CLASSIFICATION AND PROGNOSIS OF CANCER

The present invention relates to the classification of cancers, in particular prostate cancers, using samples from patients. In particular, the invention provides methods for identifying potentially aggressive prostate cancers to determine which cancers are or will become aggressive (and hence require treatment) and which will remain indolent (and will therefore not require treatment). The present invention is therefore useful to identify patients with a poor prognosis. The specific population of cancer identified by the present invention is referred to herein as DESNT cancer. The invention also provides biomarker panels useful in the diagnosis and prognosis of cancer.

Skip to: Description  ·  Claims  · Patent History  ·  Patent History
Description

The present invention relates to the classification of cancers, in particular prostate cancers, using samples from patients. In particular, the invention provides methods for identifying potentially aggressive prostate cancers to determine which cancers are or will become aggressive (and hence require treatment) and which will remain indolent (and will therefore not require treatment). The present invention is therefore useful to identify patients with a poor prognosis. The specific population of cancer identified by the present invention is referred to herein as DESNT cancer.

A common method for the diagnosis of prostate cancer is the measure of prostate specific antigen (PSA) in blood. However, as many as 50-80% of PSA-detected prostate cancers are biologically irrelevant, that is, even without treatment, they would never have caused any symptoms. Radical treatment of early prostate cancer, with surgery or radiotherapy, should ideally be targeted to men with significant cancers, so that the remainder, with biologically ‘irrelevant’ disease, are spared the side-effects of treatment. Accurate prediction of individual prostate cancer behaviour at the time of diagnosis is not currently possible, and immediate radical treatment for most cases has been a common approach. Put bluntly, many men are left impotent or incontinent as a result of treatment for a ‘disease’ that would not have troubled them. A large number of prognostic biomarkers have been proposed for prostate cancer. A key question is whether these biomarkers can be applied to PSA-detected, early prostate cancer to distinguish the clinically significant cases from those with biologically irrelevant disease. Validated methods for detecting aggressive cancer early could lead to a paradigm-shift in the management of early prostate cancer.

A critical problem in the clinical management of prostate cancer is that it is highly heterogeneous. Accurate prediction of individual cancer behaviour is therefore not achievable at the time of diagnosis leading to substantial overtreatment. It remains an enigma that, in contrast to many other cancer types, stratification of prostate cancer based on unsupervised analysis of global expression patterns has not been possible: for breast cancer, for example, ERBB2 overexpressing, basal and luminal subgroups can be identified.

There remains in the art a need for a more reliable diagnostic test for prostate cancer and to better assist in distinguishing between aggressive cancer, which may require treatment, and non-aggressive cancer, which perhaps can be left untreated and spare the patient any side effects from unnecessary interventions.

The present invention provides an algorithm-based molecular diagnostic assay for predicting whether a patient is a member of a poor prognosis category of human prostate cancer designated DESNT. In some embodiments, the expression levels of certain genes (such as those listed in Table 2 or Table 3) may be used alone or in combination to predict whether the cancer is a DESNT cancer. The algorithm-based assay and associated information provided by the practice of the methods of the present invention facilitate optimal treatment decision making in prostate cancer. For example, such a clinical tool would enable physicians to identify patients who have a high risk of having aggressive disease and who therefore need radical and/or aggressive treatment.

The present inventors have applied a Bayesian clustering procedure called Latent Process Decomposition (LPD, Simon Rogers, Mark Girolami, Colin Campbell, Rainer Breitling, “The Latent Process Decomposition of cDNA Microarray Data Sets”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 2, pp. 143-156, April-June 2005, doi:10.1109/TCBB.2005.29) identifying a common process, designated DESNT, in four independent prostate cancer transcriptome datasets. DESNT cancers are characterized by down-regulation of a core set of genes, many encoding proteins involved in the cytoskeleton machinery, ion transport and cell adhesion. For the three datasets with linked PSA failure data following prostatectomy patients with DESNT cancers exhibited a very poor outcome relative to non-DESNT patients (p=2.65×10−5, p=7.74×10−9, and p=4.28×10−5). DESNT cancers can therefore be considered aggressive prostate cancers, since they result in very poor outcomes for the patient. The results demonstrate the existence of a novel poor prognosis category of human prostate cancer, and assists in the targeting of therapy, helping avoid treatment-associated morbidity in men with indolent disease. Unlike in Rogers et al., the present inventors performed an analysis to determine the correlation of the groups with survival and to provide a definition of signature genes for each process. The inventors also conducted the analysis on a much larger set of cancers and multiple datasets and were surprisingly able, for the first time, to not only identify a process that is common across different datasets, but furthermore to invariably correlate this particular group with a poor cancer prognosis. The present inventors also discovered that the contribution of this process to a given expression profile can be used to determine the prognosis of the cancer, optionally in combination with other markers for prostate cancer such as tumour stage, Gleason score and PSA. Notably, the methods of the present invention are not simple hierarchical clustering methods, and allow a much more detailed and accurate analysis of patient samples that such prior art methods. For the first time, the present inventors have provided a method that allows a reliable prediction of cancer progression, whereas methods of the prior art could not be used to detect cancer progression, since there was nothing to indicate such a correlation could be made.

The present inventors also wished to develop a classifier that, unlike LPD, was not computer processing intensive and that could be applied to a wider range of datasets and to individual cancers. Therefore, the present invention also provides a method for identifying a gene signature that can be used in a random forest classification to identify DESNT cancers.

The present inventors have used additional mathematical techniques to provide further methods of prognosis and diagnosis, and also provide biomarkers and biomarker panels useful in identifying patients with a poor prognosis,

As used herein, “DESNT” cancer refers to prostate cancer with a poor prognosis and one that requires treatment. “DESNT status” refers to whether or not the cancer is predicted to progress (or, for historical data, has progressed), hence a step of determining DESNT status refers to predicting whether or not a cancer will progress and hence require treatment. Progression may refer to elevated PSA, metastasis and/or patient death. The present invention is useful in identifying patients with a potentially poor prognosis and recommending them for treatment.

In a first aspect of the invention, there is provided a method of classifying cancer (such as prostate cancer), for example diagnosing aggressive cancer (such as aggressive prostate cancer) in a patient, or identifying a patient with a poor prognosis for cancer, (i.e. a patient with DESNT cancer) comprising:

    • a) determining the level of expression of a plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • b) conducting a statistical Bayesian clustering analysis or other clustering analyses on the patient expression profile and a reference dataset for the same plurality of genes from different patients;
    • c) optionally repeating the analysis step b) multiple times; and
    • d) classifying the cancer, determining whether the patient has cancer, or determining whether the patient has a poor prognosis (i.e. the patient has DESNT cancer).

This method and variants thereof are hereafter referred to as Method 1.

In a second aspect of the invention, there is provided a method of classifying prostate cancer, for example diagnosing aggressive prostate cancer in a patient, or identifying a patient with a poor prognosis for prostate cancer, (i.e. a patient with DESNT prostate cancer) comprising:

    • a) providing a reference dataset where DESNT status of each patient sample in the dataset is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes, wherein the plurality of genes comprises at least 5, at least 10, at least 20, at least 30, at least 40 or at least 45 genes selected from the group listed in Table 2 or at least 5, at least 10, at least 15 or at least 20 genes selected from the group listed in Table 3;
    • c) optionally:
      • (i) determining the expression status of at least 1 further, different, gene in the patient sample as a control, wherein the control gene is not a gene listed in Table 2 or Table 3;
      • (ii) determining the relative levels of expression of the plurality of genes and of the control gene(s); and
    • d) using the expression status of those selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the reference dataset to obtain a predictor for DESNT cancer;
    • e) determining the expression status of the same plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • f) optionally normalising the patient expression profile to the reference dataset; and
    • g) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

This method and variants thereof are hereafter referred to as Method 2.

In a third aspect of the invention, there is provided a method of classifying cancer (such as prostate cancer), for example diagnosing aggressive cancer in a patient (such as aggressive prostate cancer), or identifying a patient with a poor prognosis for cancer, (i.e. a patient with DESNT cancer) comprising:

    • a) providing a reference dataset where DESNT status (i.e. cancer classification) of each patient sample in the dataset is known (for example as determined by LPD analysis);
    • b) selecting from this dataset of a plurality of genes;
    • c) using the expression status of those selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancers;
    • d) determining the expression status of the same plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • e) optionally normalising the patient expression profile to the reference dataset; and
    • f) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

This method and variants thereof are hereafter referred to as Method 3.

In a fourth aspect of the invention, there is provided a method of classifying prostate cancer, for example diagnosing aggressive cancer in a patient (such as aggressive prostate cancer), or identifying a patient with a poor prognosis for cancer, (i.e. a patient with DESNT cancer) comprising:

    • a) providing one or more reference datasets where DESNT status of each patient sample in the datasets is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes whose expression statuses are known to vary between DESNT and non-DESNT cancer (for example a plurality of genes listed in Table 4, for example at least 100, at least 200, at least 300, at least 400, at least 500 or at least 1000 genes listed in Table 4);
    • c) applying a LASSO logistic regression model analysis on the selected genes to identify a subset of the selected genes that identify DESNT cancer;
    • d) using the expression status of this subset of selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancers;
    • e) determining the expression status of the subset of selected genes in a sample obtained from the patient to provide a patient expression profile;
    • f) optionally normalising the patient expression profile to the reference dataset(s); and
    • g) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

This method and variants thereof are hereafter referred to as Method 4.

In a fifth aspect of the invention, there is provided a biomarker panel comprising the genes listed in Table 2 as a predictor for the progression of cancer, or as a classifier of cancer. In particular, the genes listed in Table 2 can be used to predict progression of cancer (such as prostate cancer). Down-regulation of these genes is predictor of cancer progression. Generally, in embodiments of the invention, at least 5, at least 10, at least 20, at least 30 or at least 40 of the genes from Table 2 will be used. In some embodiments, all 45 genes from Table 2 will be used. This panel is therefore useful in diagnosing aggressive cancer in a patient, in particular aggressive prostate cancer, although progression of other cancer types can be predicted using the same biomarker panel.

In a sixth aspect of the invention, there is provided a biomarker panel comprising the genes listed in Table 3 as a predictor for the progression of cancer, or as a classifier of cancer. In particular, the genes listed in Table 3 can be used to predict progression of cancer. Generally, in embodiments of the invention, at least 5, at least 10, or at least 15 of the genes from Table 3 will be used. In some embodiments, all 20 genes from Table 3 will be used. This panel is of particular relevance to prostate cancer, and is therefore useful in predicting prostate cancer progression in a patient.

In a seventh aspect of the invention, there is provided a biomarker panel comprising the genes listed in Table 1 as a predictor for the progression of cancer, or as a classifier of cancer. In particular, the genes listed in Table 1 can be used to predict progression of cancer. Generally, in embodiments of the invention, at least 5, at least 10, or at least 15, at least 20, at least 50, at least 100, at least 200, at least 300 or at least 400 of the genes from Table 1 will be used. In some embodiments, all 500 genes from Table 1 will be used. This panel is of particular relevance to prostate cancer, and is therefore useful in predicting prostate cancer progression in a patient. The choice of genes used from Table 1 may be determined using a method as described herein. In some embodiments of the invention, a biomarker panel is generated according to a method of the invention involving determining predictors for cancer. Such an analysis can be done on any set of genes. Preferably the set of genes from which the biomarker panel is selected comprises at least 1000 randomly selected genes. In some embodiments, the genes are not housekeeping genes (for example none of the genes listed in Table 6).

The panels defined above may be referred to collectively herein as “the biomarker panels”.

In a further aspect of the invention there is provided a method of diagnosing, screening or testing for cancer (such as prostate cancer), in particular aggressive or DESNT cancer (such as aggressive or DESNT prostate cancer), comprising detecting, in a sample, the level of expression of all or a selection of the genes from the biomarker panels. In some embodiments, the biological sample is a prostate tissue biopsy (such as a suspected tumour sample), saliva, a blood sample, or a urine sample. Preferably the sample is a tissue sample from a prostate biopsy, a prostatectomy specimen (removed prostate) or a TURP (transurethral resection of the prostate) specimen.

There is also provided one or more genes in the biomarker panels for use in diagnosing cancer (such as prostate cancer), in particular aggressive cancer (such as aggressive prostate cancer). There is also provided the use of one or more genes in the biomarker panels in methods of detecting or diagnosing such cancers, as well as methods of detecting or diagnosing such cancers using one or more genes in the biomarker panels.

There is also provided one or more genes in the biomarker panels for use in predicting progression of cancer (such as prostate cancer), in particular aggressive cancer (such as aggressive prostate cancer). There is also provided the use of one or more genes in the biomarker panel in methods of predicting progression of cancer, as well as methods of predicting cancer progression using one or more genes in the biomarker panels.

There is also provided one or more genes in the biomarker panels for use in classifying cancer (such as prostate cancer). There is also provided the use of one or more genes in the biomarker panel in classifying cancer, as well as methods of classifying cancer using one or more genes in the biomarker panels.

There is further provided a kit of parts for testing for prostate cancer comprising a means for detecting the level of expression of one or more genes in the biomarker panels in a biological sample. The kit may also comprise means for detecting the level of expression of one or more control genes not present in the biomarker panels.

There is also provided a method of distinguishing between aggressive and non-aggressive prostate cancer, comprising detecting the level of expression of one or more genes in the biomarker panels in a biological sample. Optionally the expression levels of each of the genes measured is compared with a reference. The reference may be a control or housekeeping gene. In some embodiments, the control genes are selected from the genes listed in Table 6 or Table 7. The control genes of Table 7 are of particular relevance to prostate cancer. The control genes of Table 6 are useful more broadly.

There is still further provided methods of diagnosing aggressive cancer, methods of classifying cancer, methods of prognosing cancer, and methods of predicting cancer progression comprising detecting the level of expression of one or more genes in the biomarker panels in a biological sample. Optionally the method further comprises comparing the expression levels of each of the quantified genes with a reference.

In a still further aspect of the invention there is provided a method of treating prostate cancer in a patient, comprising proceeding with treatment for prostate cancer if aggressive prostate cancer or cancer with a poor prognosis is diagnosed or suspected. In the invention, the patient has been diagnosed as having aggressive prostate cancer or as having a poor prognosis using one of the methods of the invention. In some embodiments, the method of treatment may be preceded by a method of the invention for diagnosing, classifying, prognosing or predicting progression of cancer (such as prostate cancer) in a patient, or a method of identifying a patient with a poor prognosis for prostate cancer, (i.e. identifying a patient with DESNT prostate cancer).

BRIEF DESCRIPTION OF THE FIGURES AND TABLES

FIG. 1. Latent Process Decomposition (LPD), gene correlations and clinical outcome.

FIG. 2. Genes commonly down regulated in DESNT poor prognosis prostate cancer.

FIG. 3. Comparison of RF-DESNT and non-RF-DESNT cancers in The Cancer Genome Atlas dataset.

FIG. 4. Example computer apparatus.

FIG. 5. Log-likelihood plots.

FIG. 6. Latent Process Decomposition (LPD) analysis of transcriptome datasets.

FIG. 7, Analysis of outcome for DESNT cancers identified by LPD.

FIG. 8. Correlations of Gene Expression of DESNT cancers identified by LPD classification.

FIG. 9. Detection of DESNT cancers by RF classification using the 20 gene signature.

FIG. 10 Analysis of outcome for DESNT cancers identified by RF classification.

FIG. 11. Correlations of Gene Expression of DESNT cancers identified by RF classification.

FIG. 12. Distribution of LPD runs.

FIG. 13. LPD decomposition of the MSKCC dataset.

FIG. 14. Stratification of prostate cancer based on the percentage of DESNT cancer present.

FIG. 15. Nomogram model developed to predict PSA free survival at 1, 3, 5 and 7 years for LPD.

FIG. 16. Cox Model for LPD.

Table 1: 500 gene probes that vary most across prostate cancers.

Table 2: 45 commonly downreglated genes in 80/100 from CancerMap, Stephenson, MSKCC and Klein datasets.

Table 3: 20 random forest genes.

Table 4: 1669 genes that vary between DESNT and non-DESNT cancer.

Table 5: 35 commonly downregulated genes in 67/100 from CamCap, Stephenson, MSCKSS and Klein datasets.

Table 6: General control/housekeeping genes.

Table 7: Control/housekeeping genes for prostate cancer.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides methods, biomarker panels and kits useful in predicting cancer progression.

In one embodiment of the invention, there is provided a method of classifying cancer, diagnosing aggressive cancer, or identifying a patient with a poor prognosis for cancer, (i.e. a patient with DESNT cancer) comprising:

    • a) determining the level of expression of a plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • b) conducting a statistical Bayesian clustering analysis or other clustering analyses on the patient expression profile and a reference dataset for the same plurality of genes from different patients;
    • c) optionally repeating the analysis step b) multiple times; and
    • d) classifying the cancer, determining whether the patient has aggressive cancer, or determining whether the patient has a poor prognosis (i.e. the patient has DESNT cancer).

This method is of particular relevance to prostate cancer, but it can be applied to other cancers.

In embodiments where the analysis step b) of Method 1 is repeated, different initial random seeds may be used each time the analysis is run.

The step a) of Method 1 of determining the level of expression of a plurality of genes may be carried out on genes whose expression levels are known to vary across cancers. For example, the level of expression may be determined for at least 50, at least 100, at least 200 or most preferably at least 500 genes there are known to vary across cancers. The skilled person can determine which genes should be measured, for example using previously published dataset(s) for patients with cancer and choosing a group of genes whose expression levels vary across different cancer samples. In particular, the choice of genes is determined based on the amount by which their expression levels are known to vary across difference cancers.

Variation across cancers refers to variations in expression seen for cancers having the same tissue origin (e.g. prostate, breast, lung etc). For example, the variation in expression is a difference in expression that can be measured between samples taken from different patients having cancer of the same tissue origin. When looking at a selection of genes, some will have the same or similar expression across all samples. These are said to have little or low variance. Others have high levels of variation (high expression in some samples, low in others).

A measurement of how much the expression levels vary across prostate cancers can be determined in a number of ways known to the skilled person, in particular statistical analyses. For example, the skilled person may consider a plurality of genes in each of a plurality of cancer samples and select those genes for which the standard deviation or inter-quartile range of the expression levels across the plurality of samples exceeds a predetermined threshold. The genes can be ordered according to their variance across samples or patients, and a selection of genes that vary can be made. For example, the genes that vary the most can be used, such as the 500 genes showing the most variation. Of course, it is not vital that the genes that vary the most are always used. For example, the top 500 to 1000 genes could be used. Generally, the genes chosen will all be in the top 50% of genes when they are according to variance. What is important is the expression levels vary across the reference dataset. The selection of genes is without reference to clinical aggression. This is known as unsupervised analysis. The skilled person is aware how to select genes for this purpose.

Step b) requires the use of one or more reference datasets. Preparation of the reference datasets will generally not be part of the method, since reference datasets are available to the skilled person. When using a previously obtained reference dataset (or even a reference dataset obtained de novo in step b) of Method 1), normalisation of the levels of expression for the plurality of genes in the patient sample to the reference dataset may be required to ensure the information obtained for the patient sample was comparable with the reference dataset. Normalisation techniques are known to the skilled person, for example, Robust Multi-Array Average, Froze Robust Multi-Array Average or Probe Logarithmic Intensity Error when complete microarray datasets are available. Quantile normalisation can also be used. Normalisation may occur after the first expression profile has been combined with the reference dataset to provide a combined dataset that is then normalised.

Methods of normalisation generally involve correction of the measured levels to account for, for example, differences in the amount of RNA assayed, variability in the quality of the RNA used, etc, to put all the genes being analysed on a comparable scale. The control genes (also referred to as housekeeping genes) are useful as they are known not to differ in expression status under the relevant conditions (e.g. DESNT cancer). Exemplary housekeeping genes are known to the skilled person, and they include RPLP2, GAPDH, PGK1 Alas1, TBP1, HPRT, K-Alpha 1, and CLTC. In some embodiments, the housekeeping genes are those listed in Table 6 or Table 7. Table 7 is of particular relevance to prostate cancer. Preferred embodiments of the invention use at least 2 housekeeping genes for normalisation.

Step a) of Method 1 may involve a single expression profile from a single patient. Alternatively, two or more expression profiles from different patients undergoing diagnosis could be used. Such an approach is useful when diagnosing a number of patients simultaneously. The method may include a step of assigning a unique label to each of the patient expression profiles to allow those expression profiles to be more easily identified in the analysis step.

In some embodiments, in particular those relating to prostate cancer, the level of expression is determined for a plurality of genes selected from the list in Table 1.

In some embodiments, step a) of Method 1 involves determining the level of expression at least 20, at least 50, at least 100, at least 200 or at least 500 genes selected from the list in Table 1. As the number of genes increases, the accuracy of the test may also increase. In a preferred embodiment, at least all 500 genes are selected from the list in Table 1. However, the method does not need to be restricted to the genes of Table 1.

In some cases, information on the level of expression of many more genes may be obtained in step a) of Method 1, such as by using a microarray that determines the level of expression of a much larger number of genes. It is even possible to obtain the entire transcriptome. However, it is only necessary to carry out the subsequent analysis steps on a subset of genes whose expression levels are known to vary across prostate cancers. Preferably, the genes used will be those whose expression levels vary most across prostate cancers (i.e. expression varies according to cancer aggression), although this is not strictly necessary, provided the subset of genes is associated with differential expression levels across cancers (such as prostate cancers).

The actual genes on which the analysis is conducted will depend on the expression level information that is available, and it may vary from dataset to dataset. It is not necessary for this method step to be limited to a specific list of genes. However, the genes listed in Table 1 can be used.

Thus step a) of Method 1 may include the determination of a much larger number of genes that is needed for the rest of the method. The method may therefore further comprise a step of selecting, from the expression profile for the patient sample, a subset of genes whose expression level is known to vary across prostate cancers. Said subset may be the at least 20, at least 50, at least 100, at least 200 or at least 500 genes selected from Table 1.

In preferred embodiments, the Bayesian clustering analysis is a latent process decomposition (LPD) analysis. Such mathematical models are known to a person of skill in the art and are described in, for example, Simon Rogers, Mark Girolami, Colin Campbell, Rainer Breitling, “The Latent Process Decomposition of cDNA Microarray Data Sets”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 2, pp. 143-156, April-June 2005, doi:10.1109/TCBB.2005.29. Alternative Bayesian clustering algorithms that could be used include: Dirichlet Process Mixture Models, Bayesian Hierarchical Clustering, Bayesian Multi-topic Microarray Analysis with Hyperparameter Reestimation, Bayesian Mixture Models, a Markov Chain Monte Carlo approach to LPD, or a marginalized variational Bayesian approach.

When an LPD analysis is carried out on the reference dataset, which includes, for a plurality of patients, information on the expression levels for a number of genes whose expression levels vary significantly across prostate cancers, it is possible to identify a population of patients that all exhibit DESNT (aggressive or poor prognosis) cancer. The LPD analysis groups the patients into “processes”. The present inventors have surprisingly discovered that when the LPD analysis is carried out using genes whose expression levels are known to vary across prostate cancers, one particular patient population (or process) is identified that is substantially always associated with a negative outcome for the patient (i.e. a DESNT/aggressive cancer). Even more surprisingly, this process is present even across multiple different datasets.

In the development of the present invention, the inventors performed an LDP analysis using between 3 and 8 underlying processes contributing to the overall expression profile as indicated from log-likelihood plots (FIGS. 1b, 5). Following decomposition of each dataset, cancers were assigned to individual processes based on their highest pi value yielding the results shown in FIG. 1a and FIG. 6. pi is the contribution of each process i to the expression profile of an individual cancer: sum of pi over all processes=1. However, the highest pi value does not always need to be used and pi can be defined differently, and skilled person would be aware of possible variations. For example, pi can be at least 0.1, at least 0.2, at least 0.3, at least 0.4 or preferably at least 0.5.

Indeed, as demonstrated in Example 2, pi is a continuous variable and is a measure of the contribution of a given process to the expression profile of a given sample. The higher the contribution of the DESNT process (so the higher the value of pi for the DESNT process contributing to the expression profile for a given sample), the greater the chance the cancer will have a poor outcome. As demonstrated and indicated in Example 2, for a given sample, a number of different processes can contribute to an expression profile. It is not always necessary for the DESNT process to be the most dominant (i.e. to have to highest pi value of all the processes contributing to the expression profile) for a poor outcome to be predicted. However, the higher the pi value the worse the patient outcome; not only in reference to PSA but also metastasis and death are also more likely. In some embodiments, the contribution of the DESNT process to the overall expression profile for a given cancer may be determined when assessing the likelihood of a cancer being DESNT. In some embodiments, the prediction of cancer progression may be done in further combination with one or more of stage of the tumour, Gleason score and/or PSA score. Therefore, in some embodiments, the step of determining the cancer prognosis may comprise a step of determining the pi value for the DESNT process for the expression profile and, optionally, further determining the stage of the tumour, the Gleason score of the patient and/or PSA score of the patient.

In some embodiments, the step of grouping individual patient expression profiles comprises, for each expression profile, using the LDP analysis to determine the contribution (p) of each group to the overall expression profile for each patient expression profile (wherein the sum of all pi values for a given expression profile is 1). The patient expression profile may be assigned to an individual group according to the group that contributes the most to the overall expression profile (in other words, the patient expression profile is assigned to the group with the highest pi value). In some embodiments, each group is assigned either DESNT or a non-DESNT status. Cancer progression in the patient can be predicted according to the contribution (pi value) of the DESNT process to the overall expression profile. In some embodiments, DESNT cancer is predicted when the pi value for the DESNT process for the patient cancer sample is at least 0.1, at least 0.2, at least 0.3, at least 0.4 or at least 0.5.

In FIG. 1a, the “pi” value is shown on the vertical axis. Each column represents as single patient. Following LPD of each dataset, cancers were assigned to individual processes based on their highest pi value yielding the results shown in this Figure. pi is the contribution of each process i to the expression profile of an individual cancer: sum of pi over all processes=1.

The reference dataset may have been obtained previously and, in general, the obtaining of these datasets is not part of the claimed method. However, in some embodiments, the method may further comprise obtaining the additional datasets for inclusion in the LPD analysis. The reference dataset is in the form of a plurality of expression profiles that comprises the same genes measured in the patient sample.

In any of the Methods described herein, there are four main ways in which it is possible to identify a DESNT cancer or a DESNT cancer group:

    • (i) correlations of gene expression levels with DESNT cancer groups in another dataset or datasets;
    • (ii) demonstration of overlaps of differentially expressed genes between DESNT and non-DESNT cancers with a core down-regulated gene set;
    • (iii) its poorer clinical outcome; and
    • (iv) LPD on a combined reference and unknown patient dataset with DESNT status assigned if the patient dataset clusters with the known DESNT group.

In the first (i) method, after the LPD analysis has been conducted, the patient samples are grouped together in different processes. For the patients in each process the level of expression for each gene is averaged. The averaged expression levels are then correlated with data from other datasets, where the presence of DESNT cancer is known. Hence the process in the new dataset associated with DESNT cancer can be determined. That new dataset can then be used in the method of the invention, since when the new dataset includes one or more unknown patient samples, a determination can be made as to whether the unknown patient sample(s) groups with the DESNT process or not (i.e. is assigned to the same process/group as the DESNT process/group). Alternatively, it is possible to correlate the expression of genes in the sample to the average gene expression level in the DESNT group. In this way, it is possible to carry out a correlation on a single unknown specimen.

In the second (ii) method, it is necessary to have a reference set of genes that is known to have altered expression (for example be down-regulated) in the DESNT cancer. This may have been obtained previously by conducting an LPD analysis on a plurality of datasets to determine the processes in each dataset. In that method, a common process can be identified based on gene correlations using the method described above. A subset of genes is identified that is consistently down-regulated in each expression profile of the DESNT process compared to non-DESNT processes of each dataset. In the analysis conducted by the present inventors, 45 genes were most commonly found to be downregulated 40 in at least 80 out of 100 runs of the LPD analysis for each of 4 datasets analysed (Table 2). However, different genes might be identified if different datasets are used. It is likely there will be considerable overlap between the genes identified when different datasets are used. For example, in a second analysis performed by the investigators using a different combination of datasets 35 genes were found to be down regulated in at least 67 of 100 runs of the LPD analysis of each dataset (Table 5). There was a 27 gene overlap with the 45 commonly down-regulated genes identified in the first analysis.

Once the core down-regulated gene set is obtained, method (ii) can be carried out. In particular, DESNT cancer can be identified by demonstrating an overlap between the core down-regulated set of genes and the differentially expressed genes in one of the groups from the test dataset. “Overlap” may be 50%, 60%, 70%, 80%, 90% or 100% overlap. Preferably the overlap is at least 67%. The core down-regulated gene set may comprise at least 5, at least 10, at least 20, at least 30 or at least 40 genes. For example, the core down-regulated gene set may comprise the 45 genes of Table 1.

In one embodiment of the invention, there is therefore provided a method of classifying cancer, comprising comparing in a patient sample the level of expression of at least 5, at least 10, at least 20, at least 30, at least 40 or all 45 genes from Table 2 with the level of expression of the same genes in a healthy patient, or a patient not having aggressive or DESNT cancer. Alternatively, the method may comprise comparing in a patient sample the level of expression of at least 5, at least 10, at least 20, at least 30, or all 35 genes from Table 5. If the level of expression at least 50%, 60%, 70%, or 80% of genes in the patient sample is lower than in the control or reference genes, DESNT cancer is present and cancer progression is predicted.

When the new (test) dataset includes one or more unknown patient samples, a determination can be made as to whether the unknown patient sample(s) groups with the DESNT process or not.

In the third (iii) method, the DESNT cancer process identified by LPD is associated with poorer clinical outcome, for example patient death or cancer relapse when compared to non-DESNT cancer. Again, when the new (test) dataset includes one or more unknown patient samples, a determination can be made as to whether the unknown patient sample(s) groups with the DESNT process or not using this method (iii).

In the fourth (iv) method, it is not possible to run the LPD analysis on a single expression profile for the plurality of genes from a single patient sample and determine if that individual patient has DESNT cancer. Rather, in one method of the invention, it is necessary for the expression profile from the patient sample to be included in an analysis of a larger dataset. For example, step b) of Method 1 (the LPD analysis step) can therefore be conducted simultaneously on the patient expression profile and the reference dataset. In other words, the patient expression profile can be combined with the reference dataset prior to LPD analysis. If the additional patient sample groups with the DESNT cancer process, then the patient has DESNT cancer.

Thus, in one embodiment of the invention, the method comprises the steps of

    • a) determining the level of expression of a plurality of genes in a sample obtained from the patient to provide a first expression profile;
    • b) combining the first expression profile with a reference dataset, the reference dataset comprising expression profiles for the same plurality of genes obtained from different patients to obtain a combined dataset, optionally wherein the clinical outcome of the patients in the reference dataset is known;
    • c) conducting an LPD analysis on the combined dataset;
    • d) identifying a process (patient group) from the LPD analysis that is associated with DESNT cancer; and
    • e) classifying the cancer or determining the presence or absence of DESNT cancer in the patient by determining whether or not the patient sample is in the process (patient group) associated with DESNT cancers.

As already noted, some of the methods of the invention can be carried out on multiple patient samples simultaneously. For example, level of expression of a plurality of genes in a sample may be determined in at least two samples obtained from at least two different patients to provide expression profiles for each patient.

The methods of the invention may also comprise assigning a unique label to the one or more patient expression profiles so they can be more easily identified during the analysis step.

In methods of the invention, identifying a process/patient group associated with DESNT cancer can be done using one of the first three methods mentioned above, specifically (i) correlation of gene expression levels with DESNT cancer groups in other datasets, (ii) demonstration of overlaps of differentially expressed genes between DESNT and non-DESNT cancers with a core down-regulated gene set, (iii) association with its poorer clinical outcome.

Assignment of an individual cancer as DESNT can be achieved using method (iv); carrying out LPD on a combined reference & patient dataset to determine if the patient dataset clusters with the known DESNT group. Method (iii) requires the clinical outcome of the patients in the reference dataset to be known.

By “clinical outcome” it is meant that for each patient in the reference dataset whether the cancer has progressed. For example, as part of an initial assessment, those patients may have prostate specific antigen (PSA) levels monitored. When it rises above a specific level, this is indicative of relapse and hence disease progression. Histopathological diagnosis may also be used. Spread to lymph nodes, and metastasis can also be used, as well as death of the patient from the cancer (or simply death of the patient in general) to define the clinical endpoint. Gleason scoring, cancer staging and multiple biopsies (such as those obtained using a coring method involving hollow needles to obtain samples) can be used. Clinical outcomes may also be assessed after treatment for prostate cancer. This is what happens to the patient in the long term. Usually the patient will be treated radically (prostatectomy, radiotherapy) to effectively remove or kill the prostate. The presence of a relapse or a subsequent rise in PSA levels (known as PSA failure) is indicative of progressed cancer. The DESNT cancer population identified using the method of the invention comprises a subpopulation of cancers that will progress more quickly.

Combinations of such methods (i), (ii) (iii) and (iv) may be used, and the skilled person is familiar with how to determine patient outcome for the patients in the reference dataset.

Accordingly, any of the methods of the invention may be carried out in patients in whom DESNT cancer is suspected. Importantly, the present invention allows a prediction of cancer progression before treatment of cancer is provided. This is particularly important for prostate cancer, since many patients will undergo unnecessary treatment for prostate cancer when the cancer would not have progressed even without treatment.

Additionally, the accuracy of the diagnosis can be increased by repeating the analysis, since the results of LPD can differ slightly each time the analysis is run even when the same data is being analysed. Often the variation is due to a different starting point of a random number generator (used as seed values) being used in each run of the LPD process and so even for a repeated run over the same dataset, multiple different outcomes can arise. Thus, carrying out the analysis a plurality of times and referring to the modal (most frequent) or mean (average) value can be beneficial. In some embodiments, the LPD analysis is carried out at least 2, 3, 5 or at least 20 times. In some embodiments, the analysis is carried out at least 50 times. In preferred embodiments, the analysis is carried out at least 100 times (i.e. it is repeated at least 99 times).

In embodiments where the analysis step is repeated, the step of determining whether the cancer is DESNT may require a comparison between the number of times the cancer is indicated as DESNT, and the number of times the cancer is indicated as non-DESNT (i.e. indolent or non-aggressive prostate cancer). For example, a determination that a patient has aggressive cancer may require the cancer to be DESNT in at least 50% of the analysis steps undertaken. In preferred embodiments, the cancer must be DESNT in at least 60%, or in more preferred embodiments, in at least 70%. In the most preferred embodiments, the cancer is DESNT in at least 67% of the analyses.

When the LPD analysis is undertaken, it splits the patients in the dataset being analysed into a number of processes (groups). In some embodiments of the invention, the step of determining whether a specific patient, whose clinical outcome is not known, has DESNT cancer requires the process (for example, the patient group associated with aggressive cancer) to be known. A patient sample added to the reference data set can then be present within the aggressive cancer (DESNT) group (or not, as the case may be) to determine whether the patient has aggressive cancer.

However, as noted above, it is not always necessary to know in advance the clinical outcome of the patients in the reference datasets. Either or both of these two methods for determining the presence of DESNT cancer can be used:

    • (i) correlations of gene expression levels with DESNT cancer groups in other datasets; or
    • (ii) demonstration of overlaps of differentially expressed genes between DESNT and non-DESNT cancers with a core down-regulated gene set.

The assignment of an individual cancer as DESNT can be achieved by carrying out LPD on a combined reference & patient dataset to determine if the patient dataset clusters with the known DESNT group.

Ideally, the presence or absence DESNT cancer in the reference datasets is determined using up to three of these methods:

    • i. correlations of gene expression levels with DESNT cancer groups in another dataset or datasets,
    • ii. demonstration of overlaps of differentially expressed genes between DESNT and non-DESNT cancers with a core down-regulated gene set,
    • iii. correlation with clinical outcome.

The step of determining the level of expression of a plurality of genes in the patient sample can be done by any suitable means known to a person of skill in the art, such as those discussed elsewhere herein, or methods as discussed in any of Prokopec S D, Watson J D, Waggott D M, Smith A B, Wu A H, Okey A B et al. Systematic evaluation of medium-throughput mRNA abundance platforms. RNA 2013; 19: 51-62; Chatterjee A, Leichter A L, Fan V, Tsai P, Purcell R V, Sullivan M J et al. A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients. Sci Rep 2015; 5: 10438; Pollock J D. Gene expression profiling: methodological challenges, results, and prospects for addiction research. Chem Phys Lipids 2002; 121: 241-256; Mantione K J, Kream R M, Kuzelova H, Ptacek R, Raboch J, Samuel J M et al. Comparing bioinformatic gene expression profiling methods: microarray and RNA-Seq. Med Sci Monit Basic Res 2014; 20: 138-142; Casassola A, Brammer S P, Chaves M S, Ant J. Gene expression: A review on methods for the study of defense-related gene differential expression in plants. American Journal of Plant Research 2013; 4, 64-73; Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 2011; 12: 87-98.

In embodiments of the invention, the analysis step in any of the methods can be computer implemented. The invention also provides a computer readable medium programmed to carry out any of the methods of the invention.

In a further embodiment of the invention, there is provided a method of classifying prostate cancer, for example diagnosing aggressive prostate cancer in a patient, or identifying a patient with a poor prognosis for prostate cancer, (i.e. a patient with DESNT prostate cancer) comprising:

    • a) providing a reference dataset where DESNT status of each patient sample in the dataset is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes, wherein the plurality of genes comprises at least 5, at least 10, at least 20, at least 30, at least 40 or at least 45 genes selected from the group listed in Table 2 or at least 5, at least 10, at least 15 or at least 20 genes selected from the group listed in Table 3;
    • c) optionally:
      • (i) determining the expression status of at least 1 further, different, gene in the patient sample as a control, wherein the control gene is not a gene listed in Table 2 or Table 3;
      • (ii) determining the relative levels of expression of the plurality of genes and of the control gene(s); and
    • d) using the expression status of those selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancer;
    • e) determining the expression status of the same plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • f) optionally normalising the patient expression profile to the reference dataset; and
    • g) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

This method and variants thereof are hereafter referred to as Method 2. The genes of Table 2 were identified by the inventors by conducting an LPD analysis on multiple datasets and determining genes that were commonly down-regulated in the DESNT groups. The genes of Table 3 were identified by the inventors by conducting a LASSO analysis as described in Method 4.

In a preferred embodiment, the control genes used in step (i) are selected from the housekeeping genes listed in Table 6 or Table 7. Table 7 is particularly relevant to prostate cancer. In some embodiments of the invention, at least 1, at least 2, at least 5 or at least 10 housekeeping genes. Preferred embodiments use at least 2 housekeeping genes. Step (ii) above may comprise determining a ratio between the test genes and the housekeeping genes.

In a further method of the invention, there is provided a method of diagnosing aggressive cancer in a patient (such as aggressive prostate cancer), or identifying a patient with a poor prognosis for cancer, (i.e. a patient with DESNT cancer) comprising:

    • a) providing a reference dataset where DESNT status of each patient sample in the dataset is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes;
    • c) using the expression status of those selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancers;
    • d) determining the expression status of the same plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • e) optionally normalising the patient expression profile to the reference dataset; and
    • f) applying the predictor to the patient expression profile to determine whether the patient's cancer is DESNT or non-DESNT.

This method and variants thereof are hereafter referred to as Method 3.

In an additional method of the invention, there is provided a method of diagnosing aggressive cancer in a patient (such as aggressive prostate cancer), or identifying a patient with a poor prognosis for cancer, (i.e. a patient with DESNT cancer) comprising:

    • a) providing one or more reference datasets where DESNT status of each patient sample in the datasets is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes whose expression statuses are known to vary between DESNT and non-DESNT cancer (for example a plurality of genes listed in Table 4, for example at least 100, at least 200, at least 300, at least 400, at least 500, or at least 1000 genes listed in Table 4);
    • c) applying a LASSO logistic regression model analysis on the selected genes to identify a subset of the selected genes that [best] identify DESNT cancer;
    • d) using the expression status of this subset of selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancers;
    • e) determining the expression status of the subset of selected genes in a sample obtained from the patient to provide a patient expression profile;
    • f) optionally normalising the patient expression profile to the reference dataset(s); and
    • g) applying the optimal predictor to the patient expression profile to determine whether the patient's cancer is DESNT or non-DESNT.

This method and variants thereof are hereafter referred to as Method 4.

DESNT patient populations identified using methods involving Random Forest analysis are referred to as “RF-DESNT”. DESNT patient populations identified using methods involving LPD analysis are referred to as “LPD-DESNT”.

The presents inventors wished to develop a classifier that, unlike LPD, was not computer processing intensive and that could be applied to a wider range of datasets. Methods 2 to 4 provide such solutions, and can be used to predict cancer progression. Therefore, the present invention provides a method for identifying a gene signature that can be used in random forest classification to identify RF-DESNT cancers and predict cancer progression.

Supervised machine learning algorithms or general linear models are used to produce a predictor of DESNT status. The preferred approach is random forest analysis but alternatives such as support vector machines, neural networks, naive Bayes classifier, or nearest neighbour algorithms could be used. Such methods are known and understood by the skilled person.

Random forest analysis can be used to predict whether a cancer is DESNT or not. Methods 2 to 4 above require considerably less computing power than Method 1 and hence can be carried out more easily.

A random forest analysis is an ensemble learning method for classification, regression and other tasks, which operates by constructing a multitude of decision trees during training and outputting the class that is the mode of the classes (classification) or mean prediction (regression) of the individual decision trees. Accordingly, a random forest corrects for overfitting of data to any one decision tree.

A decision tree comprises a tree-like graph or model of decisions and their possible consequences, including chance event outcomes. Each internal node of a decision tree typically represents a test on an attribute or multiple attributes (for example whether an expression level of a gene in a cancer sample is above a predetermined threshold), each branch of a decision tree typically represents an outcome of a test, and each leaf node of the decision tree typically represents a class (classification) label.

In a random forest analysis, an ensemble classifier is typically trained on a training dataset (also referred to as a reference dataset) where the DESNT group, for example as determined by LPD, is known. The training produces a model that is a predictor for membership of DESNT or non-DESNT. The groups identified by RF can be referred to as RF-DESNT and RF-non-DESNT). Once trained the random forest classifier can then be applied to a dataset from an unknown sample. This step is deterministic i.e. if the classifier is subsequently applied to the same dataset repeatedly, it will consistently sort each cancer of the new dataset into the same class each time.

The ensemble classifier acts to classify each cancer sample in the new dataset as either a RF-DESNT cancer or a RF-non-DESNT cancer. Accordingly, when the random forest analysis is undertaken, the ensemble classifier splits the cancers in the dataset being analysed into a number of classes. The number of classes may be 2 (i.e. the ensemble classifier may group or classify the patients in the dataset into a DESNT class, or DESNT group, containing the DESNT cancers and a non-DESNT class, or non-DESNT group, containing other cancers).

Each decision tree in the random forest is an independent predictor that, given a cancer sample, assigns it to one of the classes which it has been trained to recognize, i.e. DESNT/non-DESNT. Each node of each decision tree comprises a test concerning one or more genes of the same plurality of genes as obtained in the cancer sample from the patient. Several genes may be tested at the node. For example, a test may ask whether the expression level(s) of one or more genes of the plurality of genes is above a predetermined threshold.

Variations between decision trees will lead to each decision tree assigning a sample to a class in a different way. The ensemble classifier takes the classification produced by all the independent decision trees and assigns the sample to the class on which the most decision trees agree.

The plurality of genes for which the level of expression is determined in step b) of Method 2, 3 or 4 (and on which the decisions of the random forest analysis are based) can be chosen using any suitable method. One possible method is to apply an LPD analysis or other Bayesian statistical analysis to a training dataset and determine the cancers that are assigned to the DESNT group/process. Then to select those genes that are shown to be consistently down-regulated in DESNT cancers compared to non-DESNT cancer. This down-regulation may be consistent across several different datasets on which LPD analysis has been conducted. In some embodiments, the plurality of genes used in step b) of Methods 2 3 and 4 comprises at least 5, at least 10, at least 15, at least 20, at least 30, at least 40 or at least 45 genes. In particular, the plurality of genes used in step b) of Method 2 and Method 3 comprises at least 5, at least 10, at least 15, at least 20, at least 30, at least 40, or all 45 genes listed in Table 2.

Another possible method (as in Method 4) is to perform a least absolute shrinkage and selection operator (LASSO) analysis on a training dataset and to select those genes that are found to best characterise DESNT membership. A logistic regression model is derived with a constraint on the coefficients such that the sum of the absolute value of the model coefficients is less than some threshold. This has the effect of removing genes that either don't have the ability to predict DESNT membership or are correlated with the expression of a gene already in the model. LASSO is a mathematical way of finding the genes that are most likely to distinguish the DESNT vs non-DESNT samples in a training or reference dataset. The subset of genes is step e) of Method 4 may comprise at least 5, at least 10, at least 15, or at least 20 genes. In a particular embodiment, steps a) and b) of Method 4 are not required, and instead the method can begin at step c) of Method 4 using at least 5, at least 10, at least 15 or at least 20 of the subset of genes identified in Table 3.

When devising Method 4, the present inventors carried out the following steps. As a starting point all genes with significantly altered expression in DESNT cancers (compared to Non-DESNT cancers) that were generally present in at least two of the five datasets analysed by the inventors (genes in total) were identified. A representative DESNT LPD classification for carrying out LASSO was chosen from the analysed MSKCC dataset. In practice, the DESNT classification used could use a representative run, selected for example by the mean p-value of some statistical test, or a summary of all the runs of some description, for example DESNT status is assigned to a sample if in at least 50% of runs it is assigned as DESNT.

A LASSO logistic regression model was used to predict DESNT membership in the MSKCC dataset leading to the selection of a set of 20 genes that characterized DESNT membership. These genes are listed in Table 3. Removal of these 20 genes from the 1669 gene and repetition of this procedure identified further sets of genes that could characterise DESNT memberships. Additional sets of genes could be obtained by carrying out the same analyses using other datasets that have been analysed by LPD as a starting point.

The invention provides a further list of genes that are associated with or predictive of DESNT cancer or cancer progression. For example, in one embodiment, a LASSO analysis can be used to provide an expression signature that is indicative or predictive of DESNT cancer, in particular DESNT prostate cancer. The expression signature may also be considered a biomarker panel, and comprises at least 5, at least 10, at least 12, at least 15 or all 20 genes selected from the group consisting of the genes listed in Table 3.

Note that in any methods of the invention, the statistical analysis can be conducted on the level of expression of the genes being analysed, or the statistical analysis can be conducted on a ratio calculated according to the relative level of expression of the genes and of any control genes.

For example, with reference to method 1, the method may comprise the steps of:

    • a) determining the level of expression of a plurality of genes in a sample obtained from the patient to provide a patient expression profile;
    • b) determining the expression status of at least 1 further, different, gene in the patient sample as a control, wherein the control genes are not any of the genes whose level of expression is determined in step a);
    • c) determining the relative levels of expression of the plurality of genes and of the control gene(s);
    • d) providing a reference dataset comprising expression profiles from different patients and determining the relative levels of expression of the same plurality of genes used in step a) and the same control gene or control genes used in step b);
    • e) conducting a statistical Bayesian clustering analysis or other clustering analyses on the relative expression levels obtained in steps c) and d);
    • f) optionally repeating the analysis step e) multiple times; and
    • g) classifying the cancer, determining whether the patient has cancer, or determining whether the patient has a poor prognosis (i.e. the patient has DESNT cancer).

With reference to method 2, the method may comprise the steps of:

    • a) providing a reference dataset where DESNT status of each patient sample in the dataset is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes, wherein the plurality of genes comprises at least 5, at least 10, at least 20, at least 30, at least 40 or at least 45 genes selected from the group listed in Table 2 or at least 5, at least 10, at least 15 or at least 20 genes selected from the group listed in Table 3;
    • c) determining the expression status of at least 1 further, different, gene in the patient sample as a control;
    • d) determining the relative levels of expression of the plurality of genes and of the control gene(s);
    • e) using the relative levels of expression to apply a supervised machine learning algorithm (for example random forest analysis) on the reference dataset to obtain a predictor for DESNT cancer;
    • f) determining the relative levels of expression of the same plurality of genes and control genes in a sample obtained from the patient to provide a patient expression profile;
    • g) optionally normalising the patient expression profile to the reference dataset; and
    • h) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

With reference to method 3, the method may comprise the steps of:

    • a) providing a reference dataset where DESNT status (i.e. cancer classification) of each patient sample in the dataset is known (for example as determined by LPD analysis);
    • b) selecting from this dataset of a plurality of genes;
    • c) determining the expression status of at least 1 further, different, gene in the patient sample as a control;
    • d) determining the relative levels of expression of the plurality of genes and of the control gene(s);
    • e) using the relative expression levels of those selected genes to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancers;
    • f) providing a patient expression profile comprising the relative levels of expression in a sample obtained from the patient, wherein the relative levels of expression is obtained using the same plurality of genes selected in step b) and the same control gene(s) used in step d);
    • g) optionally normalising the patient expression profile to the reference dataset; and
    • h) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

With reference to method 4, the method may comprise the steps of:

    • a) providing one or more reference datasets where DESNT status of each patient sample in the datasets is known (for example as determined by LPD analysis);
    • b) selecting from this dataset a plurality of genes whose expression statuses are known to vary between DESNT and non-DESNT cancer (for example a plurality of genes listed in Table 4, for example at least 100, at least 200, at least 300, at least 400, at least 500 or at least 1000 genes listed in Table 4);
    • c) applying a LASSO logistic regression model analysis on the selected genes to identify a subset of the selected genes that identify DESNT cancer;
    • d) determining the expression status of at least 1 further, different, gene in the patient sample as a control;
    • e) determining the relative levels of expression of the subset of genes and of the control gene(s);
    • f) using the relative expression levels to apply a supervised machine learning algorithm (for example random forest analysis) on the dataset to obtain a predictor for DESNT cancers;
    • g) providing a patient expression profile comprising the relative levels of expression in a sample obtained from the patient, wherein the relative levels of expression are obtained using the same subset of genes selected in step c) and the same control gene(s) used in step e);
    • h) optionally normalising the patient expression profile to the reference dataset(s); and
    • i) applying the predictor to the patient expression profile to classify the cancer, determine the presence of aggressive cancer, or determining whether the patient has a poor prognosis (i.e. determine whether the patient's cancer is DESNT or non-DESNT).

In any of the above methods, the control gene or control genes may be selected from the genes listed in Table 6 or Table 7.

Datasets

The present inventors used MSKCC, CancerMap, Stephenson, CamCap and TOGA datasets in their analysis. However, other suitable datasets are and will become available skilled person. Generally, the datasets comprise a plurality of expression profiles from patient or tumour samples. The size of the dataset can vary. For example, the dataset may comprise expression profiles from at least 20, optionally at least 50, at least 100, at least 200, at least 300, at least 400 or at least 500 patient or tumour samples. Preferably the dataset comprises expression profiles from at least 500 patients or tumours.

In some embodiments, the methods of the invention use expression profiles from multiple datasets. For example, in some embodiments, the methods use expression profiles from at least 2 datasets, each data set comprising expression profiles from at least 250 patients or tumours.

The patient or tumour expression profiles may comprise information on the levels of expression of a subset of genes, for example at least 10, at least 40, at least 100, at least 500, at least 1000, at least 1500, at least 2000, at least 5000 or at least 10000 genes. Preferably, the patient expression profiles comprise expression data for at least 500 genes. In the analysis steps of the various Methods of the invention, any selection of a subset of genes will be taken from the genes present in the datasets.

Classification of Cancer

The methods and biomarkers disclosed herein are useful in classifying cancers according to their likelihood of progression (and hence are useful in the prognosis of cancer). The present invention is particularly focused on prostate cancer, but the methods can be used for other cancers. In particular, the list of genes in Table 2, for example, has been found to be indicative of progression of a range of cancers, including prostate cancer. Cancers that are likely or will progress are referred to by the inventors as DESNT cancers. References to DESNT cancer herein refer to cancers that are predicted to progress. References to DESNT status herein refer to an indicator of whether or not a cancer will progress. Aggressive cancers are cancers that progress.

Cancer types that can be classified according to methods of the invention include acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy-cell tumor, head cancer, hyperplasia, hyperplastic comeal nerve tumor, in situ carcinoma, intestinal ganglioneuroma, islet cell tumor, Kaposi's sarcoma, kidney cancer, larynx cancer, leiomyomater tumor, liver cancer, lung cancer, lymphomas, malignant carcinoid, malignant hypercalcemia, malignant melanomas, marfanoid habitus tumor, medullary carcinoma, metastatic skin carcinoma, mucosal neuromas, mycosis fungoide, myelodysplastic syndrome, myeloma, neck cancer, neural tissue cancer, neuroblastoma, osteogenic sarcoma, osteosarcoma, ovarian tumor, pancreas cancer, parathyroid cancer, pheochromocytoma, polycythemia vera, primary brain tumor, prostate cancer, rectum cancer, renal cell tumor, retinoblastoma, rhabdomyosarcoma, seminoma, skin cancer, small-cell lung tumor, soft tissue sarcoma, squamous cell carcinoma, stomach cancer, thyroid cancer, topical skin lesion, veticulum cell sarcoma, or Wilm's tumor.

Of particular relevance to the present invention is prostate cancer, colorectal cancer and breast cancer.

References herein are made to “aggressive cancer” including “aggressive prostate cancer”. Aggressive prostate cancer can be defined as a cancer that requires treatment to prevent, halt or reduce disease progression and potential further complications (such as metastases or metastatic progression). Ultimately, aggressive prostate cancer is prostate cancer that, if left untreated, will spread outside the prostate and may kill the patient. The present invention is useful in detecting some aggressive cancers, including aggressive prostate cancers.

Prostate cancer can be classified according to The American Joint Committee on Cancer (AJCC) tumour-nodes-metastasis (TNM) staging system. The T score describes the size of the main (primary) tumour and whether it has grown outside the prostate and into nearby organs. The N score describes the spread to nearby (regional) lymph nodes. The M score indicates whether the cancer has metastasised (spread) to other organs of the body:

T1 tumours are too small to be seen on scans or felt during examination of the prostate—they may have been discovered by needle biopsy, after finding a raised PSA level. T2 tumours are completely inside the prostate gland and are divided into 3 smaller groups:

    • T2a—The tumour is in only half of one of the lobes of the prostate gland;
    • T2b—The tumour is in more than half of one of the lobes;
    • T2c—The tumour is in both lobes but is still inside the prostate gland.

T3 tumours have broken through the capsule (covering) of the prostate gland—they are divided into 2 smaller groups:

    • T3a—The tumour has broken through the capsule (covering) of the prostate gland;
    • T3b—The tumour has spread into the seminal vesicles.

T4 tumours have spread into other body organs nearby, such as the rectum (back passage), bladder, muscles or the sides of the pelvic cavity. Stage T3 and T4 tumours are referred to as locally advanced prostate cancer.

Lymph nodes are described as being ‘positive’ if they contain cancer cells. If a lymph node has cancer cells inside it, it is usually bigger than normal. The more cancer cells it contains, the bigger it will be:

    • NX—The lymph nodes cannot be checked;
    • N0—There are no cancer cells in lymph nodes close to the prostate;
    • N1—There are cancer cells present in lymph nodes.

M staging refers to metastases (cancer spread):

    • M0—No cancer has spread outside the pelvis;
    • M1—Cancer has spread outside the pelvis;
    • M1a—There are cancer cells in lymph nodes outside the pelvis;
    • M1b—There are cancer cells in the bone;
    • M1c—There are cancer cells in other places.

Prostate cancer can also be scored using the Gleason grading system, which uses a histological analysis to grade the progression of the disease. A grade of 1 to 5 is assigned to the cells under examination, and the two most common grades are added together to provide the overall Gleason score. Grade 1 closely resembles healthy tissue, including closely packed, well-formed glands, whereas grade 5 does not have any (or very few) recognisable glands. Scores of less than 6 have a good prognosis, whereas scores of 6 or more are classified as more aggressive. The Gleason score was refined in 2005 by the International Society of Urological Pathology and references herein refer to these scoring criteria (Epstein J I, Allsbrook W C Jr, Amin M B, Egevad L L; ISUP Grading Committee. The 2005 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason grading of prostatic carcinoma. Am J Surg Pathol 2005; 29(9):1228-42). The Gleason score is detected in a biopsy, i.e. in the part of the tumour that has been sampled. A Gleason 6 prostate may have small foci of aggressive tumour that have not been sampled by the biopsy and therefore the Gleason is a guide. The lower the Gleason score the smaller the proportion of the patients will have aggressive cancer. Gleason score in a patient with prostate cancer can go down to 2, and up to 10. Because of the small proportion of low Gleasons that have aggressive cancer, the average survival is high, and average survival decreases as Gleason increases due to being reduced by those patients with aggressive cancer (i.e. there is a mixture of survival rates at each Gleason score).

Prostate cancers can also be staged according to how advanced they are. This is based on the TMN scoring as well as any other factors, such as the Gleason score and/or the PSA test. The staging can be defined as follows:

Stage I:

    • T1, N0, M0, Gleason score 6 or less, PSA less than 10
    • OR
    • T2a, N0, M0, Gleason score 6 or less, PSA less than 10

Stage IIA:

    • T1, N0, M0, Gleason score of 7, PSA less than 20
    • OR
    • T1, N0, M0, Gleason score of 6 or less, PSA at least 10 but less than 20:
    • OR
    • T2a or T2b, N0, M0, Gleason score of 7 or less, PSA less than 20

Stage IIB:

    • T2c, N0, M0, any Gleason score, any PSA
    • OR
    • T1 or T2, N0, M0, any Gleason score, PSA of 20 or more:
    • OR
    • T1 or T2, N0, M0, Gleason score of 8 or higher, any PSA

Stage III:

    • T3, N0, M0, any Gleason score, any PSA

Stage IV:

    • T4, N0, M0, any Gleason score, any PSA
    • OR
    • Any T, N1, M0, any Gleason score, any PSA:
    • OR
    • Any T, any N, M1, any Gleason score, any PSA

In the present invention, an aggressive cancer is defined functionally or clinically: namely a cancer that can progress. This can be measured by PSA failure. When a patient has surgery or radiation therapy, the prostate cells are killed or removed. Since PSA is only made by prostate cells the PSA level in the patient's blood reduces to a very low or undetectable amount. If the cancer starts to recur, the PSA level increases and becomes detectable again. This is referred to as “PSA failure”. An alternative measure is the presence of metastases or death as endpoints.

Increase in Gleason and stage as defined above can also be considered as progression. However, a DESNT characterisation is independent of Gleason, stage and PSA. It provides additional information about the development of aggressive cancer in addition to Gleason, stage and PSA. It is therefore a useful independent predictor of outcome. Nevertheless, DESNT status can be combined with Gleason, tumour stage and/or PSA.

Thus, the methods of the invention provide methods of classifying cancer, some methods comprising determining the expression level or expression status of a one or members of a biomarker panel. The panel of genes may be determined using a method of the invention. In some embodiments, the panel of genes may comprise at least 5, at least 10, at least 15 or all 20 of the genes listed in Table 3. The panel of genes may comprise at least 5, at least 10, at least 20, at least 30, at least 40 or all 45 genes listed in Table 2. Other biomarker panels of the invention, or those generated using methods of the invention, may also be used.

The cancer may be described as progressive when the status of one or more of those genes (for example at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or 100% of the genes) is considered to have an abnormal status. An abnormal status can be defined as an expression status (for example as determined by the level of expression, by DNA methylation or other epigenetic factors) that differs from a healthy or non-progressive cancer state. This may be determined according to a previously determined reference expression status of the same genes being analysed, or may be achieved by determining the status of one or more control or housekeeping genes. Housekeeping genes are generally considered to be expressed at the same levels in progressed and non-progressed patients. Therefore, it is possible to determine the ratio of the test genes to your control genes. The ratio would be different in normal and progressed tissue. As noted above, the housekeeping genes of Table 6 or Table 7 can be used.

For example, in one embodiment, a cancer is defined as progressive or potentially/likely to be progressive when at least 50%, at least 60%, at least 70%, at least 80% or at least 90% of at least 15 genes listed in Table 3 are determined to have an abnormal expression status (for example at least 80% of at least 15 genes in Table 3). In another embodiment, a cancer is defined as progressive or potentially/likely to be progressive when at least 50%, at least 60%, at least 70%, at least 80% or at least 90% of at least 40 genes listed in Table 2 are determined to have an abnormal expression status (for example at least 80% of at least 40 genes in Table 2).

Determining the expression status of a gene may comprise determining the level of expression of the gene. Expression status and levels of expression as used herein can be determined by methods known the skilled person. For example, this may refer to the up or down-regulation of a particular gene or genes, as determined by methods known to a skilled person. Epigenetic modifications may be used as an indicator of expression, for example determining DNA methylation status, or other epigenetic changes such as histone marking, RNA changes or conformation changes. Epigenetic modifications regulate expression of genes in DNA and can influence efficacy of medical treatments among patients. Aberrant epigenetic changes are associated with many diseases such as, for example, cancer. DNA methylation in animals influences dosage compensation, imprinting, and genome stability and development. Methods of determining DNA methylation are known to the skilled person (for example methylation-specific PCR, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, use of microarrays, reduced representation bisulfate sequencing (RRBS) or whole genome shotgun bisulfate sequencing (NGBS). In addition, epigenetic changes may include changes in conformation of chromatin.

The expression status of a gene may also be judged examining epigenetic features. Modification of cytosine in DNA by, for example, methylation can be associated with alterations in gene expression. Other way of assessing epigenetic changes include examination of histone modifications (marking) and associated genes, examination of non-coding RNAs and analysis of chromatin conformation. Examples of technologies that can be used to examine epigenetic status are provided in the following publications:

  • 1. Zhang, G. & Pradhan, S. Mammalian epigenetic mechanisms. IUBMB life (2014).
  • 2. Grønbæk, K. et al. A critical appraisal of tools available for monitoring epigenetic changes in clinical samples from patients with myeloid malignancies. Haematologica 97, 1380-1388 (2012).
  • 3. Ulahannan, N. & Greally, J. M. Genome-wide assays that identify and quantify modified cytosines in human disease studies. Epigenetics Chromatin 8, 5 (2015).
  • 4. Crutchley, J. L., Wang, X., Ferraiuolo, M. A. & Dostie, J. Chromatin conformation signatures: ideal human disease biomarkers? Biomarkers (2010).
  • 5. Esteller, M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet. 8, 286-298 (2007).

If an expression status is found to be abnormal, this refers to a situation in which the biomarker's status in a particular sample differs from the status generally found in average samples (i.e. healthy samples or samples obtained from patients that do not have DESNT cancer). In the present invention, the presence of an abnormal expression status can be indicative of DESNT cancer. For example, an abnormal status might be determined using epigenetic factors or determining the level of gene expression (for example RNA level). With reference to the genes listed in Table 2, a decrease in gene expression or a change in expression status that results in a decrease in expression of that gene is indicative of DESNT cancer. Thus, the presence of an abnormal expression status in at least 5, at least 10, at least 20, at least 30, at least 40 or all 45 genes listed in Table 2 is indicative of DESNT cancer. Alternatively, a threshold may be determined by the skilled person that is an indicative measure of the expression status of at least 5, at least 10, at least 20, at least 30, at least 40 or all 45 genes listed in Table 2. If, for a given patient sample, the average expression status is below said threshold (due to a decrease in expression of one or more genes, or preferably the majority of the genes being analysed), this is indicative of DESNT cancer.

In some embodiments, a decrease in the expression status or level of expression of at least 5, at least 10, at least 20, at least 30, at least 40 or all 45 genes listed in Table 2 is indicative of DESNT cancer.

In some cases, a new biomarker panel may have been generated using the methods of the invention, and that used to classify cancer. For example, in a second analysis performed by the investigators using a different combination of datasets 35 genes were found to be down regulated in at least 67 of 100 runs of the LPD analysis of each dataset (Table 5). There was a 27 gene overlap with the 45 commonly down-regulated genes identified in the first analysis. Therefore, the biomarker panel may comprise at least 5, at least 10, at least 20, at least 30 or all 35 genes listed in table 5.

Usually, in order to determine if an expressions status is abnormal, it is necessary to include in the method a determination of the expression status of at least 1 control gene in the patient sample. Based on the expression status of the at least 1 control gene, an index value for the prognostic genes can be determined. If the index value is below a certain threshold, because of a decrease in expression of the prognostic genes, this is indicative of cancer progression or predictive of cancer progression (i.e. DESNT cancer). Said threshold is determined by normalising the expression levels of the prognostic genes using the 1 or more control genes and determining if at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 95% of the prognostic genes have a decreased expression level. In some embodiments, 100% of the prognostic genes having a decreased expression level is indicative or predictive of cancer progression (i.e. DESNT cancer).

In one embodiment of the invention, the method comprises:

    • a) enriching a biological sample for an analyte of interest (for example RNA, DNA or protein); and
    • b) determining the epigenetic status of the analyte of interest in the enriched sample.

Proteins can also be used to determine expression levels, and suitable method are known to the skilled person. This is also discussed further below.

Apparatus and Media

The present invention also provides an apparatus configured to perform any method of the invention.

FIG. 4 shows an apparatus or computing device 100 for carrying out a method as disclosed herein. Other architectures to that shown in FIG. 3 may be used as will be appreciated by the skilled person.

Referring to the Figure, the meter 100 includes a number of user interfaces including a visual display 110 and a virtual or dedicated user input device 112. The meter 100 further includes a processor 114, a memory 116 and a power system 118. The meter 100 further comprises a communications module 120 for sending and receiving communications between processor 114 and remote systems. The meter 100 further comprises a receiving device or port 122 for receiving, for example, a memory disk or non-transitory computer readable medium carrying instructions which, when operated, will lead the processor 114 to perform a method as described herein.

The processor 114 is configured to receive data, access the memory 116, and to act upon instructions received either from said memory 116, from communications module 120 or from user input device 112. The processor controls the display 110 and may communicate date to remote parties via communications module 120.

The memory 116 may comprise computer-readable instructions which, when read by the processor, are configured to cause the processor to perform a method as described herein.

The present invention further provides a machine-readable medium (which may be transitory or non-transitory) having instructions stored thereon, the instructions being configured such that when read by a machine, the instructions cause a method as disclosed herein to be carried out.

Other Methods and Uses of the Invention

The methods of the invention may be combined with a further test to further assist the diagnosis, for example a PSA test, a Gleason score analysis, or a determination of the staging of the cancer. In PSA methods, the amount of prostate specific antigen in a blood sample is quantified. Prostate-specific antigen is a protein produced by cells of the prostate gland. If levels are elevated in the blood, this may be indicative of prostate cancer. An amount that constitutes “elevated” will depend on the specifics of the patient (for example age), although generally the higher the level, the more like it is that prostate cancer is present. A continuous rise in PSA levels over a period of time (for example a week, a month, 6 months or a year) may also be a sign of prostate cancer. A PSA level of more than 4 ng/ml or 10 ng/ml, for example, may be indicative of prostate cancer, although prostate cancer has been found in patients with PSA levels of 4 or less.

In some embodiments of the invention, the methods are able to differentially diagnose aggressive cancer (such as aggressive prostate cancer) from non-aggressive cancer. This can be achieved by determining the DESNT status of the cancer. Alternatively or additionally, this may be achieved by comparing the level of expression found in the test sample for each of the genes being quantified with that seen in patients presenting with a suitable reference, for example samples from healthy patients, patients suffering from non-aggressive cancer, or using the control or housekeeping genes as discussed herein. In this way, unnecessary treatment can be avoided and appropriate treatment can be administered instead (for example antibiotic treatment for prostatitis, such as fluoxetine, gabapentin or amitriptyline, or treatment with an alpha reductase inhibitor, such as Finasteride).

In one embodiment of the invention, the method comprises the steps of:

    • 1) detecting RNA in a biological sample obtained from a patient; and
    • 2) quantifying the expression levels of each of the RNA molecules.

The RNA transcripts detected correspond to the biomarkers being quantified (and hence the genes whose expression levels are being measured). In some embodiments, the RNA being detected is the RNA (e.g. mRNA, lncRNA or small RNA) corresponding to at least 40 genes listed in Table 2 (optionally at least all of the genes listed in Table 2), or at least 15 genes listed in Table 3 (optionally all of the genes listed in Table 3). Such methods may be undertaken on a sample previously obtained from a patient, optionally a patient that has undergone a DRE to massage the prostate and increase the amount of RNA in the resulting sample. Alternatively, the method itself may include a step of obtaining a biological sample from a patient.

In one embodiment, the RNA transcripts detected correspond to a selection or all of the genes listed in Table 1. A subset of genes can then be selected for further analysis, such as LDP analysis.

In some embodiments of the invention, the biological sample may be enriched for RNA (or other analyte, such as protein) prior to detection and quantification. The step of enrichment is optional, however, and instead the RNA can be obtained from raw, unprocessed biological samples, such as whole urine. The step of enrichment can be any suitable pre-processing method step to increase the concentration of RNA (or other analyte) in the sample. For example, the step of enrichment may comprise centrifugation and filtration to remove cells from the sample.

In one embodiment of the invention, the method comprises:

    • a) enriching a biological sample for RNA by amplification, filtration or centrifugation, optionally wherein the biological sample has been obtained from a patient that has undergone DRE;
    • b) detecting RNA transcripts in the enriched sample; and
    • c) quantifying the expression levels of each of the detected RNA molecules.

The step of detection may comprise a detection method based on hybridisation, amplification or sequencing, or molecular mass and/or charge detection, or cellular phenotypic change, or the detection of binding of a specific molecule, or a combination thereof. Methods based on hybridisation include Northern blot, microarray, NanoString, RNA-FISH, branched chain hybridisation assay analysis, and related methods. Methods based on amplification include quantitative reverse transcription polymerase chain reaction (qRT-PCT) and transcription mediated amplification, and related methods. Methods based on sequencing include Sanger sequencing, next generation sequencing (high throughput sequencing by synthesis) and targeted RNAseq, nanopore mediated sequencing (MinION), Mass Spectrometry detection and related methods of analysis. Methods based on detection of molecular mass and/or charge of the molecule include, but is not limited to, Mass Spectrometry. Methods based on phenotypic change may detect changes in test cells or in animals as per methods used for screening miRNAs (for example, see Cullen & Arndt, Immunol. Cell Biol., 2005, 83:217-23). Methods based on binding of specific molecules include detection of binding to, for example, antibodies or other binding molecules such as RNA or DNA binding proteins.

In some embodiments, the method may comprise a step of converting RNA transcripts into cDNA transcripts. Such a method step may occur at any suitable time in the method, for example before enrichment (if this step is taking place, in which case the enrichment step is a cDNA enrichment step), before detection (in which case the detection step is a step of cDNA detection), or before quantification (in which case the expression levels of each of the detected RNA molecules by counting the number of transcripts for each cDNA sequence detected).

Methods of the invention may include a step of amplification to increase the amount of RNA or cDNA that is detected and quantified. Methods of amplification include PCR amplification.

In some methods of the invention, detection and quantification of cDNA-binding molecule complexes may be used to determine gene expression. For example, RNA transcripts in a sample may be converted to cDNA by reverse-transcription, after which the sample is contacted with binding molecules specific for the genes being quantified, detecting the presence of a of cDNA-specific binding molecule complex, and quantifying the expression of the corresponding gene.

There is therefore provided the use of cDNA transcripts corresponding to one or more genes identified in the biomarker panels, for use in methods of detecting, diagnosing or determining the prognosis of prostate cancer, in particular prostate cancer.

Once the expression levels are quantified, a diagnosis of cancer (in particular aggressive prostate cancer) can be determined. The methods of the invention can also be used to determine a patient's prognosis, determine a patient's response to treatment or to determine a patient's suitability for treatment for cancer, since the methods can be used to predict cancer progression.

The methods may further comprise the step of comparing the quantified expression levels with a reference and subsequently determining the presence or absence of cancer, in particular aggressive prostate cancer.

Analyte enrichment may be achieved by any suitable method, although centrifugation and/or filtration to remove cell debris from the sample may be preferred. The step of obtaining the RNA from the enriched sample may include harvesting the RNA from microvesicles present in the enriched sample.

The step of sequencing the RNA can be achieved by any suitable method, although direct RNA sequencing, RT-PCR or sequencing-by-synthesis (next generation, or NGS, high-throughput sequencing) may be preferred. Quantification can be achieved by any suitable method, for example counting the number of transcripts identified with a particular sequence. In one embodiment, all the sequences (usually 75-100 base pairs) are aligned to a human reference. Then for each gene defined in an appropriate database (for example the Ensembl database) the number of sequences or reads that overlap with that gene (and don't overlap any other) are counted. To compare a gene between samples it will usually be necessary to normalise each sample so that the amount is the equivalent total amount of sequenced data. Methods of normalisation will be apparent to the skilled person.

As would be apparent to a person of skill in the art, any measurements of analyte concentration may need to be normalised to take in account the type of test sample being used and/or and processing of the test sample that has occurred prior to analysis.

The level of expression of a gene can be compared to a control to determine whether the level of expression is higher or lower in the sample being analysed. If the level of expression is higher in the sample being analysed relative to the level of expression in the sample to which the analysed sample is being compared, the gene is said to be up-regulated. If the level of expression is lower in the sample being analysed relative to the level of expression in the sample to which the analysed sample is being compared, the gene is said to be down-regulated.

In embodiments of the invention, the levels of expression of genes can be prognostic. As such, the present invention is particularly useful in distinguishing prostate cancers requiring intervention (aggressive prostate cancer), and those not requiring intervention (indolent or non-aggressive prostate cancer), avoiding the need for unnecessary procedures and their associated side effects. The most likely use of the present invention will be the use of the 500 gene panel to determine if an additional patient sample is DESNT by LPD analysis, the use of the 45 gene panel to determine if a patent is DESNT by measuring down-regulation of genes in the patient sample, and use of the 20 gene panel by RF analysis.

In some embodiments of the invention, the biomarker panels may be combined with another test such as the PSA test, PCA3 test, Prolaris, or Oncotype DX test. Other tests may be a histological examination to determine the Gleason score, or an assessment of the stage of progression of the cancer.

In a still further embodiment of the invention there is provided a method for determining the suitability of a patient for treatment for prostate cancer, comprising classifying the cancer according to a method of the invention, and deciding whether or not to proceed with treatment for prostate cancer if cancer progression is diagnosed or suspected, in particular if aggressive prostate cancer is diagnosed or suspected.

There is also provided a method of monitoring a patient's response to therapy, comprising classifying the cancer according to a method of the invention using a biological sample obtained from a patient that has previously received therapy for prostate cancer (for example chemotherapy and/or radiotherapy). In some embodiments, the method is repeated in patients before and after receiving treatment. A decision can then be made on whether to continue the therapy or to try an alternative therapy based on the comparison of the levels of expression. For example, if DESNT cancer is detected or suspected after receiving treatment, alternative treatment therapies may be used. The method can be repeated to see if the treatment is successful at downgrading a patient's cancer from DESNT to non-DESNT.

In one embodiment, there is therefore provided a method comprising:

    • a) conducting a diagnostic method of the invention of a sample obtained from a patient to determine the presence or absence of a DESNT cancer (such as DESNT prostate cancer);
    • b) providing treatment for cancer where DESNT cancer is found or suspected;
    • c) subsequently conducting a diagnostic method of the invention of a further sample obtained from a patient to determine the presence or absence of a DESNT cancer; and
    • d) maintaining, changing or withdrawing the therapy for cancer.

In some embodiments of the invention, the methods and biomarker panels of the invention are useful for individualising patient treatment, since the effect of different treatments can be easily monitored, for example by measuring biomarker expression in successive urine samples following treatment. The methods and biomarkers of the invention can also be used to predict the effectiveness of treatments, such as responses to hormone ablation therapy.

In another embodiment of the invention there is provided a method of treating or preventing cancer in a patient (such as aggressive prostate cancer), comprising conducting a diagnostic method of the invention of a sample obtained from a patient to determine the presence or absence of a DESNT cancer, and, if DESNT caner is detected or suspected, administering cancer treatment. Methods of treating prostate cancer may include resecting the tumour and/or administering chemotherapy and/or radiotherapy to the patient.

The methods of treating cancer of the present invention are particularly useful in the treatment of aggressive prostate cancer. In some embodiments, the methods of treatment are performed on patients who have been identified as having DESNT cancer.

If possible, treatment for prostate cancer involves resecting the tumour or other surgical techniques. For example, treatment may comprise a radical or partial prostatectomy, trans-urethral resection, orchiectomy or bilateral orchiectomy. Treatment may alternatively or additionally involve treatment by chemotherapy and/or radiotherapy. Chemotherapeutic treatments include docetaxel, abiraterone or enzalutamide.

Radiotherapeutic treatments include external beam radiotherapy, pelvic radiotherapy, post-operative radiotherapy, brachytherapy, or, as the case may be, prophylactic radiotherapy. Other treatments include adjuvant hormone therapy (such as androgen deprivation therapy, cryotherapy, high-intensity focused ultrasound, immunotherapy, brachytherapy and/or administration of bisphosphonates and/or steroids.

In another embodiment of the invention, there is provided a method identifying a drug useful for the treatment of cancer, comprising:

    • a) conducting a diagnostic method of the invention of a sample obtained from a patient to determine the presence or absence of a DESNT cancer;
    • b) administering a candidate drug to the patient;
    • c) subsequently conducting a diagnostic method of the invention on a further sample obtained from a patient to determine the presence or absence of a DESNT cancer; and
    • d) comparing the finding in step (a) with the finding in step (c), wherein a reduction in the prevalence or likelihood of DESNT cancer identifies the drug candidate as a possible treatment for cancer.

Biological Samples

Methods of the invention may comprise steps carried out on biological samples. The biological sample that is analysed may be a urine sample, a semen sample, a prostatic exudate sample, or any sample containing macromolecules or cells originating in the prostate, a whole blood sample, a serum sample, saliva, or a biopsy (such as a prostate tissue sample or a tumour sample). Most commonly for prostate cancer the biological sample is from a prostate biopsy, prostatectomy or TURP. The method may include a step of obtaining or providing the biological sample, or alternatively the sample may have already been obtained from a patient, for example in ex vivo methods. The samples are considered to be representative of the level of expression of the relevant genes in the potentially cancerous prostate tissue, or other cells within the prostate, or microvesicles produced by cells within the prostate or blood or immune system. Hence the methods of the present invention may use quantitative data on RNA produced by cells within the prostate and/or the blood system and/or bone marrow in response to cancer, to determine the presence or absence of prostate cancer.

The methods of the invention may be carried out on one test sample from a patient. Alternatively, a plurality of test samples may be taken from a patient, for example at least 2, 3, 4 or 5 samples. Each sample may be subjected to a separate analysis using a method of the invention, or alternatively multiple samples from a single patient undergoing diagnosis could be included in the method.

Further Analytical Methods Used in the Invention

The level of expression of a gene or protein from a biomarker panel of the invention can be determined in a number of ways. Levels of expression may be determined by, for example, quantifying the biomarkers by determining the concentration of protein in the sample, if the biomarkers are expressed as a protein in that sample. Alternatively, the amount of RNA or protein in the sample (such as a tissue sample) may be determined. Once the level of expression has been determined, the level can optionally be compared to a control. This may be a previously measured level of expression (either in a sample from the same subject but obtained at a different point in time, or in a sample from a different subject, for example a healthy subject or a subject with non-aggressive cancer, i.e. a control or reference sample) or to a different protein or peptide or other marker or means of assessment within the same sample to determine whether the level of expression or protein concentration is higher or lower in the sample being analysed. Housekeeping genes can also be used as a control. Ideally, controls are a protein or DNA marker that generally does not vary significantly between samples.

Other methods of quantifying gene expression include RNA sequencing, which in one aspect is also known as whole transcriptome shotgun sequencing (WTSS). Using RNA sequencing it is possible to determine the nature of the RNA sequences present in a sample, and furthermore to quantify gene expression by measuring the abundance of each RNA molecule (for example, mRNA or microRNA transcripts). The methods use sequencing-by-synthesis approaches to enable high throughout analysis of samples.

There are several types of RNA sequencing that can be used, including RNA PolyA tail sequencing (there the polyA tail of the RNA sequences are targeting using polyT oligonucleotides), random-primed sequencing (using a random oligonucleotide primer), targeted sequence (using specific oligonucleotide primers complementary to specific gene transcripts), small RNA/non-coding RNA sequencing (which may involve isolating small non-coding RNAs, such as microRNAs, using size separation), direct RNA sequencing, and real-time PCR. In some embodiments, RNA sequence reads can be aligned to a reference genome and the number of reads for each sequence quantified to determine gene expression. In some embodiments of the invention, the methods comprise transcription assembly (de-novo or genome-guided).

RNA, DNA and protein arrays (microarrays) may be used in certain embodiments. RNA and DNA microarrays comprise a series of microscopic spots of DNA or RNA oligonucleotides, each with a unique sequence of nucleotides that are able to bind complementary nucleic acid molecules. In this way the oligonucleotides are used as probes to which the correct target sequence will hybridise under high-stringency condition. In the present invention, the target sequence can be the transcribed RNA sequence or unique section thereof, corresponding to the gene whose expression is being detected. Protein microarrays can also be used to directly detect protein expression. These are similar to DNA and RNA microarrays in that they comprise capture molecules fixed to a solid surface.

Capture molecules include antibodies, proteins, aptamers, nucleic acids, receptors and enzymes, which might be preferable if commercial antibodies are not available for the analyte being detected. Capture molecules for use on the arrays can be externally synthesised, purified and attached to the array. Alternatively, they can be synthesised in-situ and be directly attached to the array. The capture molecules can be synthesised through biosynthesis, cell-free DNA expression or chemical synthesis. In-situ synthesis is possible with the latter two.

Once captured on a microarray, detection methods can be any of those known in the art. For example, fluorescence detection can be employed. It is safe, sensitive and can have a high resolution. Other detection methods include other optical methods (for example colorimetric analysis, chemiluminescence, label free Surface Plasmon Resonance analysis, microscopy, reflectance etc.), mass spectrometry, electrochemical methods (for example voltametry and amperometry methods) and radio frequency methods (for example multipolar resonance spectroscopy).

Methods for detection of RNA or cDNA can be based on hybridisation, for example, Northern blot, Microarrays, NanoString, RNA-FISH, branched chain hybridisation assay, or amplification detection methods for quantitative reverse transcription polymerase chain reaction (qRT-PCR) such as TaqMan, or SYBR green product detection. Primer extension methods of detection such as: single nucleotide extension, Sanger sequencing. Alternatively, RNA can be sequenced by methods that include Sanger sequencing, Next Generation (high throughput) sequencing, in particular sequencing by synthesis, targeted RNAseq such as the Precise targeted RNAseq assays, or a molecular sensing device such as the Oxford Nanopore MinION device. Combinations of the above techniques may be utilised such as Transcription Mediated Amplification (TMA) as used in the Gen-Probe PCA3 assay which uses molecule capture via magnetic beads, transcription amplification, and hybridisation with a secondary probe for detection by, for example chemiluminescence.

RNA may be converted into cDNA prior to detection. RNA or cDNA may be amplified prior or as part of the detection.

The test may also constitute a functional test whereby presence of RNA or protein or other macromolecule can be detected by phenotypic change or changes within test cells. The phenotypic change or changes may include alterations in motility or invasion.

Commonly, proteins subjected to electrophoresis are also further characterised by mass spectrometry methods. Such mass spectrometry methods can include matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF).

MALDI-TOF is an ionisation technique that allows the analysis of biomolecules (such as proteins, peptides and sugars), which tend to be fragile and fragment when ionised by more conventional ionisation methods. Ionisation is triggered by a laser beam (for example, a nitrogen laser) and a matrix is used to protect the biomolecule from being destroyed by direct laser beam exposure and to facilitate vaporisation and ionisation. The sample is mixed with the matrix molecule in solution and small amounts of the mixture are deposited on a surface and allowed to dry. The sample and matrix co-crystallise as the solvent evaporates.

Additional methods of determining protein concentration include mass spectrometry and/or liquid chromatography, such as LC-MS, UPLC, a tandem UPLC-MS/MS system, and ELISA methods. Other methods that may be used in the invention include Agilent bait capture and PCR-based methods (for example PCR amplification may be used to increase the amount of analyte).

Methods of the invention can be carried out using binding molecules or reagents specific for the analytes (RNA molecules or proteins being quantified). Binding molecules and reagents are those molecules that have an affinity for the RNA molecules or proteins being detected such that they can form binding molecule/reagent-analyte complexes that can be detected using any method known in the art. The binding molecule of the invention can be an oligonucleotide, or oligoribonucleotide or locked nucleic acid or other similar molecule, an antibody, an antibody fragment, a protein, an aptamer or molecularly imprinted polymeric structure, or other molecule that can bind to DNA or RNA. Methods of the invention may comprise contacting the biological sample with an appropriate binding molecule or molecules. Said binding molecules may form part of a kit of the invention, in particular they may form part of the biosensors of in the present invention.

Aptamers are oligonucleotides or peptide molecules that bind a specific target molecule. Oligonucleotide aptamers include DNA aptamer and RNA aptamers. Aptamers can be created by an in vitro selection process from pools of random sequence oligonucleotides or peptides. Aptamers can be optionally combined with ribozymes to self-cleave in the presence of their target molecule. Other oligonucleotides may include RNA molecules that are complimentary to the RNA molecules being quantified. For example, polyT oligos can be used to target the polyA tail of RNA molecules.

Aptamers can be made by any process known in the art. For example, a process through which aptamers may be identified is systematic evolution of ligands by exponential enrichment (SELEX). This involves repetitively reducing the complexity of a library of molecules by partitioning on the basis of selective binding to the target molecule, followed by re-amplification. A library of potential aptamers is incubated with the target protein before the unbound members are partitioned from the bound members. The bound members are recovered and amplified (for example, by polymerase chain reaction) in order to produce a library of reduced complexity (an enriched pool). The enriched pool is used to initiate a second cycle of SELEX. The binding of subsequent enriched pools to the target protein is monitored cycle by cycle. An enriched pool is cloned once it is judged that the proportion of binding molecules has risen to an adequate level. The binding molecules are then analysed individually. SELEX is reviewed in Fitzwater & Polisky (1996) Methods Enzymol, 267:275-301.

Antibodies can include both monoclonal and polyclonal antibodies and can be produced by any means known in the art. Techniques for producing monoclonal and polyclonal antibodies which bind to a particular protein are now well developed in the art. They are discussed in standard immunology textbooks, for example in Roitt et al., Immunology, second edition (1989), Churchill Livingstone, London. The antibodies may be human or humanised, or may be from other species. The present invention includes antibody derivatives that are capable of binding to antigens. Thus, the present invention includes antibody fragments and synthetic constructs. Examples of antibody fragments and synthetic constructs are given in Dougall et al. (1994) Trends Biotechnol, 12:372-379. Antibody fragments or derivatives, such as Fab, F(ab′)2 or Fv may be used, as may single-chain antibodies (scAb) such as described by Huston et al. (993) Int Rev Immunol, 10:195-217, domain antibodies (dAbs), for example a single domain antibody, or antibody-like single domain antigen-binding receptors. In addition, antibody fragments and immunoglobulin-like molecules, peptidomimetics or non-peptide mimetics can be designed to mimic the binding activity of antibodies. Fv fragments can be modified to produce a synthetic construct known as a single chain Fv (scFv) molecule. This includes a peptide linker covalently joining VH and VL regions which contribute to the stability of the molecule.

Other synthetic constructs include CDR peptides. These are synthetic peptides comprising antigen binding determinants. These molecules are usually conformationally restricted organic rings which mimic the structure of a CDR loop and which include antigen-interactive side chains. Synthetic constructs also include chimeric molecules. Synthetic constructs also include molecules comprising a covalently linked moiety which provides the molecule with some desirable property in addition to antigen binding. For example, the moiety may be a label (e.g. a detectable label, such as a fluorescent or radioactive label), a nucleotide, or a pharmaceutically active agent.

In those embodiments of the invention in which the binding molecule is an antibody or antibody fragment, the method of the invention can be performed using any immunological technique known in the art. For example, ELISA, radio immunoassays or similar techniques may be utilised. In general, an appropriate autoantibody is immobilised on a solid surface and the sample to be tested is brought into contact with the autoantibody. If the cancer marker protein recognised by the autoantibody is present in the sample, an antibody-marker complex is formed. The complex can then be directed or quantitatively measured using, for example, a labelled secondary antibody which specifically recognises an epitope of the marker protein. The secondary antibody may be labelled with biochemical markers such as, for example, horseradish peroxidase (HRP) or alkaline phosphatase (AP), and detection of the complex can be achieved by the addition of a substrate for the enzyme which generates a colorimetric, chemiluminescent or fluorescent product. Alternatively, the presence of the complex may be determined by addition of a marker protein labelled with a detectable label, for example an appropriate enzyme. In this case, the amount of enzymatic activity measured is inversely proportional to the quantity of complex formed and a negative control is needed as a reference to determining the presence of antigen in the sample. Another method for detecting the complex may utilise antibodies or antigens that have been labelled with radioisotopes followed by a measure of radioactivity. Examples of radioactive labels for antigens include 3H, 14C and 125I.

The method of the invention can be performed in a qualitative format, which determines the presence or absence of a cancer marker analyte in the sample, or in a quantitative format, which, in addition, provides a measurement of the quantity of cancer marker analyte present in the sample. Generally, the methods of the invention are quantitative. The quantity of biomarker present in the sample may be calculated using any of the above described techniques. In this case, prior to performing the assay, it may be necessary to draw a standard curve by measuring the signal obtained using the same detection reaction that will be used for the assay from a series of standard samples containing known amounts or concentrations of the cancer marker analyte. The quantity of cancer marker present in a sample to be screened can then extrapolated from the standard curve.

Methods for determining gene expression as used in the present invention therefore include methods based on hybridization analysis of polynucleotides, methods based on sequencing of polynucleotides, proteomics-based methods, reverse transcription PCR, microarray-based methods and immunohistochemistry-based methods. References relating to measuring gene expression are also provided above.

Kit of Parts and Biosensors

In a still further embodiment of the invention there is provided a kit of parts for predicting cancer progression (detecting DESNT cancer) comprising a means for quantifying the expression or concentration of the biomarkers of the invention, or means of determining the expression status of the biomarkers of the invention. The means may be any suitable detection means. For example, the means may be a biosensor, as discussed herein. The kit may also comprise a container for the sample or samples and/or a solvent for extracting the biomarkers from the biological sample. The kit may also comprise instructions for use.

In some embodiments of the invention, there is provided a kit of parts for classifying cancer (for example, determining the likelihood of cancer progression) comprising a means for detecting the expression status (for example level of expression) of the biomarkers of the invention. The means for detecting the biomarkers may be reagents that specifically bind to or react with the biomarkers being quantified. Thus, in one embodiment of the invention, there is provided a method of diagnosing prostate cancer comprising contacting a biological sample from a patient with reagents or binding molecules specific for the biomarker analytes being quantified, and measuring the abundance of analyte-reagent or analyte-binding molecule complexes, and correlating the abundance of analyte-reagent or analyte-binding molecule complexes with the level of expression of the relevant protein or gene in the biological sample.

For example, in one embodiment of the invention, the method comprises the steps of:

    • a) contacting a biological sample with reagents or binding molecules specific for one or more of the biomarkers of the invention;
    • b) quantifying the abundance of analyte-reagent or analyte-binding molecule complexes for the biomarkers; and
    • c) correlating the abundance of analyte-reagent or analyte-binding molecule complexes with the expression level of the biomarkers in the biological sample.

The method may further comprise the step of d) comparing the expression level of the biomarkers in step c) with a reference to classify the status of the cancer, in particular to determine the likelihood of cancer progression and hence the requirement for treatment (aggressive prostate cancer). Of course, in some embodiments, the method may additionally comprise conducting a statistical analysis, such as those described in the present invention. The patient can then be treated accordingly. Suitable reagents or binding molecules may include an antibody or antibody fragment, an oligonucleotide, an aptamer, an enzyme, a nucleic acid, an organelle, a cell, a biological tissue, imprinted molecule or a small molecule. Such methods may be carried out using kits of the invention.

The kit of parts may comprise a device or apparatus having a memory and a processor. The memory may have instructions stored thereon which, when read by the processor, cause the processor to perform one or more of the methods described above. The memory may further comprise a plurality of decision trees for use in the random forest analysis.

The kit of parts of the invention may be a biosensor. A biosensor incorporates a biological sensing element and provides information on a biological sample, for example the presence (or absence) or concentration of an analyte. Specifically, they combine a biorecognition component (a bioreceptor) with a physiochemical detector for detection and/or quantification of an analyte (such as RNA or a protein).

The bioreceptor specifically interacts with or binds to the analyte of interest and may be, for example, an antibody or antibody fragment, an enzyme, a nucleic acid (such as an aptamer), an organelle, a cell, a biological tissue, imprinted molecule or a small molecule. The bioreceptor may be immobilised on a support, for example a metal, glass or polymer support, or a 3-dimensional lattice support, such as a hydrogel support.

Biosensors are often classified according to the type of biotransducer present. For example, the biosensor may be an electrochemical (such as a potentiometric), electronic, piezoelectric, gravimetric, pyroelectric biosensor or ion channel switch biosensor. The transducer translates the interaction between the analyte of interest and the bioreceptor into a quantifiable signal such that the amount of analyte present can be determined accurately. Optical biosensors may rely on the surface plasmon resonance resulting from the interaction between the bioreceptor and the analyte of interest. The SPR can hence be used to quantify the amount of analyte in a test sample. Other types of biosensor include evanescent wave biosensors, nanobiosensors and biological biosensors (for example enzymatic, nucleic acid (such as RNA or an aptamer), antibody, epigenetic, organelle, cell, tissue or microbial biosensors).

The invention also provides microarrays (RNA, DNA or protein) comprising capture molecules (such as RNA or DNA oligonucleotides) specific for each of the biomarkers being quantified, wherein the capture molecules are immobilised on a solid support. The microarrays are useful in the methods of the invention.

In one embodiment of the invention, there is provided a method of classifying prostate cancer comprising determining the expression level of one or more of the biomarkers of the invention, and optionally comparing the so determined values to a reference.

The biomarkers that are analysed can be determined according to the Methods of the invention. Alternatively, the biomarker panels provided herein can be used. At least 15 (preferably all 20) of the genes listed in Table 3 are useful in classifying prostate cancer. At least 40 (preferably all 45) of the genes listed in Table 2 are useful in classifying several different types of cancer and determining the likelihood of progression, including the classification of prostate cancer.

Features for the second and subsequent aspects of the invention are as for the first aspect of the invention mutatis mutandis.

The present invention shall now be further described with reference to the following examples, which are present for the purposes of illustration only and are not to be construed as being limiting on the invention.

In the Examples, reference is made to a number of Figures, as follows:

FIG. 1. Latent Process Decomposition (LPD), gene correlations and clinical outcome. a, LPD analysis of Affymetrix expression data from the MSKCC datasets divided the samples into eight processes, each represented here by a bar chart. Samples are represented in all eight processes and height of each bar corresponds to the proportion (p) of the signature that can be assigned to each LPD process. Samples are assigned to the LPD group in which they exhibit the highest value of pi. LPD was performed using the 500 gene probes with the greatest variation in expression between samples in the MSKCC dataset. The process containing DESNT cancers is indicated. b, List of datasets used in LPD analysis. The unique number of primary cancer and normal specimens used in LPD are indicated. FF, fresh frozen specimen; FFPE, formalin-fixed paraffin embedded specimen. The CancerMap and CamCap were not independent having 40 cancers in common. Clinical and molecular details for the CancerMap dataset are given in Supplementary Information Table 2 and Supplementary Data 1. c, Correlations of average levels of gene expression between cancers designated as DESNT. All six comparisons for the MSKCC, CancerMap, Stephenson and Klein datasets are shown. The expression levels of each gene have been normalised across all samples to mean 0 and standard deviation 1. d, Kaplan-Meier PSA failure plots for the MSKCC, CancerMap and Stephenson datasets. The number of cancers in each group is indicated in the bottom right corner of each Kaplan-Meier plot. The number of patients with PSA failure is indicated in parentheses.

FIG. 2. Genes commonly down regulated in DESNT poor prognosis prostate cancer. a, Number of genes with significantly altered expression in DESNT cancers compared to non-DESNT cancers (P<0.01 after correction for False Discovery Rate). 45 genes had lower expression in DESNT cancers in all four expression microarray datasets, based on a stringency requirement of being down-regulated in at least 80 of 100 independent LPD runs. b, List of the 45 genes according to biological grouping. Encoded protein functions are shown in Supplementary Information Table 3. Although some of the 45 genes are preferentially expressed in stromal tissue we found no correlation between stromal content and clinical outcome in both the CancerMap and CamCap patient series, where data on cellular composition were available. When patients were stratified into two groups (above and below median stromal content) Kaplan-Meier plots failed to show outcome difference for both the CancerMap (Log-rank test, p=0.159) and CamCap (p=0.261) patient series. c. Relationship between the genes in published poor prognosis signatures for prostate cancer and the DESNT classification for human prostate cancer, represented as a circos plot. Links to the 45 commonly down-regulated genes are shown in brown.

FIG. 3. Comparison of RF-DESNT and non-RF-DESNT cancers in The Cancer Genome Atlas dataset. A 20-gene random forest (RF) classifier was used to identify DESNT cancers (designated RF-DESNT cancers). The types of genetic alteration are shown for each gene (mutations, fusions, deletions, and overexpression). Clinical parameters including biochemical recurrence (BCR) are represented at the bottom together with groups for iCluster, methylation, somatic copy number alteration (SVNA) and mRNA7,20. When mutations and homozygous deletions for each gene were combined RF-DESNT cancers contained an excess of genetic alterations in BRCA2 (P=0.021, X2 test) and TP53 (P=0.0038), but after correcting for multiple testing these differences were not significant (P>0.05).

FIG. 5. Log-likelihood plots. The log-likelihood (vertical axis) versus number of processes (horizontal-axis) using the MAP solution (upper curve) and maximum likelihood solution (lower curve) for each dataset. For the maximum likelihood model, the peak in log-likelihood indicates the number of processes to use. For the MAP model, a Bayesian prior is used to penalize construction of an over-complex model. The log-likelihood rises to a plateau after which no further gain is to be made indicating the maximum number of processes that should be used.

FIG. 6. Latent Process Decomposition (LPD) analysis of transcriptome datasets. The MSKCC, Stephenson, CancerMap, CamCap and Klein datasets were each decomposed into the optimal number of processes indicated from their log-likelihood plot (FIG. 5). A single sample is represented across all processes and height of each bar corresponds to the proportion (pi) of the signature that can be attributed to each LPD process. Samples are assigned to the LPD group in which they exhibit the highest value of pi. For the MSKCC, CancerMap, and CamCap datasets red, blue and green denote cancers with different risks of progression based on clinical parameters as defined in the Methods. For the Stephenson dataset only pathological stage is indicated because some of the parameters required for designation into the three risk groups are missing. Clinical data from the Klein dataset is not publically available. For each dataset, the process containing DESNT cancers is indicated. Log-likelihood plots and LPD decompositions were performed using the 500 gene loci whose expression varied most in the MSKCC dataset.

FIG. 7. Analysis of outcome for DESNT cancers identified by LPD. (a-d) Kaplan-Meier PSA failure plots for the MSKCC (a), CancerMap (b), Stephenson (c), and CamCap (d) datasets. For each dataset, the cancers assigned to the DESNT process by LPD are comparing to the remaining cancers. The number of cancers in each group is indicated in the bottom right corner of each plot. The number of cancers with PSA failure is indicated in parentheses. The Kaplan-Meier plot shown represents the most frequent (mode) p-value from 100 LPD runs each performed using randomly chosen seed parameters (FIG. 12). (e-i) Multivariate analyses were performed as described in the Methods for the MSKCC (e), CancerMap (f), and Stephenson (g) datasets. For (h) multivariate analyses were performed on the combined MSKCC, CancerMap, and Stephenson datasets. (i), Multivariate analyses performed on the CamCap dataset. CamCap was analysed separately because of the 40 cancer overlap with the CancerMap dataset. Pathological Stage covariates for MSKCC and Stephenson datasets did not meet the proportional hazards assumptions of the Cox model and have been modelled as time-dependent variables, as described in the Methods.

FIG. 8. Correlations of Gene Expression of DESNT cancers identified by LPD classification. Correlations (corr.) of average levels of gene expression between cancers assigned to the DESNT process using LPD from each of the MSKCC, CancerMap, Stephenson, Klein and CamCap datasets. Data from the 500 genetic loci whose expression levels varied most in MSKCC dataset and that were used for LPD are shown. The expression levels of each gene have been normalised across all samples to mean 0 and standard deviation 1. All ten possible comparisons are presented.

FIG. 9. Detection of DESNT cancers by RF classification using the 20 gene signature. A random forest classification was performed using the signature of 20 genes identified in lasso regression analysis of the 1669 genes with significantly altered expression in DESNT cancers in at least two of the five datasets: MSKCC, CancerMap, Stephenson, Klein, and CamCap. For each dataset the reference used were the cancers for the DESNT group corresponding to the modal p-value shown in FIG. 12. The figure shows the AUC, Accuracy, Sensitivity and Specificity for each prediction. A grid showing the number of false-positive (top right) and false-negative (bottom left) assignments is shown for each dataset.

FIG. 10. Analysis of outcome for DESNT cancers identified by RF classification. (a-e) Kaplan-Meier PSA failure plots for the MSKCC (a), CancerMap (b), Stephenson (c), CamCap (d) and TOGA (e) datasets. For each dataset, the cancers assigned to DESNT using the 20 gene RF classifier are comparing to the remaining cancers. The number of cancers in each group is indicated in the bottom right corner of each plot. The number of cancers with PSA failure is indicated in parentheses. Multivariate analyses were performed as described in the Methods for the MSKCC (f), CancerMap (g), Stephenson (h), CamCap (i) and TOGA (j) datasets. Pathological Stage covariates for MSKCC and Stephenson datasets did not meet the proportional hazards assumptions of the Cox model and have been modelled as time-dependent variables, as described in the Methods.

FIG. 11. Correlations of Gene Expression of DESNT cancers identified by RF classification. Correlations of average levels of gene expression between cancers assigned to the DESNT process using RF classification from each of the MSKCC, CancerMap, Stephenson, Klein, CamCap and TOGA datasets. Data from the 500 loci whose expression levels varied most in MSKCC dataset and that were used for LPD are shown. The expression levels of each gene have been normalised across all samples to mean 0 and standard deviation 1. All 15 possible comparisons are presented. For each dataset similar correlations between DESNT processes identified by LPD and RF were observed (data not shown).

FIG. 12. Distribution of LPD runs. The distribution of the PSA failure log-rank p-values of 100 LPD restarts with random seeds, for the datasets (a) MSKCC, (b) CancerMap, (c) CamCap and (d) Stephenson. Examples of Kaplan-Meier plots corresponding to modal log-rank p values are shown in FIG. 1d and FIG. 7a-d.

FIG. 13. LPD decomposition of the MSKCC dataset. (a) Samples are represented in all eight processes and height of each bar corresponds to the proportion (Gamma, vertical axis) of the signature that can be assigned to each LPD process. The seventh row illustrates the percentage of the DESNT expression signature identified in each sample. (b) Bar chart showing the proportion of DESNT cancer present in each sample. (c,d) Pie Charts showing the composition of individual cancers. DESNT is in red. Other LPD groups are represented by different colours as indicated in the key. The numbers next the pie chart indicates which cancer it represents from the bar chart above. Individual cancers were assigned as a “DESNT cancer” when the DESNT signature was the most abundant; examples are shown in the left box (DESNT). Many other cancers contain a smaller proportion of DESNT cancer (d) and are predicted also to have a poor outcome: examples shown in larger box (c, Some DESNT).

FIG. 14. Stratification of prostate cancer based on the percentage of DESNT cancer present. For these analyses the data from the MSKCC, CancerMap, CamCap and Stephenson datasets were combined (n=517). (a) Plot showing the contribution of DESNT cancer to each cancer and the division into 4 groups. Group 1 samples have less than 0.1% DESNT cancer. (b) Kaplan-Meier plot showing the Biochemical Recurrence (BCR) free survival based on proportion of DESNT cancer present as determined by LPD. Number of cancers in each Group are indicated (bottom right) and the number of PCR failures in each group are show in parentheses. The definition of Groups 1-4 is shown in FIG. 2a. Cancers with Gamma values up to 30% DESNT (Group 2) exhibited poorer clinical outcome (X2-test, p=0.015) compared to cancers lacking DESNT (<0.1%). Cancers with the intermediate (0.3 to 0.6) and high (>0.6) values of Gamma also exhibited significantly worse outcome (respectively P=2.69×10−6 and P=2.22×10−14 compare to cancers lacking DESNT. The combined Log-rank p value=1.28×10−14.

FIG. 15. Nomogram model developed to predict PSA free survival at 1, 3, 5 and 7 years for LPD. Assessing a single patient each clinical variable has a corresponding point score (top scales). The point scores for each variable are added to produce a total points score for each patient. The predicted probability of PSA free survival at 1, 3, 5 and 7 years can be determined by drawing a vertical line from the total points score to the probability scales below.

FIG. 16. Cox Model for LPD. (a) graphical representation of HR for each covariate and 95% confidence intervals of HR. (b) HR, 95% CI and Wald test statistics of the Cox model. (c) Calibration plots for the internal validation of the nomogram, using 1000 bootstrap resamples. Solid black line represents the apparent performance of the nomogram, blue line the bias-corrected performance and dotted line the ideal performance. (d) Calibration plots for the external validation of the nomogram using the CamCap dataset. Solid line corresponds to the observed performance and dotted line to the ideal performance.

EXAMPLES Example 1

A critical problem in the clinical management of prostate cancer is that it is highly heterogeneous1,2. Accurate prediction of individual cancer behavior is therefore not achievable at the time of diagnosis leading to substantial overtreatment3,4. It remains an enigma that, in contrast to breast cancer5, unsupervised analyses of global expression profiles has not defined robust categories of prostate cancer with distinct clinical outcomes6,7. In the current study the application of an unsupervised Bayesian procedure called Latent Process Decomposition8 (LPD) identifies a common process in four independent prostate cancer transcriptome datasets. Cancers assigned to this process (designated DESNT cancers) are characterized by low expression of a core set of 45 genes, many encoding proteins involved in the cytoskeleton machinery, ion transport and cell adhesion. For the three datasets with linked PSA failure data following prostatectomy, patients with DESNT cancer exhibited very poor outcome relative to other patients (P=2.65×10−8, P=4.28×10−8, and P=2.98×10−8). Analysis of prostate cancers annotated in The Cancer Genome Atlas using a random forest classifier failed to reveal links between DESNT cancers and the presence of any particular class of genetic mutation, including ETS-gene status. Our results demonstrate the existence of a poor prognosis category of human prostate cancer and will assist in the targeting of therapy, helping avoid treatment-associated morbidity in men with indolent disease.

Most expression-based prognostic signatures for prostate cancer have in common that they were derived using supervised steps, involving either comparisons of aggressive and non-aggressive disease9,10 or the selection of genes representing specific biological functions11-14. Alternatively expression biomarkers may be linked to the presence of somatic copy number variations (SCNVs)7. LPD, based on the latent Dirchelet allocation method15, examines the structure of a dataset in the absence of knowledge of clinical outcome or biological role. In contrast to standard unsupervised clustering models (e.g. k-means and hierarchical clustering) individual cancers are not assigned to a single cluster: instead gene expression levels in each cancer are modeled via combinations of latent processes. This type of analysis should be particularly suitable for prostate cancer where the composition of individual cancers can be highly heterogeneous18,17 and where a single specimen may contain more than one contributing lineage18-20. LPD has been previously used to confirm the presence of basal and ERBB2 overexpressing subgroups in breast cancer datasets8, and to show that patients with advanced prostate cancer can be stratified into two clinically distinct categories21.

Four independent transcriptome datasets (designated MSKCC6, CancerMap, Klein22, and Stephenson23, FIG. 1b) obtained from prostatectomy specimens were analyzed. LPD was performed using between 3 and 8 underlying processes contributing to the overall expression profile as indicated from log-likelihood plots (FIG. 1b, FIG. 5). Following decomposition of each dataset, cancers were assigned to individual latent processes based on their highest pi value yielding the results shown in FIG. 1a and FIG. 6. pi is the contribution of each process i to the expression profile of an individual cancer: sum of pi over all processes=1. Searching for relationships between the decompositions one process was identified that, based on correlations of gene expression levels, appeared to be common across all four datasets (FIG. 1c). To further investigate this association, for each dataset, we identified genes that were expressed at significantly lower or higher levels (P<0.01 after correction for False Discovery Rate) in the cancers assigned to this process compared to all other cancers from the same dataset. This unveiled a shared set of 45 genes all with lower expression (FIG. 2a, Extended Data Table 1). Many of the proteins encoded by these 45 core genes are components of the cytoskeleton or regulate its dynamics, while others are involved in cell adhesion and ion transport (FIG. 2b). Eleven of the 45 genes were members of published prognostic signatures for prostate cancer (FIG. 2c, Supplementary Data 1). For example MYLK, ACTG2, and CNN1 are down-regulated in a signature for cancer metastasis24, while lower expression of TMP2 is associated with poorer outcome as part of the Oncotype DX signature25. The cancers assigned to this common process are referred to as “DESNT” (latin DEScenduNT, they descend).

Using linked clinical data available for the MSKCC expression dataset the inventors found that patients with DESNT cancer exhibited extremely poor outcome when compared to patients assigned to other processes (P=2.65×10−5, Log-rank test, FIG. 1d). Validation was provided in two further datasets where PSA failure data following prostatectomy was available (FIG. 1d): for both the Stephenson and CancerMap datasets patients with DESNT cancer exhibited very poor outcome (P=4.28×10−5 and P=2.98×10−8 respectively). In multivariate analysis including Gleason sum, Stage and PSA assignment as a DESNT cancer was an independent predictor of poor outcome in the Stephenson and CancerMap datasets (P=1.83×10−4 and P=3.66×10−3, Cox regression model) but not in the MSKCC dataset (P=0.327) (Table 8, FIG. 7). When the three datasets were combining the independent predictive value of DESNT membership was P=1.61×10−7 (FIG. 7), compared to P=1.00×10−5 for Gleason Sum. The poor prognosis DESNT process was also identified in the CamCap dataset7 (Table 8, FIGS. 7 and 8), which was excluded from the from the above analysis because it was not independent: there a substantial overlap with cancers included in CancerMap (FIG. 1b).

The inventors wished to develop a classifier that, unlike LPD, was not computer processing intensive and that could be applied both to a wider range of datasets and to individual cancers. 1669 genes with significantly altered expression between DESNT and non-DESNT cancers in at least two datasets were selected for analysis. A LASSO logistic regression model was used to identify genes that were the best predictors of DESNT membership in the MSKCC dataset leading to the selection of a set of 20 genes (Extended Data Table 2), which had a one gene overlap (ACTG2) to the 45 genes with significantly lower expression in DESNT cancers. Using random forest (RF) classification these 20 genes provided high specificity and sensitivity for predicting that individual cancers were DESNT in both the MSKCC training dataset and in three validation datasets (FIG. 9). For the two validation datasets (Stephenson and CancerMap) with linked PSA failure data the predicted cancer subgroup exhibited poorer clinical outcome in both univariate and multivariate analyses, in agreement with the results observed using LPD (Table 8, FIG. 10). When RF classification was applied to RNAseq data from 333 prostate cancers annotated by The Cancer Genome Atlas (TCGA)20 a patient subgroup was identified that was confirmed as DESNT based on: (i) correlations of gene expression levels with DESNT cancer groups in other datasets (FIG. 11); (ii) demonstration of overlaps of differentially expressed genes between DESNT and non-DESNT cancers with the core down-regulated gene set (45/45 genes); and (iii) its poorer clinical outcome (P=5.4×10−4) compared to non-DESNT patients (Table 8, FIG. 10e).

For the TCGA dataset we failed to find correlations between assignment as a DESNT cancer and the presence of any specific genetic alteration (P>0.05 after correction for False Discovery Rate, X2 test, FIG. 3). Of particular note, there was no correlation to ETS-gene status (P, =0.136, X2 test, FIG. 3). A lack of correlation between DESNT cancers and ERG-gene rearrangement, determined using the fluorescence in situ hybridization break-apart assay26, was confirmed using CancerMap samples (LPD-DESNT, P=0.549; RF-DESNT, P=0.2623, X2 test: DESNT cancers identified by LPD and by RF approaches are referred to respectively as LPD-DESNT and RF-DESNT). These observations are consistent with the lack of correlation between ERG status and clinical outcome27. Since ETS-gene alteration, found in around half of prostate cancer20,26, is considered to be an early step in prostate cancer development17,28 it is likely that changes involved in the generation of DESNT cancer represent a later event that is common to both ETS-positive and ETS-negative cancers.

For RF-DESNT cancers in the TGCA series some of the 45 core genes exhibited altered levels of CpG gene methylation compared to non-RF-DESNT cancers (Supplementary Information Table 1) suggesting a possible role in controlling gene expression. Supporting this idea, for sixteen of the 45 core genes, epigenetic down regulation in human cancer has been previously reported including six genes in prostate cancer (CLU, DPYSL3, GSTP1, KCNMA1, SNAI2, and SVIL) (FIG. 2b, Extended Data Table 1). CpG methylation of five of the genes (FBLN1, GPX3, GSTP1, KCNMA1, TIMP3) has previously been linked to cancer aggression. The down-regulation of genes determining cytoskeleton structure and involved in cell adhesion in DESNT cancers would argue against the contributions of amoeboid-type movement and mesenchymal migration in determining cancer aggression, but could reflect collective migration or expansive growth phenotypes29.

Evidence from The European Randomized study of Screening for Prostate Cancer demonstrates that PSA screening can reduce mortality from prostate cancer by 21%30. However, a critical problem with PSA screening is that it leads to the detection of up to 50% of cancers that are clinically irrelevant3,4: that is cancers that would never have caused symptoms in a man's lifetime in the absence of screening. In our study application of LPD to prostate cancer transcriptome datasets has revealed the existence of a novel poor prognosis category of prostate cancer common across all prostatectomy series examined. The DESNT cancer category was detected using data generated by several different platforms (Illumina HT12 v4 BeadChip array, RNAseq, Affymetrix arrays) and from both frozen and formalin fixed tissue. Classification of a cancer as DESNT should significantly enhance the ability to identify patients whose cancers will progress. In turn this will allow the targeting of radiotherapy, surgery and chemotherapy to men with more aggressive disease helping avoid the side effects of treatment, including impotence, in men with irrelevant cancers.

Methods

The CancerMap Dataset

Fresh prostate cancer specimens were obtained from a systematic series of patients who had undergone a prostatectomy at the Royal Marsden NHS Foundation Trust and Addenbrooke's Hospital, Cambridge. The relevant local Research Ethics Committee approved was obtained for this study. Frozen prostate slices at were collected31 and RNAs were prepared7,32 as described previously.

Expression profiles were determined as previously described32 using 1.0 Human Exon ST arrays (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's instructions. The Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay was used to generate amplified and biotinylated sense-strand DNA targets from the entire expressed genome (1.5 μg of total RNA) without bias. Manufacturer's instructions were followed for the hybridization, washing and scanning steps. Arrays were hybridized by rotating them at 60 rpm in the Affymetrix Gene Chip hybridization oven at 45° C. for 16 h. After hybridization, the arrays were washed in the Affymetrix GeneChip Fluidics station FS 450. The arrays were scanned using the Affymetrix Gene Chip scanner 3000 7G system. Data is available from the Gene Expression Omnibus: GSE (data to be released on publication).

Risk of Progression Categories

Prostatectomy risk of progression categories were defined based on the UK International Cancer Genome Consortium stratification of for prostate cancer (Chris Foster, personal communication).

Low risk PSA <= 10 ng/ml AND (Gleason = 3 + 3 OR (Gleason = 3 + 4 AND no extra capsular extension)) Medium risk 10 ng/ml < PSA <= 20 ng/ml OR (Gleason = 4 + 3 AND no extra capsular extension) OR (Gleason = 3 + 4 AND extra capsular extension) High risk PSA > 20 ng/ml OR Gleason sum > 7 OR (Gleason = 4 + 3 AND extra capsular extension) OR Seminal vesicle invasion

Additional Transcriptome Datasets

Five prostate cancer microarray datasets were analysed that will be referred to as: MSKCC, CancerMap, CamCap, Stephenson and Klein. All data analysed was from radical prostatectomy specimens. The MSKCC dataset contains 370 Affymetrix Human Exon 1.0 ST Array experiments (GEO: GSE21034)6. 50 microarrays were removed corresponding to cell-lines, xenografts and metastatic tissue. The remaining 320 microarrays represents 160 replicates from primary tumour and normal tissue samples: only one dataset from each sample was used in LPD analyses. The Stephenson dataset contains data from 78 cancers and 11 normal prostate samples obtained using Affymetrix U133A human gene arrays23. Klein consists of 182 formalin-fixed and paraffin-embedded (FFPE) primary tumour samples analysed with Affymetrix Human Exon 1.0 ST Arrays (GEO: GSE62667)22. The CamCap dataset used in our study was produced combining Illumina HumanHT-12 V4.0 expression beadchip (bead microarray) datasets (GEO: GSE70768 and GSE70769) obtained from two prostatectomy series (Cambridge and Stockholm) and consisted of 147 cancer and 73 normal samples7. The CamCap and CancerMap datasets have in common patients and thus are not independent. One RNAseq dataset consisting of 333 prostate cancers from The Cancer Genome Atlas was analysed which is referred to as TCGA20. The counts per gene supplied by TCGA were used.

Data Processing

Gene-level and exon-level expression signal estimates were derived from CEL files generated from Affymetrix GeneChip Exon 1.0 ST arrays using the robust multiarray analysis algorithm33 implemented in the Affymetrix Expression Console software package. For the bead micorarray datasets pre-normalised data was used and annotated to UCSC hg19 using illuminaHumanv4.db R annotation package. Poor quality probes (“Bad” and “No match” probes) were removed. The pre-normalised Stephenson dataset was annotated using the hgu133a.db R package. When necessary, dataset/centre batch effects were adjusted for using the ComBat algorithm34 implemented in the sva R package.

Latent Process Decomposition

Latent process decomposition (LPD)8,35, an unsupervised Bayesian approach, was used to classify samples into subgroups called processes. As in Rogers et al.35 the 500 probesets with greatest variance across the MSKCC dataset were selected for use in LPD. These probesets map to 492 genes. For each dataset all probes that map to these genes were used in LPD analyses (CancerMap: 507, CamCap:483, Stephenson: 609).

LPD can objectively assess the most likely number of processes. The inventors assessed the hold-out validation log-likelihood of the data computed at various number of processes and used a combination of both the uniform (equivalent to a maximum likelihood approach) and non-uniform (MAP approach) priors to choose the number of processes. For the MAP approach the mean parameter of the model is set to 0.1, as it has been previously observed that the value used had little impact on the results, and the variance parameter set to the value of the prior that corresponds to the maximum log-likelihood, i.e. −0.5 for MSKCC, −0.5 for CancerMap, −0.05 for CamCap, −0.75 for Stephenson and −0.3 for Klein.

For robustness, the inventors restarted LPD 100 times with different seeds, for each dataset. Out of the 100 runs the inventors selected a representative run that was used for subsequent analysis. The representative run, was the run with the survival log-rank p-value closest to the mode. For the Klein dataset, for which do not have clinical data was not available, the hold-out log-likelihood from LPD was used instead.

Statistical Tests

All statistical tests were performed in R version 3.2.2 (r-project.org/). Correlations between the expression profiles between two datasets for a particular gene set and sample subgroup were calculated as follows:

    • 1. For each gene one probeset is selected at random;
    • 2. For each probeset its distribution is transformed across all samples to a standard normal distribution;
    • 3. The average expression for each probeset across the samples in the subgroup is determined, to obtain an expression profile for the subgroup; and
    • 4. The Pearson's correlation between the expression profiles of the subgroups in the two datasets is determined.

Differentially expressed probesets were identified using a moderated t-test implemented in the limma R package36. Genes are considered significantly differentially expressed if the adjusted p-value was below 0.01 (p values adjusted using the False Discovery Rate).

Survival analyses were performed using Cox proportional hazards models and Kaplan-Meier estimator, with biochemical recurrence after prostatectomy as the end point. When several samples per patient were available, only the sample with the highest proportion of tumour tissue was used. Expression profiles from normal tissue were not included. Multivariate survival analyses were performed with the clinical covariates Gleason grade (≥7 and >7), pathological stage (T1/T2 and T3/T4) and PSA levels (≥10 and >10). The inventors modelled the variables that did not satisfy the proportional hazards assumption (T-stage in MSKCC), as a product of the variable with the heavyside function:

g ⁡ ( t ) = { 1 ,   if ⁢   t ≥ t 0 0 ,   otherwise

where t0 is a time threshold. The multiplication of a predictor with the heavyside function, divides the predictor into time intervals for which the extended Cox model computes different hazard ratios.

Driving an Optimal Predictor of DESNT Membership

To derive an optimal predictor of DESNT membership the datasets were prepared so that they were comparable: probes were only retained if the associated gene was found in every microarray platform, only one randomly chosen probe was retained per gene and the batch effects adjusted using the ComBat algorithm34. The MSKCC dataset was used as the training set and other datasets as test sets. Gene selection was performed using regularized general linear model approach (LASSO) implemented in the glmnet R package37, starting with all genes that were significantly up or down regulated in DESNT in at least two of the total of five microarray dataset (1669 genes). LASSO was run 100 times and only genes that were selected in at least 25% of runs were retained. The optimal predictor was then derived using the random forest model38 implemented in the randomForest R package39. Default parameters were used, apart from the number of trees were set to 10001 and the class size imbalance was adjusted for by down-sampling the majority class to the frequency of the minority class.

Example 2

Presence of DESNT Signature Predicts Poor Clinical Outcome.

In previous studies optimal decomposition of expression microarray datasets was performed using between 3 and 8 underlying processes. An illustration of the decomposition of the MSKCC dataset into 8 processes is shown in FIG. 13a where each process is represented by a bar chart. Samples are represented in all eight processes and height of each bar corresponds to the proportion (Gamma or pi) of the signature that can be assigned to each LPD process. LPD Process 7 illustrates the percentage of the DESNT expression signature identified in each sample, with individual cancer being assigned as a “DESNT cancer” when the DESNT signature was the most abundant as shown in FIGS. 13b and 13d. Based on PSA failure patients with DESNT cancers always exhibited poorer outcome, relative to other cancers in the same dataset. The implication is that it is the presence of regions of cancer containing the DESNT signature that conferred poor outcome. This model predicts that cancers containing smaller contribution of DESNT signature, such as those shown in FIG. 13c for the MSKCC dataset, should also exhibit poorer outcome.

To increase the power to test this prediction data from cancers from the MSKCC, CancerMap, Stephenson, and CamCap were combined (n=515). Treating the proportion of expression assigned to the DESNT process (Gamma) as a continuous variable the inventors found that it had a significant association with PSA recurrence (P=2.66×10−15, HR=1.5, 95% CI=[1.35, 1.66], Cox proportional hazard regression model). Outcome became worse as Gamma increased. This is illustrated by dividing the cancers into four groups based on the proportion of the DESNT process present (FIG. 14a), then PSA failure free survival is as follows (FIG. 14b); (i) no DESNT cancer, 74.4% at 70 months; (ii) less than 0.3 Gamma, 63.1% at 70 months; (iii) 0.3 to 0.6 Gamma, 45.5% at 70 months and (iv)>0.60 Gamma, 20.4% at 70 months (FIG. 14b). Overall 47% of cancers contained at least some DESNT cancer (FIG. 14a).

Nomogram for DESNT Predicting PSA Failure

The proportion of DESNT cancer was combined with other clinical variables (Gleason grade, PSA levels, pathological stage and the surgical margins status) in a Cox proportional hazards model and fitted to a combine dataset of 330 cancers. DESNT Gamma was an independent predictor of worse clinical outcome (P=3×10−4, HR=1.30, 95% CI=[1.13, 1.50]), FIG. 16a,b) along with Gleason grade=4+3 (P=1.8×10−3, HR=3.26, 95% CI=[1.55, 6.86]), Gleason grade>7 (P<1×10−4, HR=5.41, 95% CI=[2.46, 11.92]) pathological stage (P=2.45×10−2, HR=1.62, 95% CI=[1.06, 2.48]), and positive surgical margins (P=1.74×10−2, HR=1.69, 95% CI=[1.10, 2.60]). PSA level as a predictor was below our threshold of statistical significance (P=0.1145, HR=1.13, 95% CI=[0.97, 1.32]). Using this survival model a nomogram for use of DESNT cancer together with other variables was devised (FIG. 15, FIG. 16) to predict the risk of biochemical recurrence at 1, 3, 5 and 7 years following prostatectomy. At internal validation, the nomogram obtained a bootstrap-corrected C-index of 0.761, and at external validation, on the CamCap dataset, a C-index of 0.799.

Tables

TABLE 1 500 GENE PROBES THAT VARY IN EXPRESSION MOST ACROSS THE MSKCC DATASET HGNC Accession symbol ID TGM4 NM_003241 RLN1 NM_006911 ORM1 NM_000607 OLFM4 NM_006418 OR51E2 NM_030774 SERPINB11 NM_080475 CRISP3 NM_006061 TDRD1 NM_198795 SLC14A1 NM_001128588 IGJ NM_144646 ERG NM_001136154 GDEP NR_026555 TMEFF2 NM_016192 CST1 NM_001898 LTF NM_002343 AMACR NM_014324 SERPINA3 NM_001085 NEFH NM_021076 ACSM1 NM_052956 OR51E1 NM_152430 MT1G NM_005950 ANKRD36B NM_025190 LOC100510059 XM_003120411 PLA2G2A NM_000300 TARP NM_001003799 REXO1L1 NM_172239 ANPEP NM_001150 HLA-DRB5 NM_002125 PLA2G7 NM_001168357 NCAPD3 NM_015261 OR51F2 NM_001004753 SPINK1 NM_003122 RCN1 NM_002901 CP NM_000096 SMU1 NM_018225 ACTC1 NM_005159 AGR2 NM_006408 SLC26A4 NM_000441 IGKC BC032451 MYBPC1 NM_002465 NPY NM_000905 PI15 NM_015886 SLC22A3 NM_021977 PIGR NM_002644 APOD NM_001647 HPGD NM_000860 LEPREL1 NM_018192 LCE1D NM_178352 GSTM5 NM_000851 SLC30A4 NM_013309 SEMA3D NM_152754 CACNA2D1 NM_000722 GPR116 NM_015234 C7orf63 NM_001039706 FAM198B NM_001128424 SCD NM_005063 NR4A2 NM_006186 ARG2 NM_001172 ZNF385B NM_152520 RGS1 NM_002922 DNAH5 NM_001369 NPR3 NM_000908 RAB3B NM_002867 CHRDL1 NM_145234 ZNF208 NM_007153 MBOAT2 NM_138799 ATF3 NM_001040619 ST6GAL1 NM_173216 GDF15 NM_004864 ANXA1 NM_000700 FOLH1 NM_004476 C4B NM_001002029 ELOVL2 NM_017770 GSTM1 NM_000561 GLIPR1 NM_006851 C3 NM_000064 MYO6 NM_004999 ORM2 NM_000608 RAET1L NM_130900 PCDHB3 NM_018937 C1orf150 ENST00000366488 ALOX15B NM_001141 LSAMP NM_002338 SLC15A2 NM_021082 PCP4 NM_006198 MCCC2 NM_022132 GCNT1 NM_001097634 C5orf23 BC022250 SCGB1D2 NM_006551 CXCL2 NM_002089 AFF3 NM_001025108 ATP1B1 NM_001677 GJA1 NM_000165 PLA1A NM_015900 MPPED2 NM_001584 AMD1 NM_001634 EMP1 NM_001423 PRR16 NM_016644 CNN1 NM_001299 GHR NM_000163 ALDH1A1 NM_000689 TRIM29 NM_012101 IFNA17 NM_021268 TAS2R4 NM_016944 SEPP1 NM_001093726 GREM1 NM_013372 RASD1 NM_016084 C1S NM_201442 CLSTN2 NM_022131 DMXL1 NM_005509 HIST1H2BC NM_003526 NRG4 NM_138573 ARL17A NM_001113738 GRPR NM_005314 PART1 NR_024617 CYP3A5 NR_033807 KCNC2 NM_139136 SERPINE1 NM_000602 SLC6A14 NM_007231 EIF4A1 NM_001416 MYOF NM_013451 PHOSPHO2 NM_001008489 GCNT2 NM_145649 AOX1 NM_001159 CCDC80 NM_199511 ATP2B4 NM_001001396 UGDH NM_003359 GSTM2 NM_000848 MEIS2 NM_172316 RGS2 NM_002923 PRKG2 NM_006259 FIBIN NM_203371 FDXACB1 NM_138378 SOD2 NM_001024465 SEPT7 NM_001788 PTPRC NM_002838 GABRP NM_014211 CBWD3 NM_201453 TOR1AIP2 NM_022347 TRPC4 NM_016179 RAB27A NM_004580 CD69 NM_001781 RPL17 NM_000985 PSCA NM_005672 ATRNL1 NM_207303 MYOCD NM_001146312 MS4A8B NM_031457 TNS1 NM_022648 BAMBI NM_012342 IGF1 NM_001111283 RALGAPA1 NM_014990 S100A10 NM_002966 PMS2CL NR_002217 MMP2 NM_004530 SLC8A1 NM_021097 OAS2 NM_002535 ARRDC3 NM_020801 AMY2B NM_020978 SPARCL1 NM_001128310 IQGAP2 NM_006633 ACAD8 NM_014384 LPAR3 NM_012152 HIGD2A NM_138820 NUCB2 NM_005013 HLA-DPA1 NM_033554 SLITRK6 NM_032229 MME NM_007288 RBPMS L17325 HLA-DRB1 NM_002124 FOLH1 NM_001193471 LUZP2 NM_001009909 MSMB NM_002443 GSTT1 NM_000853 MMP7 NM_002423 ODZ1 NM_001163278 ACTB NM_001101 SPON2 NM_012445 SLC38A11 NM_173512 FOS NM_005252 OR51T1 NM_001004759 HLA-DMB NM_002118 KRT15 NM_002275 ITGA8 NM_003638 CXADR NM_001338 LYZ NM_000239 CEACAM20 NM_001102597 C8orf4 NM_020130 DPP4 NM_001935 PGC NM_002630 C15orf21 NR_022014 CHORDC1 NM_012124 LRRN1 NM_020873 MT1M NM_176870 EPHA6 NM_001080448 PDE11A NM_001077197 TMSB15A NM_021992 LYPLA1 NM_006330 FOSB NM_006732 F5 NM_000130 C15orf48 NM_032413 MIPEP NM_005932 HSD17B6 NM_003725 SLPI NM_003064 CD38 NM_001775 MMP23B NM_006983 OR51A7 NM_001004749 CFB NM_001710 CCL2 NM_002982 POTEM NM_001145442 TPMT NM_000367 FAM3B NM_058186 FLRT3 NM_198391 ATP8A2 NM_016529 PRIM2 NM_000947 ADAMTSL1 NM_001040272 NELL2 NM_001145108 RPS4Y1 NM_001008 CD24 NM_013230 GOLGA6L9 NM_198181 ZFP36 NM_003407 TRIB1 NM_025195 BNIP3 NM_004052 KL NM_004795 PDE5A NM_001083 DCN NM_001920 LDHB NM_001174097 PCDHB5 NM_015669 ACADL NM_001608 ZNF99 NM_001080409 CPNE4 NM_130808 CCDC144B NR_036647 SLC26A2 NM_000112 CYP1B1 NM_000104 SELE NM_000450 CLDN1 NM_021101 KRT13 NM_153490 SFRP2 NM_003013 SLC25A33 NM_032315 HSD17B11 NM_016245 HSD17B13 NM_178135 UGT2B4 NM_021139 CTGF NM_001901 SCIN NM_001112706 C10orf81 NM_001193434 CYR61 NM_001554 PRUNE2 NM_015225 IFI6 NM_002038 MYH11 NM_022844 PPP1R3C NM_005398 KCNH8 NM_144633 ZNF615 NM_198480 ERV3 NM_001007253 F3 NM_001993 TTN NM_133378 LYRM5 NM_001001660 FMOD NM_002023 NEXN NM_144573 IL28A NM_172138 FHL1 NM_001159702 CXCL10 NM_001565 CXCR4 NM_001008540 OR51L1 NM_001004755 SLC12A2 NM_001046 AGAP11 NM_133447 SLC27A2 NM_003645 AXGP1 NM_001185 VCAN NM_004385 ERAP2 NM_022350 KRT17 NM_000422 SLC2A12 NM_145176 CCL4 NM_002984 RPF2 NM_032194 SLC45A3 NM_033102 SEC11C NM_033280 IFIT1 NM_001548 PAK1IP1 NM_017906 HIST1H3C NM_003531 ERRFI1 NM_018948 ADAMTS1 NM_006988 TRIM36 NM_018700 FLNA NM_001456 CCND2 NM_001759 IFIT3 NM_001031683 FN1 NM_212482 PRY NM_004676 HSPB8 NM_014365 CD177 NM_020406 TP63 NM_003722 IFI44 NM_006417 COL12A1 NM_004370 EDNRA NM_001957 PCDHB2 NM_018936 HLA-DRA NM_019111 TUBA3E NM_207312 ASPN NM_017680 FAM127A NM_001078171 DMD NM_000109 DHRS7 NM_016029 ANO7 NM_001001891 MEIS1 NM_002398 TSPAN1 NM_005727 CNTN1 NM_001843 TRIM22 NM_006074 GSTA2 NM_000846 SORBS1 NM_001034954 GPR81 NM_032554 CSRP1 NM_004078 C3orf14 AF236158 TPM2 NM_003289 REPS2 NM_004726 EAF2 NM_018456 CAV1 NM_001172895 PRUNE2 NM_015225 TMEM178 NM_152390 MFAP4 NM_001198695 SYNM NM_145728 EFEMP1 NM_004105 RND3 NM_005168 SCNN1A NM_001038 B3GNT5 NM_032047 LMOD1 NM_012134 UBC NM_021009 LMO3 NM_018640 LOX NM_002317 NFIL3 NM_005384 C11orf92 NR_034154 C11orf48 NM_024099 BCAP29 NM_018844 EPCAM NM_002354 PTGDS NM_000954 ASB5 NM_080874 TUBA1B NM_006082 SERHL NR_027786 ITGA5 NM_002205 SPARC NM_003118 C7 NM_000587 NTN4 NM_021229 FAM36A NM_198076 CNTNAP2 NM_014141 SC4MOL NM_006745 CH17-189H20.1 AK000992 TRGC2 ENST00000427089 RAP1B NM_015646 SLC4A4 NM_001098484 LCE2D NM_178430 EGR1 NM_001964 MT1L NR_001447 SCUBE2 NM_020974 FAM55D NM_001077639 PDK4 NM_002612 CXCL13 NM_006419 CACNA1D NM_000720 GPR160 NM_014373 CPM NM_001874 PTGS2 NM_000963 TSPAN8 NM_004616 BMP5 NM_021073 GOLGA8A NR_027409 OR4N2 NM_001004723 FAM135A NM_001105531 DYNLL1 NM_001037494 DSC3 NM_024423 C4orf3 NM_001001701 HIST1H2BK NM_080593 LCN2 NM_005564 STEAP4 NM_024636 RPS27L NM_015920 TRPM8 NM_024080 ID2 NM_002166 LUM NM_002345 EDNRB NM_001122659 PGM5 NM_021965 SFRP4 NM_003014 STEAP1 NM_012449 FADS2 NM_004265 CXCL11 NM_005409 CWH43 NM_025087 SNRPN BC043194 GPR110 NM_153840 THBS1 NM_003246 SPOCK1 NM_004598 GSTP1 NM_000852 OAT NM_000274 HIST2H2BF NM_001024599 ACSM3 NM_005622 GLB1L3 NM_001080407 SLC5A1 NM_000343 OR4N4 NM_001005241 MAOB NM_000898 BZW1 NM_014670 GENSCAN00000007309 GENSCAN00000007309 IFI44L NM_006820 KRT5 NM_000424 SCN7A NM_002976 GOLM1 NM_016548 HIST4H4 NM_175054 IL7R NM_002185 CSGALNACT1 NM_018371 A2M NM_000014 LRRC9 AK128037 ARHGEF38 NM_017700 ACSL5 NM_016234 SGK1 NM_001143676 TMEM45B NM_138788 AHNAK2 NM_138420 NEDD8 NM_006156 GREB1 NM_014668 UBQLN4 NM_020131 SDHC NM_003001 TCEAL2 NM_080390 SLC18A2 NM_003054 HIST1H2BE NM_003523 RARRES1 NM_206963 PLN NM_002667 OGN NM_033014 GPR110 NM_025048 CLGN NM_001130675 NIPAL3 NM_020448 ACTG2 NM_001615 RCAN3 NM_013441 KLK11 NM_001167605 HMGCS2 NM_005518 EML5 NM_183387 EDIL3 NM_005711 PIGH NM_004569 GLYATL1 NM_080661 FGFR2 NM_000141 SNAI2 NM_003068 CALCRL NM_005795 MON1B NM_014940 PVRL3 NM_015480 VGLL3 NM_016206 SULF1 NM_001128205 LIFR NM_002310 SH3RF1 AB062480 C12orf75 NM_001145199 GNPTAB NM_024312 CALM2 NM_001743 KLF6 NM_001300 C7orf58 NM_024913 RDH11 NM_016026 NR4A1 NM_002135 RWDD4 NM_152682 ABCC4 NM_005845 ZNF91 NM_003430 GABRE NM_004961 SLC16A1 NM_001166496 DEGS1 NM_003676 CLDN8 NM_199328 HAS2 NM_005328 ODC1 NM_002539 REEP3 NM_001001330 LYRM4 AF258559 PPFIA2 NM_003625 PGM3 NM_015599 ZDHHC8P1 NR_003950 C6orf72 AY358952 HIST1H2BD NM_138720 TES NM_015641 PDE8B NM_003719 DNAJB4 NM_007034 RGS5 NM_003617 EPHA3 NM_005233 COX7A2 NR_029466 MT1H NM_005951 HIST2H2BE NM_003528 TGFB3 NM_003239 VEGFA NM_001025366 CRISPLD2 NM_031476 TFF1 NM_003225 LOC100128816 AY358109 SYT1 NM_00135805 CPE NM_001873 LOC286161 AK091672 NAALADL2 NM_207015 TMPRSS2 NM_001135099 SERPINF1 NM_002615 EPHA7 NM_004440 SDAD1 NM_018115 SOX14 NM_004189 RPL35 NM_007209 HSPA1B NM_005346 MSN NM_002444 MTRF1L NM_019041 PTN NM_002825 CAMKK2 NM_006549 RBM7 NM_016090 OR52H1 NM_001005289 C1R NM_001733 CHRNA2 NM_000742 MRPL41 NM_032477 PROM1 NM_001145847 LPAR6 NM_005767 SAMHD1 NM_015474 SCNN1G NM_001039 DNAJC10 NM_018981 MOXD1 NM_015529 HIST1H2BG NM_003518 ID1 NM_181353 SEMA3C NM_006379

TABLE 2 45 GENES COMMONLY DOWNREGULATED IN THE MSKCC, KLEIN, CANCERMAP AND STEPHENSON DATASETS (AT LEAST 80/100 LPD RUNS) C7 CSRP1 GPX3 EPAS1 CRISPLD2 PCP4 JAM3 FBLN1 LMOD1 CNN1 ETS2 ACTN1 MYLK ATP2B4 SPG20 CLU ILK CDC42EP3 ACTG2 PPAP2B STOM GSTP1 MYL9 SORBS1 STAT5B PLP2 ITGA5 TIMP3 PALLD PDK4 TPM2 RBPMS TNS1 SVIL FERMT2 FLNA CALD1 SNAI2 TPM1 TGFBR3 KCNMA1 ACTA2 PDLIM1 DPYSL3 VCL

TABLE 3 20 GENES IDENTFIED BY LASSO ANLAYSIS FROM THE 1669 GENES IDENTIFED IN TABLE 4 DST CYP27A1 SP100 ALDH2 MME CHRDL1 RND3 PARM1 WDR59 S100A13 THSD4 ACTG2 ZNF532 LDHB MSRA GSTM4 PLEKHA6 DLG5 CDK6 EPHX2

TABLE 4 1669 GENES THAT EXHIBIT SIGNIFICANTLY DIFFERENT EXPRESSION BETWEEN DESNT AND NON-DESNT CANCERS IN AT LEAST TWO DATASETS LPP CX3CL1 NSFL1C PFKFB3 USP11 CCND2 CLIC4 UGP2 RGL1 CCDC69 PER3 DLD FBXO7 DKC1 MFN2 ATAD1 TRIM29 RFWD2 C11orf54 S100A13 WLS UTY CHD1 EIF5 AOC3 ATP2B4 SQRDL EMP2 SPRY1 ZNF589 STMN1 ATF3 FBXO18 COPZ2 SLC2A5 CTNNB1 SETD5 MITF GON4L WSB1 ALDH3A2 FBXW4 CAT ABR TNKS TMF1 ST8SIA1 TPP2 GALM MBTPS1 WDR19 MSRB2 NR4A1 ID1 FAM129A ECHDC2 SLC38A2 ZCCHC11 MBNL2 SPTBN1 CASC3 PCDH9 ACTA2 CCT3 STK24 TRIP11 FLOT1 RBMS3 FHL2 MADD ITSN1 PI4KA PIAS2 DGKA SPG11 WIPF1 EYA4 SCYL3 NFAT5 RYK VCL CCDC121 RBPMS DLX1 TPST1 CAPNS1 GPR161 TFDP1 SERINC3 SIK2 FAM198B MGP METTL3 ACTC1 PREX2 RBBP6 ACOX1 TAB2 SMC1A RFC2 BRE PRRG4 CRTAP LYST SMARCA2 KCNMB1 SNAI2 ZC3H18 ANKRD12 NUB1 PPIC TCF7L2 LMBRD1 ANKRD34B SLC1A1 APEX1 FOXN3 NCOA1 FBLN1 TJP2 SF3A1 GABBR1 MEF2A AMT CNOT1 SET DVL2 ATP2A2 PPP1R10 PI15 EPS15 LONRF3 PPAP2B IL4R CDK5RAP2 ROCK2 LARGE MATR3 UBE2E3 CDH11 FBXO32 DHX9 RARA PARP6 SKP2 ILF3 SP110 RAB2A STAU1 SVIL ANXA7 TUBB WAC CAST ZMYND8 MAPKAPK2 PMP22 PDSS2 PEX10 LRP1 EP400 MTMR9 ATP10D KIF1B LRPPRC RAB27A TCF12 AFF1 GLIPR2 USP9X PBRM1 COX7A1 LASP1 TSPAN13 PCBP1 GLT8D1 SLC41A1 ANAPC1 GPBP1L1 NUP214 NRBP1 AIMP2 CLK1 METTL7A LGALS3BP WDR11 YTHDC1 CDC45 GNG12 CDC5L LTBP1 PRMT1 SFXN3 HEG1 KLF3 FAM13B POGZ BNC2 BAG3 SON MORF4L2 LRP10 ADAMTS1 PRDM2 EPC2 ACSS3 TRAF3IP2 AMFR SERPING1 EFEMP1 PER1 RUVBL1 MSN PKP1 COX11 GPM6B GTF2I GCNT2 PARM1 PPP1R15A UBR2 STARD13 PCDH7 MANBAL SLC22A17 VEZF1 FGA MXI1 RBMS1 FYTTD1 SSTR1 APP MYLK MYH11 STAT3 ROBO1 AMMECR1 TEAD1 DMD ZYG11B CDH7 MTUS1 VSIG2 WDFY3 RBAK KCTD9 SH3RF1 TCF20 HEPH TRERF1 NDRG2 SORBS2 CUL3 VPS13D C2orf43 DNAJB5 FAF1 ATOX1 BIN1 ADRA1A MDH1 POPDC2 TGFBI WHSC1L1 PITPNC1 HSPB1 SCMH1 APCDD1 LRPAP1 PDLIM4 C9orf72 PPP1R15B PPARD ZNF483 AHNAK2 ARID1B AGL SYNE1 USP25 C9orf3 NAMPT ACTR3 ERC1 ELF1 GAB1 EXOSC10 NID1 ITGB4 CBX7 LIMK2 CELF2 PINK1 ZNF207 SF3B1 SMC6 LEPREL1 DYRK1A MEIS2 PLD3 PDS5A FAM124A NBEAL1 MT1M HIPK1 TP53BP1 TRPM7 IRF2BP2 RNF213 EPB41L5 TSPYL2 TTC17 PTGDS NF1 MED13 LPAR1 TMEM51 RHOT1 JAZF1 NBAS ASAP1 DDX42 PDE8A IGF1R DYNLT1 SMAD3 TACC2 CLSPN KPNA6 TNPO1 SYNM HERC4 PRKCD CELF1 CAP2 MPHOSPH8 TSPAN18 MYL9 SERPINB1 SMG6 SLC37A3 RNF185 PYGL JUST UBA6 HSPA9 PDZRN4 DICER1 SEC31A KCNAB1 SAP130 HSD17B11 DPYSL3 VWA5A TP53INP2 CLU CTSB ALAS1 DDX17 PELI1 PDGFC SS18 MAPKAP1 STOM FST MYADM ARSJ JUNG ST5 SNX2 EGFR CLASP1 SMURF2 PSIP1 CCNL1 FLNA PARP14 RB1 ELOVL6 ZFP36L1 PPFIBP1 PRICKLE2 DHX8 KHDRBS3 TLN1 DDX24 YY1AP1 AGPAT1 JAK2 CAV1 RAPH1 NEO1 CD99L2 FN1 SETD3 DCN CPT1A SMNDC1 TLE4 PRUNE2 PPFIBP2 BRIX1 VPS45 TGFB3 CCNI LMNA SLK UBE4B GSTP1 IP6K2 BTBD7 USO1 TTC14 ENSA APOBEC3C WBP5 HFE ATP12A DNAH10 THOC2 GBP1 PDS5B SLC25A23 CSDE1 NCOA7 CTDSP2 LATS1 PTEN DDR2 FAM65A TMLHE C16orf45 CEBPB ANG HP1BP3 WDR1 DYM SPATS2L C7 VEGFA PRPF4B TBX3 COL4A6 MAP1B MED13L PSMC4 AKAP11 MON2 TIMP3 SH3BP5 PAXIP1 STAT5B PIK3C3 ZC3H7A PLCL1 CDC73 NEBL MYOCD CLIP1 RCAN3 KIAA0513 ACSS2 ZYX ARHGEF7 CDKL5 NUP98 BPTF PDCD6IP LPHN2 DLG1 DST NSF NIPAL3 ZMYM4 RTN4 KIAA1109 EFS KPNA1 ITM2C CYB5B UBQLN1 ASPH TRIM38 TTLL7 DIP2C CREG1 EPB41L1 APOL1 MLXIP NCK1 SH3BGRL MSRB3 NUCKS1 TOPBP1 ZEB2 FAM114A1 PITRM1 PSMD1 NHS BAZ1B PDK4 PJA2 PLEKHO1 RBM3 ADHFE1 ZNF460 LMOD1 TNFRSF1A UTP14A ARIH1 NFX1 ZRANB2 JPH2 CACNA1D CAPN7 OGN NFIX ORMDL1 WRNIP1 MTMR3 HIF1A ANXA11 CDK4 YWHAB TMEM43 AKAP7 SLIT2 PAN3 CACHD1 PIK3R1 ROR2 NID2 CSRNP1 CCDC91 UACA MCAM CXCL12 TCIRG1 NHLRC2 FREM2 YEATS2 BACH1 TPM1 MAEA SCP2 PALLD MAP1LC3B SYNE2 MAP4K4 HBP1 ZBTB20 MATN2 ASXL2 ATF6 GEM MKX DZIP1 NOL8 LMO3 DES LMO4 SLC10A7 PAPD4 CBLB CD81 SLC7A8 MAPKAPK5 SLC16A2 PTGS2 PDGFRA PCNA CDC42BPB ZFYVE9 UBR4 KPNB1 USP24 RSPO3 ACOX2 NIPBL PDE5A MSMB TNFRSF19 C1S AP2B1 EIF4A2 ANO5 FERMT2 TNFRSF10B UBE3C ANGPT1 SRI NFATC3 DUOX1 PDLIM3 IK LIMA1 AFF3 PSMA4 B4GALT5 BCLAF1 TSC22D3 TUBB6 EPAS1 MAP3K4 NT5C2 POLDIP3 SMG7 PTPRA PHF21A MARK3 MME MIER1 TOP2A QKI MRPL10 SLC8A1 CYP27A1 RHOJ DCAF7 THBS1 PCM1 SEMA3C ACIN1 NDEL1 CHRDL1 FGFR2 NSD1 MKL2 DCBLD1 APBB1 NUMB AASS TRIM33 GGA2 VAPA MAX ZNF516 TMBIM1 INO80 PCP4 CWC27 CMIP KIF20A CLIC6 RELA FBXO11 IER3 FAM127B STAT2 CLK4 DEDD PIK3CA PDK2 ABCC13 LITAF RCC2 FLOT2 AFAP1L2 MACF1 DMXL2 AKAP13 TRIP6 ETS2 TGFBR2 TPR PRNP MEIS1 F5 RDH10 TRIP12 RALGAPA2 USH2A CTNS RPRD2 EPHX2 PTK2 LRRN1 THSD4 TEX2 PER2 NXF1 CHMP1A ITSN2 SETBP1 SNX9 CPE TTLL13 RICTOR CPM FBXO17 LRCH2 IREB2 ATP1A1 HS1BP3 TTBK2 ALMS1 VAMP3 MAPK14 GPX3 ITIH5 DHX36 DDHD2 YAP1 OGDHL CSNK1D PSME1 DDX3Y TMEM185A NUP153 SRPX TNRC6A ZFP36 PPFIA1 ARHGAP1 USP48 SNRNP200 PGM5 HOXD10 SSX2IP MYO6 COL6A1 ADH5 LONRF1 IGF1 UBE2C PYGM GJA1 PTK2B PRKAR1A KANK1 CMBL ITGB1 BAZ2B REST ILK PRPF8 HECTD1 B3GALT2 UBR3 ABI2 CALU LRP6 PIGT ABHD6 ATP8B1 MAGI2 TOMM34 OLFML3 ITGB8 PLP2 DSTN PARD3 PRPF3 HSPB6 XRN2 BCAS1 ATG9A KDM3B MTMR8 ATP6V0E1 ID4 S100A16 RALGAPB ABI1 COL6A3 ZNF451 CCDC80 GDAP1 EIF4EBP2 ITGB3 LSAMP KLHL5 RC3H2 ITPK1 RYBP LDHB AKT3 DOPEY1 TAGLN IFI16 MAPK1IP1L TIMP2 SLMO2 TRMU ETV5 PKN2 MMP19 FLNC RNF217 SPAG9 KAT2B NKAIN1 TCERG1 YPEL5 DOCK1 CCT6A PUM2 OGDH NFE2L1 ADAR VPS37A KANK2 CCNT2 YWHAH IARS USP34 REV1 NUDT5 STARD4 KDM3A ZNF655 YME1L1 CASP14 SORT1 STK4 CKAP5 CDKN1B TCF21 KIF2A CYB5R2 DDX19B ANXA4 ATF7IP HLF IL17RA ZMYND11 ROCK1 CFL2 ARHGAP26 RAB7A MYH9 STXBP1 ATG2B PPP1R12A CDK12 TIMP1 ENAH SCARA3 SDCCAG8 TIMELESS DKK3 RGN SKP1 NPC2 LRP2 DDX3X SEC24B SBNO1 MPDZ GPBP1 BOD1 CHST3 SCAMP1 CAV2 PCNX SLC1A5 ANXA2 GSTM4 OTUB1 C11orf57 DCBLD2 SPEG MAP4 ANKRD17 AQR LGALS1 EFTUD1 CDC42SE2 ZNF234 LCLAT1 FOXO4 IVNS1ABP NR2C2 TOR1AIP1 KCNJ8 CYB5R3 LIX1L BCOR SORBS3 AXIN2 C16orf62 NISCH KCNMA1 DPT PPP1R3B SPTA1 SESTD1 GMPR CNOT4 RAB11FIP2 FAM127A TIA1 CALD1 CIZ1 GDPD1 SNX33 CHMP2B OTUD4 NVL EML4 NCK2 OPA1 ITPR2 KLHDC2 EPS15L1 HADHA ARHGAP17 NIN VDAC3 ARHGAP10 USP30 ARL6IP1 LRRC41 GADD45B CD59 RNF216 CDC42EP3 HOOK3 BIN3 AES KCTD10 PARN MPZL2 CD74 SMAD4 CNN2 GSTM2 EDARADD TSPAN31 ZSCAN18 TMED10 HPS1 AFF4 SMARCA5 CTSA FOSL2 CASP7 DIXDC1 CLCN6 ADCY5 CYP20A1 WDR26 GSTK1 FMNL2 LRRC16A SERINC1 RDX VAMP2 CTTNBP2NL RASA1 NPHP3 SKIL SSFA2 RABGAP1L LDB3 MAF TNRC6B GNAO1 GGT7 RNF121 RAD50 PRKCB SYTL4 YTHDC2 GCLC FLII CEP350 EAF2 ATM TMEM63A PTPLA ARRB1 MAT2A TAPBP FYCO1 S100A6 NFKBIZ PAK1IP1 LGALS3 BCL6 MEF2C RBM4 CYTH3 TNC CDC27 RUFY3 N4BP2L2 MTPAP MKLN1 DEK CAPRIN1 COMMD6 NPAS2 CD47 CD44 TRA2B ATF2 BCL7B MID2 MAML2 PEA15 VILL EXOC4 MAPK10 ADCY8 SRGN NUFIP2 RRM1 NFIB DIRAS2 MBNL1 R3HDM1 LIMS2 REL GLI3 CD40 TUBA1A ALDH1A2 FNBP1L NETO2 MRVI1 GLG1 PUS7 EEA1 MRAS TTLL5 GIT2 SUPT4H1 SUN1 UTP18 CA11 REXO2 ZCCHC24 GNL2 GATAD2B PDHA1 PTPRG AKT2 RIC3 FAT1 COMMD1 MSL2 KIF16B KLF4 ACOX3 AUTS2 DHX15 ARID4B MFAP4 ARPP19 TBC1D14 MLLT10 PSAP TBC1D1 EFHD2 AOX1 GAS1 PSMC5 HNRNPU CUL1 MAN1A2 EIF4G2 SOS1 STRN3 DYNC1H1 ATXN2 SORBS1 TTC28 CSTB ZNF280D GPR124 RBM23 TSHZ3 EXOC7 CALCOCO2 MMP2 MAPK1 OAZ1 RRAS ELP3 PPARGC1A HK1 ZEB1 TBC1D5 NFKBIA CEP120 GNS DMTF1 DIP2B ARNT SCPEP1 SCN7A STAM2 EP300 PTPN14 STK38L HELZ BBS2 DOCK9 DUSP1 FGF2 ATP2B1 CPEB3 EGR1 AFTPH USP4 RHOA DLG5 GIGYF2 PARVA CHD9 GAS6 SMARCC2 CDC42BPA TBL1X GSTM5 SCRN1 NEU1 PRPSAP1 PAICS SUPT16H PTPRM ACO1 SMURF1 STAT6 IL13RA1 TGFB1I1 TRAK2 RHOBTB3 STXBP6 EIF5B MEF2D BHLHE40 MED21 PRRG1 GGCT SERPINH1 MCL1 CHMP1B UCK2 STX12 ASH1L CLINT1 SMAD2 RBL2 TNKS2 FXYD6 TMEM165 ATP8B2 LAPTM4A ATL3 SMC5 TOP1 AP3B1 NT5DC3 KIAA1033 ANO4 CREB3L2 ASAP2 SETX LBR CALCOCO1 LAMP1 ZNFX1 ABCC9 LRCH3 PSME4 MTOR NR4A3 TRPC4 CDC42EP4 FOSB PTRF ZC3H13 GLIPR1 CDC42EP5 NR4A2 PLSCR1 COQ10B TPM2 ANPEP FRMD6 NCAPD2 POLR2A IFI35 CHRM1 NEIL3 ACACB SETD2 DNAJB1 CNN3 HNRNPM ITM2B ZNF611 SEC63 PRKDC EIF4G3 VIM PCDH15 ALOX15B INO80D C1R RIN2 GNAI2 IMMT BBX TMEM55A NFIA STXBP3 SLFN5 SPATA6 PAGE4 EXOC1 ERAP1 PRPS2 JARID2 JAM3 EPHA3 ARHGAP20 A2M DNAJC13 PIBF1 CDC37L1 TBCK ZNF396 GALNT8 ASCC3 ITCH RARS2 DAB2 ARL6IP5 TBCEL SLMAP TGFBR1 DAAM2 HMGXB4 SOS2 IDE FUBP1 FBN1 CORO1C LARP6 TSC1 TECPR2 RBBP7 PHF11 NEXN GNAL IFNAR1 NEK7 GPATCH8 TACC1 ATP1A2 PUM1 GTF3C2 FAM160B1 IDS SLC39A14 BTG2 APOOL EPRS IL6ST LAMB2 FAM107B SH3PXD2B VPS39 NCBP1 MORC3 TTLL4 KIF15 SUPT6H ZNF384 AHCYL1 NOTCH2 TGFBR3 TNRC6C IPO8 EARS2 AP3D1 KRT15 STX6 SECISBP2L SAT2 WNK1 ANKRD40 JMJD1C TEP1 CALM1 UBP1 HIPK3 PLXDC2 IRS1 COL6A2 WDR12 SENP7 KBTBD2 PHF1 CD63 ADD1 TCEAL2 COPS3 PYGB SBF2 TSG101 STAT5A DENND4A STAM BNIP2 TRAPPC10 PBX1 EYA1 HDDC2 NNT EMP3 PNMA1 KLF9 HERPUD2 C15orf41 NPTN RND3 SHKBP1 FBXO31 ZNF3 SWAP70 DENND5A SMOC1 FNBP1 TRIO ROS1 SLC18A2 AHR PPIP5K2 HSPB8 DUSP3 FHL1 LDB1 HIST1H4C RASD2 TTLL3 ITGA7 PLEKHA6 SIN3A FAM20B MRGPRF RAB8B SMTN EZH1 CAP1 MY01D PLEK2 KHDRBS1 MYO9A PRKD1 PDE4D PHF3 JUN DERA LSM14A XPO7 GPRC5B KRT23 CHURC1 ENTPD4 COPA SLC12A4 KCNS3 PRKACA SPON1 LNPEP ACADVL CSRP1 M6PR DDX1 HERC1 C10orf76 CAPZB VPS53 MYCBP2 POLR2B ANXA1 ZZEF1 ZNF318 PCDH18 HEXB C11orf30 OTUD5 CYR61 SNTB2 PHC3 KIF4A UBE2E1 PRPSAP2 SPRY2 RGS2 RBM5 AMOT SNRNP40 USP14 TGFB2 TMEM109 ARRDC3 WWTR1 STAG1 CST3 TINAGL1 MYO1C SPTAN1 REV3L DAAM1 ARPC2 CSNK2B PRPF18 ANTXR2 PLEKHA5 OSMR GSN AGFG1 LDB2 PKD2 ITGA9 SAMD8 SLC15A2 C2orf88 TMEM59 RLF UBAP1 PDE11A TMEM220 REPS1 GPRASP1 STX7 SMG1 TNS1 RAF1 XRCC5 PPWD1 CDKAL1 VPS4B DCUN1D4 GNG2 PTN FNBP4 TMEM35 SLC25A12 ITGA5 BIRC6 KIF14 DARS UFC1 TBC1D23 PCGF5 DAPK3 EMP1 RBPMS2 TEAD3 CTGF MSRA KIF5B ZHX2 KRT5 PPP1R7 ZFR NPAT ABCB11 ARMCX1 KIAA0430 PRDM8 SLC4A7 PSMB7 CISD1 ACTN1 SNX19 JAK1 RHOB DRAM2 SMARCA4 CNPY2 CD38 WBP2 MED12 PTTG1IP EHD2 TCF4 SEC24A QRICH1 PHIP RNF38 ITGA1 STRBP TRPS1 FOXJ3 SP100 KLF8 ALDH2 SPEN NPR2 DEPDC1B TMEM47 CYLD TET2 XYLB CDK6 MYL6 UBAP2L EXT1 TRO MIB1 SIDT1 EPHB6 XRN1 TLE2 PAK3 CD46 SRD5A2 ZFAND5 PPP3CB RAP1A TCF25 IGFBP5 OSBPL9 PDLIM1 SPARCL1 MTMR12 PITPNB CYC1 CNOT6 NCKAP1 GDAP2 USP53 ZNF185 DCP1A PLAGL1 FABP3 SOD2 DCTN1 ACTG2 FAM160B2 VAMPS MTR TP63 PTP4A2 BMPR2 SPOP SF3B3 VPS13C SMAD9 SHISA5 CHD2 CCDC25 WDR59 BIRC5 CREBBP LZTFL1 SERPINF1 SPOCK3 ITPR1 LAMA4 MXRA5 CAMK2G FCHSD2 ZNF148 G3BP1 GTF3C3 MCC EHBP1 CNN1 SOX4 CRIM1 PREPL ETV6 DPYD AEBP2 MAP3K7 CREB1 MAN2A1 FUBP3 TBC1D9B ASB2 ZFC3H1 MYOF HNRNPA2B1 QSER1 RSRC2 ARFGEF2 ZBTB4 IQGAP1 SGCB PIP4K2A MPPED2 SMARCA1 SEC23A CHMP7 BOC NFYC UBC RCBTB2 AP1G1 PHACTR2 VPS41 SPRED1 IL1R1 RQCD1 AKIRIN2 PPP1CB CRISPLD2 CRY2 FZD7 ARHGEF12 SLC22A3 GABARAPL1 MAP4K5 ADSL FGFR1 GNG4 DCUN1D1 FASTKD2 STK38 GALC XPC ASNS CTNNA1 RNF11 SENP6 KDSR FNDC3B NFE2L2 GABARAPL2 ERBB2IP RARRES2 ESYT2 GBF1 PPIL4 CDS2 TRIP13 SYNRG CYP3A5 RABGAP1 SHOC2 ZNF532 HUWE1 EDNRA DDX5 PTPRK STIM1 EPCAM MARVELD1 AHI1 ABCA8 EPB41L2 CCDC88A GRAMD3 TRIP10 SLAIN2 YPEL3 AZGP1 SLC14A1 SCAPER NCAPG2 NEK1 RAB3GAP2 KDM2A DCAF8 MYO15B ZNF638 FAM69A RAD54L2 RIMKLB CRTC3 WFDC2 L3MBTL4

TABLE 5 35 GENES COMMONLY DOWNREGULATED IN THE MSKCC, KLEIN, CAMCAP AND STEPHENSON DATASETS (AT LEAST 67/100 LPD RUNS) 35 genes 67 of 100 ACTN1 ANXA2 HSPB8 ILK CSRP1 FERMT2 ATP2B4 ACTG2 PCP4 MYLK CNN1 JAM3 LMOD1 TPM2 SORBS1 MYH11 DPYSL3 VCL LPAR1 MYL9 STOM FBLN1 KCNMA1 PALLD GSTP1 C7 TGFB3 RND3 CXCL12 ITGA5 PTRF ACTA2 TGFBR3 FZD7 FLNA

TABLE 6 Example Control Genes: House Keeping Control genes HPRT 18S rRNA RPL9 PFKP H2A.X RPL23a B2M 28s rRNA SRP14 EF-1d IMP RPL37 TBP PBGD RPL24 IMPDH1 accession RPS11 GAPDH ACTB RPL22 IDH2 number RPS3 ALAS1 UBC RPS29 KGDHC X56932 SDHB RPLP2 rb 23 kDa RPS16 SRF7 ODC-AZ SNRPB KLK3_ex2-3 TUBA1 RPL4 RPLP0 PDHA1 SDH KLK3_ex1-2 RPS9 RPL6 ALDOA PLA2 TCP20 SDH1 TFR OAZ1 COX !V PMI1 CLTC GPI RPS13 RPS12 AST SRP75 PSMB2 RPL27 LDHA MDH RPL3 PSMB4 RPS20 PGAM1 EIF4A1 RPL32 RAB7A RPL30 PGK1 FH RPL7a REEP5 RPL13A VIM ATP5F1 RNAP II RPL10

TABLE 7 Example Control Genes: Prostate specific control transcripts KLK2 PCGEM1 TGM4 PSCA HOXB13 SPINK1 KLK3 PCA3 RLN1 NKX3.1 PMEPA1 KLK4 TMPRSS2 ACPP SPDEF PAP FOLH1(PSMA) TMPRSS2/ERG PTI-1 PMA STEAP1

TABLE 8 Poor clinical outcome of patients with DESNT cancers For each dataset comparisons were made between PSA failures reported for DESNT and non-DESNT cancers. LPD, Latent Process Decomposition; RF, Random Forest. For LPD the log-rank P-values represent the modal LPD run selected from the 100 independent LPD runs as described in the Methods. For multivariate analyses Gleason, PSA at diagnosis and Pathological Stage are included for all datasets with the exception of the TCGA dataset where only Gleason and Clinical Stage data were available. The full analyses are presented in FIG. 7. Dataset Univariate p-value Multivariate p-value Latent Process Decomposition MSKCC 2.65 × 10−5 3.27 × 10−1 CancerMap 2.98 × 10−8 3.66 × 10−3 Stephenson 4.28 × 10−5 1.21 × 10−4 CamCap 1.22 × 10−3 2.90 × 10−2 Random Forest MSKCC 1.85 × 10−3 6.05 × 10−1 CancerMap 4.80 × 10−4 1.45 × 10−2 Stephenson 1.75 × 10−4 4.56 × 10−4 CamCap 1.61 × 10−5 1.31 × 10−4 TCGA 5.41 × 10−4 2.59 × 10−2

Extended Data Tables

Extended data Table 1: Genes with altered expression in the DESNT cancer group. For each dataset the genes with significantly altered expression (p<0.05) in the DESNT cancer group compared to the non-DESNT group were calculated: p-values were corrected for multiple testing. LPD was re-run 100 times for each dataset using different randomly chosen seed values. The results for the 45 genes that had altered expression in at least 80/100 runs for all four datasets are listed. The precise number of runs in which each gene has significantly altered expression is presented. All genes were down regulated in the DESNT cancer group. The emphases represent genes whose products are components of or linked to the: Cytoskeleton (bold); Adhesion, Integrins and Extracellular Matrix (underlined), Transcription Factors and Translational Regulators (double underlined), and Ion Channels (dashed underlined). Symbols: * Down regulation by CpG Methylation in Cancer; ** Down regulation by CpG Methylation in Prostate Cancer; † CpG Methylation Associated with Poor Outcome; ‡ Prostate Cancer Functional Connectivity Hub; and ∥ Gene-gene Interaction Focus for Prostate Cancer.

Gene MSKCC CancerMap Stephenson Klein ACTA2 100 92 100 98 ACTG2 100 98 100 98 ACTN1 100 92 100 100 100 92 100 100 C7 100 89 100 100 CALD1 100 92 92 100 CDC42EP3 100 92 100 95 CLU** 100 92 100 100 CNN1 100 92 100 98 CRISPLD2 100 92 100 98 CSRP1*‡ 100 93 100 100 DPYSL3** 100 92 100 86 EPAS1*∥ 100 92 100 100 ETS2 100 92 100 100 FBLN1*† 100 92 100 100 FERMT2 100 92 100 100 FLNA 100 92 100 98 GPX3*† 100 92 100 100 GSTP1**† 100 92 100 81 ILK 100 92 100 100 ITGA5 100 92 100 100 JAM3* 92 85 100 100 100 92 100 99 LMOD1 100 92 100 91 MYL9 100 92 100 98 MYLK*‡ 100 92 100 98 PALLD 100 92 100 100 PCP4 100 92 100 100 PDK4 100 83 100 96 PDLIM1 100 91 100 81 PLP2 100 92 100 100 PPAP2B 100 92 100 100 RBPMS 100 92 100 100 SNAI2** 100 93 100 91 SORBS1* 100 92 100 98 SPG20* 100 92 100 100 STAT5B 100 92 100 100 100 92 100 100 SVIL** 100 83 100 100 TGFBR3 100 92 93 87 TIMP3*† 100 92 100 97 TNS1 100 92 100 100 TPM1* 100 92 100 100 TPM2 100 92 100 80 VCL 100 92 100 100

Extended Data Table 2: Twenty Gene Random Forest Classifier.

A list of 1669 genes with significantly altered expression in DESNT cancers in at least two of the five datasets (MSKCC, CancerMap, Stephenson, Klein, and CamCap) was used as a starting point. Applying a lasso logistic regression model to predict DESNT membership in the MSKCC dataset leading to the selection of a set of 20 genes shown in this table. For each gene, its importance as a variable when performing random forest classification is also recorded.

Gene Variable Importance DST 2.146140965 CHRDL1 1.758974273 THSD4 1.561264948 GSTM4 1.550345548 CYP27A1 1.408713974 RND3 1.339094656 ACTG2 1.304989674 PLEKHA6 0.735553263 SP100 0.680938431 PARM1 0.671688267 ZNF532 0.630661162 DLG5 0.492853186 ALDH2 0.481637788 WDR59 0.467824475 LDHB 0.449345969 CDK6 0.351043941 MME 0.275274353 S100A13 0.250416073 MSRA 0.229702526 EPHX2 0.213536527

Supplementary Information Tables

Supplementary Information Table 1: Differential methylation, The differential methylation between DENST and non-DESIST cancers identified in the TCCA dataset is presented. DESIST cancer were identified using the 20-gene signature show in Extended Data Table 2 using random forest classification. We then applied a method to detect Differentially Methylated Regions (DMR) implemented in the R package “methyAnalysis” (bioconductor.org/packages/release/bioc/html/methyAnalysis.html). The significant results are listed.

Num. Gene Distance Min Min Chr Start End Probes Symbol TSS* Promoter P-value P-adjust 1 56992372 56992372 1 PPAP2B 52885 FALSE 1.71E−28 4.92E−27 1 92197531 92197531 1 TGFBR3 130072 FALSE 1.56E−12 7.59E−12 1 92295946 92295946 1 TGFBR3 31657 FALSE 3.72E−16 2.56E−15 1 203598330 203599089 7 ATP2B4 2415 FALSE 7.48E−25 1.23E−23 1 203605590 203605590 1 ATP2B4 9675 FALSE 1.34E−26 2.70E−25 1 203670963 203671140 2 ATP2B4 19093 FALSE 1.44E−39 4.05E−37 10 29923736 29924258 3 SVIL 0 TRUE 1.11E−29 4.22E−28 10 29936149 29948428 3 SVIL 76302 FALSE 2.48E−35 3.09E−33 10 29981216 29981216 1 SVIL 43514 FALSE 4.12E−21 4.57E−20 10 79150517 79150517 1 KCNMA1 247060 FALSE 3.38E−22 4.17E−21 10 79396584 79396793 3 KCNMA1 784 FALSE 1.08E−12 5.32E−12 10 97049610 97049610 1 PDLIM1 1295 FALSE 2.64E−29 8.99E−28 10 97169147 97175479 4 SORBS1 6351 FALSE 1.75E−33 1.31E−31 11 67350976 67350976 1 GSTP1 −90 TRUE 1.65E−14 9.79E−14 11 67351271 67352041 6 GSTP1 205 FALSE 1.03E−36 1.92E−34 11 134020750 134020750 1 JAM3 81930 FALSE 4.58E−28 1.29E−26 12 54811762 54812085 3 ITGA5 965 FALSE 4.27E−27 9.99E−26 13 36919344 36919960 6 SPG20 686 FALSE 8.29E−18 6.41E−17 14 69443362 69443362 1 ACTN1 921 FALSE 5.45E−35 6.12E−33 15 63345124 63345124 1 TPM1 4488 FALSE 1.25E−12 6.11E−12 16 84870066 84870203 2 CRISPLD2 16479 FALSE 1.14E−25 2.00E−24 16 84918794 84918851 2 CRISPLD2 65207 FALSE 7.28E−18 5.79E−17 2 46526843 46527098 2 EPAS1 2302 FALSE 7.50E−10 3.02E−09 2 218767655 218767655 1 TNS1 881 FALSE 9.13E−16 6.24E−15 20 35169380 35169594 3 MYL9 −293 TRUE 6.90E−31 3.09E−29 22 45899736 45899736 1 FBLN1 1017 FALSE 6.75E−35 6.89E−33 3 123339417 123339568 2 MYLK 0 TRUE 9.65E−23 1.27E−21 3 123414733 123414733 1 MYLK 5623 FALSE 1.68E−32 1.18E−30 3 123535716 123535716 1 MYLK 14614 FALSE 1.31E−33 1.23E−31 3 123602485 123602485 1 MYLK 664 FALSE 3.14E−32 2.07E−30 4 169664785 169664785 1 PALLD 112017 FALSE 2.54E−26 4.99E−25 4 169737224 169737224 1 PALLD 184456 FALSE 1.02E−26 2.12E−25 4 169754328 169754534 2 PALLD 1172 FALSE 9.98E−11 4.27E−10 4 169770092 169770092 1 PALLD 16936 FALSE 2.81E−24 4.37E−23 5 40933444 40982092 2 C7 23845 FALSE 3.70E−10 1.51E−09 7 134575145 134575524 5 CALD1 110981 FALSE 1.24E−22 1.62E−21 7 134626083 134626083 1 CALD1 8344 FALSE 1.31E−15 8.70E−15 8 27468981 27469186 3 CLU 82 FALSE 7.22E−28 1.84E−26 8 30243241 30243260 2 RBPMS 1297 FALSE 2.72E−15 1.74E−14 8 30254923 30254923 1 RBPMS 12979 FALSE 8.21E−29 2.56E−27 8 30290489 30290489 1 RBPMS 48545 FALSE 2.39E−11 1.06E−10 8 30419935 30419935 1 RBPMS 84620 FALSE 6.82E−32 4.25E−30 X 153598077 153598077 1 FLNA 4929 FALSE 1.28E−10 5.39E−10

Supplementary Information Table 2: Clinical Characteristics of the CancerMap Dataset

Category Count/Median (Range) Patients 154 Age at prostatectomy 62 (21-74) PSA at prostatectomy 7.9 (2.4-40) Follow up time (months) 56 (1-129) Recurrence Event Yes 35 No 102 Unknown 17 Gleason 6 40 7 (3 + 4) 83 7 (4 + 3) 20 8 4 9 7 Stage T1c 1 T2a 6 T2b 3 T2c 49 T2x 26 T3a 50 T3b 17 T4x 2

Supplementary Information Table 3: Functions of Differentially Expressed Genes.

List of the 45 genes commonly down-regulated in DESNT cancers identified in the MSKCC, Stephenson, CancerMap, and Klein datasets.

Gene Identity Notes ACTA2 Smooth muscle actin alpha Actin cytoskeleton and cell motility; marker for myofibroblasts 2 ACTG2 Smooth muscle actin Cytoskeletal component, involved in cell motility - expression is gamma 2 actually widespread. ACTN1 Actinin alpha 1 Alpha actinin is an actin-binding protein with multiple roles in different cell types. In nonmuscle cells, the cytoskeletal isoform is found along microfilament bundles and adherens-type junctions, where it is involved in binding actin to the membrane. In contrast, skeletal, cardiac, and smooth muscle isoforms are localized to the Z- disc and analogous dense bodies, where they help anchor the myofibrillar actin filaments. This gene encodes a nonmuscle, cytoskeletal, alpha actinin isoform and maps to the same site as the structurally similar erythroid beta spectrin gene.[2] ATPase plasma membrane Intracellular Ca homeostasis Ca2+ transporting 4 C7 complement component 7 Complement system activation; poteintial link to adhesion via vitronectin receptor CALD1 Caldesmon calmodulin- and actin-binding protein that plays an essential role in the regulation of smooth muscle and nonmuscle contraction CDC42EP3 Binds to and negatively regulates CDC42, small GTPase involved in actin filament assembly in filopodia CLU Clusterin CLU is a molecular chaperone responsible for aiding protein folding of secreted proteins; clearance of cellular debris and apoptosis CNN1 calponin 1 calponin 1 functions as an inhibitory regulator of smooth muscle contractility through inhibiting actomyosin interactions.[2][23][24]In this regulation, binding of Ca2+-calmodulin and PKC phosphorylation dissociate calponin 1 from the actin filament and facilitate smooth muscle contraction.[25] CRISPLD2 Cysteine-rich secretory Secretory protein; aka late gestation lung-1. Involved in regulation of protein LCCL domain- cell migration containing 2 CSRP1 cysteine and glycine rich CSRP1 is a member of the CSRP family of genes encoding a group of protein 1 LIM domain proteins, which may be involved in regulatory processes important for development and cellular differentiation. The LIM/double zinc-finger motif found in CRP1 is found in a group of proteins with critical functions in gene regulation, cell growth, and somatic differentiation Other genes in the family include CSRP2 and CSRP3.[3] DPYSL3 dihydropyrimidinase like 3 Putative tumour suppressor; stabilizer of focal adhesion complexes - link to cell migration EPAS1 Endothelial PAS domain- HIF2-alpha - a key transcription factor regulating cellular responses containing protein to hypoxia 1 (EPAS1, also known as hypoxia-inducible factor- 2alpha (HIF-2alpha)) ETS2 Ets-2 Member of the c-Ets family of transcription factors FBLN1 fibulin 1 Fibulin-1 is a secreted glycoprotein that is found in association with extracellular matrix structures including fibronectin-containing fibers, elastin-containing fibers and basement membranes. Fibulin-1 binds to a number of extracellular matrix constituents including fibronectin,[3] nidogen-1, and the proteoglycan, versican.[3][4] Fibulin-1 is also a blood protein capable of binding to fibrinogen.[5] FERMT2 fermitin family member 2 FERMT2 is a component of extracellular matrix structures in mammalian cells and is required for proper control of cell shape change.[4] FLNA filamin A Actin-binding protein, or filamin, is a 280-kD protein that crosslinks actin filaments into orthogonal networks in cortical cytoplasm and participates in the anchoring of membrane proteins for the actin cytoskeleton. Remodeling of the cytoskeleton is central to the modulation of cell shape and migration. Filamin A, encoded by the FLNA gene, is a widely expressed protein that regulates reorganization of the actin cytoskeleton by interacting with integrins, transmembrane receptor complexes, and second messengers.[supplied by OMIM][3] GPX3 Glutathione peroxidase-3 Aka Plasma, or Extracellular glutathione peroxidase; involved in detoxification of hydrogen peroxide GSTP1 Glutathione transferase Pi 1 Glutathione S-transferases (GSTs) are a family of enzymes that play an important role in detoxification by catalyzing the conjugation of many hydrophobic and electrophilic compounds with reduced glutathione. ILK Integrin-linked kinase Associates with beta-1 integrin, role in adhesion, migration survival etc ITGA5 Integrin alpha-5 With integrin beta 1 constitutes fibronectin receptor; involved in adhesion, migration, signallingh JAM3 Junctional adhesion Aka JAM-C; Cell-cell interactions via tight junctions; important in molecule-3 platelet-leukocyte interactions, via Mac-1 Calcium-activated Voltage-gated potassium channel potassium channel subunit alpha-1 LMOD1 Leiomodin-1 Smooth muscle actin and tropomyosin-binding MYL9 Myosin light chain 9 Muscle contraction, binds Ca and acted on by MLCK MYLK Myosin light chain kinase MLCK; Ca/Calmodulin-dependent PALLD Palladin Palladin is a component of actin-containing microfilaments that control cell shape, adhesion, and contraction.[4] PCP4 Purkinje cell protein-4 PCP4 accelerates both the association and dissociation of calcium (Ca2+) with calmodulin(CaM), which is postulated to influence the activity of CaM-dependent enzymes, especially CaM kinase II (CaMK-II) PDK4 Pyruvate Regulation of krebs cycle; located in the matrix of the mitochondria dehydrogenase lipoamide k and inhibits the pyruvate dehydrogenase complex by inase isozyme 4, phosphorylating one of its subunits, reducing the conversion of mitochondrial pyruvate to acetyl-CoA PDLIM1 PDZ and LIM domain Binds to alpha actinin-1 and actin filaments, regulating cell migration protein 1 PLP2 Proteolipid protein 2 Interaction with chemokine resptor CCR1 and regulation of cell migration PPAP2B Lipid phosphate member of the phosphatidic acid phosphatase (PAP) family. PAPs phosphohydrolase 3 convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. RBPMS RNA-binding protein with a member of the RRM family of RNA-binding proteins: regulates multiple splicing development of gastrointestinal smooth muscle. SNAI2 Zinc finger protein SNAI2 member of the Snail family of C2H2-type zinc finger transcription factors. The encoded protein acts as a transcriptional repressor that binds to E-box motifs and is also likely to repress E- cadherin transcription in breast carcinoma. SORBS1 CAP/Ponsin protein, also CAP/Ponsin is part of a small family of adaptor proteins that known as Sorbin and SH3 regulate cell adhesion, growth factor signaling domain-containing protein and cytoskeletal formation 1 SPG20 Spartin protein may be involved in endosomal trafficking, microtubule dynamics, or both functions STAT5B Signal transducer and Transcription factor that mediates the signal transduction triggered activator of transcription 5B by various cell ligands, such as IL2, IL4, CSF1, and different growth hormones Stomatin also known Integral membrane protein, regulator of ion channels as human erythrocyte integral membrane protein band 7 SVIL Supervilin Actin-binding protein that also has nuclear localization signal; Its function may include recruitment of actin and other cytoskeletal proteins into specialized structures at the plasma membrane and in the nuclei of growing cells TGFBR3 Betaglycan TGFbeta Betaglycan also known as Transforming growth factor beta receptor Receptor III III (TGFBR3), is a cell-surface chondroitin sulfate/heparan sulfate proteoglycan >300 kDa in molecular weight. Betaglycan binds to various members of the TGF-beta superfamily of ligands via its core protein, and bFGF via its heparan sulfate chains. It is not involved directly in TGF-beta signal transduction but by binding to various member of the TGF-beta superfamily at the cell surface it acts as a reservoir of ligand for TGF-beta receptors.[1][2] TIMP3 Tissue inhibitor of A negative regulator of MMPs and also certain other ADAM and metalloproteinase-3 ADAMTS metalloproteinases; involved in regulation of ECM remodelling and cell signalling TNS1 Tensin-1 A cytoskeletal regulator found in focal adhesions, crossslinks actin filaments and has SH2 domain so probaly involved in cell signalling; a recent paper on it positively regulating RhoA TPM1 Tropomyosin alpha-1 chain actin-binding protein involved in the contractile system of striated and smooth muscles and the cytoskeleton of non-muscle cells TPM2 β-Tropomyosin, also known B-tropomyosin is striated muscle-specific coiled coil dimer that as tropomyosin beta chain functions to stabilize actin filaments and regulate muscle contraction. VCL Vinculin vinculin is a membrane-cytoskeletal protein in focal adhesion plaques that is involved in linkage ofintegrin adhesion molecules to the actin cytoskeleton

SUPPLEMENTARY DATA Supplementary Data 1: Clinical and molecular characteristics of samples in the CancerMap dataset. Note this table has been divided to enable the information to be presented in this application. Each row comprises the columns Row, Sample ID, Donor ID, Batch, Material Type, Extraction Method, Centre, ERG FISH status, Tumour percentage, Ethnicity, Age at Diagnosis, Pathology Stage, Pathology sub stage, PSA pre-prostatectomy, Gleason Score, Margins, Extra Capsular Extension, BCR FreeTime months, BCR Event and ICGC category. Row Sample ID Donor ID Batch Material_Type Extraction_Method 1 TB08.0234_v1 TB08.0234 CamFinal Normal Qiagen miRNA kit 2 TB08.0234_v3 TB08.0234 CamFinal Normal Qiagen miRNA kit 3 TB08.0262_v3 TB08.0262 CamFinal Tumour Qiagen miRNA kit 4 TB08.0268_v3 TB08.0268 CamFinal Low Tumour Qiagen miRNA kit 5 TB08.0271_v1 TB08.0271 CamFinal Low Tumour Qiagen miRNA kit 6 TB08.0311_v2 TB08.0311 CamFinal Tumour Qiagen miRNA kit 7 TB08.0311_v3 TB08.0311 CamFinal Low Tumour Qiagen miRNA kit 8 TB08.0327_v1 TB08.0327 CamFinal Tumour Qiagen miRNA kit 9 TB08.0341_v1 TB08.0341 CamFinal Normal Qiagen miRNA kit 10 TB08.0341_v5 TB08.0341 CamFinal Tumour Qiagen miRNA kit 11 TB08.0359_v16 TB08.0359 CamFinal Normal Qiagen miRNA kit 12 TB08.0359_v2 TB08.0359 CamFinal Stroma Qiagen miRNA kit 13 TB08.0368_v14 TB08.0368 CamFinal Normal Qiagen miRNA kit 14 TB08.0429_v7 TB08.0429 CamFinal Low Tumour Qiagen miRNA kit 15 TB08.0489_v5 TB08.0489 CamFinal Normal Qiagen miRNA kit 16 TB08.0489_v13 TB08.0489 CamFinal Tumour Qiagen miRNA kit 17 TB08.0501_v8 TB08.0501 CamFinal Tumour Qiagen miRNA kit 18 TB08.0519_v14 TB08.0519 CamFinal Tumour Qiagen miRNA kit 19 TB08.0533_v6 TB08.0533 CamFinal Tumour Qiagen miRNA kit 20 TB08.0588_v1 TB08.0588 CamFinal Tumour Qiagen miRNA kit 21 TB08.0589_v1 TB08.0589 CamFinal Tumour Qiagen miRNA kit 22 TB08.0589_v2 TB08.0589 CamFinal Low Tumour Qiagen miRNA kit 23 TB08.0589_v4 TB08.0589 CamFinal Stroma Qiagen miRNA kit 24 TB08.0589_v5 TB08.0589 CamFinal Low Tumour Qiagen miRNA kit 25 TB08.0598_v12 TB08.0598 CamFinal Tumour Qiagen miRNA kit 26 TB08.0609_v11 TB08.0609 CamFinal Low Tumour Qiagen miRNA kit 27 TB08.0667_v9 TB08.0667 CamFinal Tumour Qiagen miRNA kit 28 TB08.0667_v6 TB08.0667 CamFinal Stroma Qiagen miRNA kit 29 TB08.0689_v14 TB08.0689 CamFinal Tumour Qiagen miRNA kit 30 TB08.0689_v15 TB08.0689 CamFinal Tumour Qiagen miRNA kit 31 TB08.0689_v2 TB08.0689 CamFinal Tumour Qiagen miRNA kit 32 TB08.0689_v8 TB08.0689 CamFinal Tumour Qiagen miRNA kit 33 TB08.0691_v13 TB08.0691 CamFinal Tumour Qiagen miRNA kit 34 TB08.0716_v18 TB08.0716 CamFinal Stroma Qiagen miRNA kit 35 TB08.0719_v11 TB08.0719 CamFinal Tumour Qiagen miRNA kit 36 TB08.0731_v13 TB08.0731 CamFinal Low Tumour Qiagen miRNA kit 37 TB08.0816_v2 TB08.0816 CamFinal Low Tumour Qiagen miRNA kit 38 TB08.0817_v14 TB08.0817 CamFinal Tumour Qiagen miRNA kit 39 TB08.0848_v10 TB08.0848 CamFinal Tumour Qiagen miRNA kit 40 TB08.0869_v4 TB08.0869 CamFinal Low Tumour Qiagen miRNA kit 41 TB08.0869_v6 TB08.0869 CamFinal Low Tumour Qiagen miRNA kit 42 TB08.0869_v7 TB08.0869 CamFinal Low Tumour Qiagen miRNA kit 43 TB08.0870_v18 TB08.0870 CamFinal Low Tumour Qiagen miRNA kit 44 TB08.0872_v2 TB08.0872 CamFinal Tumour Qiagen miRNA kit 45 TB08.0877_v19 TB08.0877 CamFinal Tumour Qiagen miRNA kit 46 TB08.0879_v11 TB08.0879 CamFinal Low Tumour Qiagen miRNA kit 47 TB08.0884_v2 TB08.0884 CamFinal Normal Qiagen miRNA kit 48 TB08.0927_v5 TB08.0927 CamFinal Tumour Qiagen miRNA kit 49 TB08.0943_v7 TB08.0943 CamFinal Stroma Qiagen miRNA kit 50 TB08.0958_v12 TB08.0958 CamFinal Tumour Qiagen miRNA kit 51 TB08.0958_v13 TB08.0958 CamFinal Tumour Qiagen miRNA kit 52 TB08.0973_v9 TB08.0973 CamFinal Tumour Qiagen miRNA kit 53 TB08.0978_v7 TB08.0978 CamFinal Tumour Qiagen miRNA kit 54 TB08.0978_v8 TB08.0978 CamFinal Tumour Qiagen miRNA kit 55 TB08.0978_v9 TB08.0978 CamFinal Tumour Qiagen miRNA kit 56 TB08.0986_v2 TB08.0986 CamFinal Tumour Qiagen miRNA kit 57 TB08.0987_v6 TB08.0987 CamFinal Tumour Qiagen miRNA kit 58 TB08.0993_v12 TB08.0993 CamFinal Low Tumour Qiagen miRNA kit 59 TB08.0997_v6 TB08.0997 CamFinal Stroma Qiagen miRNA kit 60 TB08.0999_v11 TB08.0999 CamFinal Tumour Qiagen miRNA kit 61 TB08.0999_v2 TB08.0999 CamFinal Tumour Qiagen miRNA kit 62 TB08.1015_v10 TB08.1015 CamFinal Tumour Qiagen miRNA kit 63 TB08.1015_v11 TB08.1015 CamFinal Tumour Qiagen miRNA kit 64 TB08.1015_v9 TB08.1015 CamFinal Tumour Qiagen miRNA kit 65 TB08.1019_v1 TB08.1019 CamFinal Low Tumour Qiagen miRNA kit 66 TB08.1019_v14 TB08.1019 CamFinal Low Tumour Qiagen miRNA kit 67 TB08.1019_v15 TB08.1019 CamFinal Tumour Qiagen miRNA kit 68 TB08.1019_v2 TB08.1019 CamFinal Tumour Qiagen miRNA kit 69 TB08.1026_v17 TB08.1026 CamFinal Tumour Qiagen miRNA kit 70 TB08.1044_v7 TB08.1044 CamFinal Tumour Qiagen miRNA kit 71 TB08.1053_v5 TB08.1053 CamFinal Tumour Qiagen miRNA kit 72 TB08.1063_v16 TB08.1063 CamFinal Tumour Qiagen miRNA kit 73 TB08.1063_v8 TB08.1063 CamFinal Tumour Qiagen miRNA kit 74 TB08.1083_v3 TB08.1083 CamFinal Tumour Qiagen miRNA kit 75 TB08.1116_v2 TB08.1116 CamFinal Low Tumour Qiagen miRNA kit 76 TB08.1116_v3 TB08.1116 CamFinal Tumour Qiagen miRNA kit 77 TB08.1116_v9 TB08.1116 CamFinal Tumour Qiagen miRNA kit 78 TB08.1159_v2 TB08.1159 CamFinal Normal Qiagen miRNA kit 79 TB08.0601_v16 TB08.0601 CamFinal Normal Qiagen miRNA kit 80 TB09.0217_v16 TB09.0217 CamFinal Tumour Qiagen miRNA kit 81 TB09.0217_v7 TB09.0217 CamFinal Tumour Qiagen miRNA kit 82 TB09.0219_v13 TB09.0219 CamFinal Low Tumour Qiagen miRNA kit 83 TB09.0219_v2 TB09.0219 CamFinal Low Tumour Qiagen miRNA kit 84 TB09.0219_v21 TB09.0219 CamFinal Tumour Qiagen miRNA kit 85 TB09.0219_v8 TB09.0219 CamFinal Low Tumour Qiagen miRNA kit 86 TB09.0238_v12 TB09.0238 CamFinal Stroma Qiagen miRNA kit 87 TB09.0238_v18 TB09.0238 CamFinal Tumour Qiagen miRNA kit 88 TB09.0238_v5 TB09.0238 CamFinal Tumour Qiagen miRNA kit 89 TB09.0272_v6 TB09.0272 CamFinal Tumour Qiagen miRNA kit 90 TB09.0272_v7 TB09.0272 CamFinal Tumour Qiagen miRNA kit 91 TB09.0295_v2 TB09.0295 CamFinal Tumour Qiagen miRNA kit 92 TB09.0413_v11 TB09.0413 CamFinal Tumour Qiagen miRNA kit 93 TB09.0413_v8 TB09.0413 CamFinal Low Tumour Qiagen miRNA kit 94 TB09.0443_v3 TB09.0443 CamFinal Low Tumour Qiagen miRNA kit 95 TB09.0443_v8 TB09.0443 CamFinal Tumour Qiagen miRNA kit 96 TB09.0448_v8 TB09.0448 CamFinal Tumour Qiagen miRNA kit 97 TB09.0462_v7 TB09.0462 CamFinal Low Tumour Qiagen miRNA kit 98 TB09.0471_v11 TB09.0471 CamFinal Tumour Qiagen miRNA kit 99 TB09.0504_v4 TB09.0504 CamFinal Tumour Qiagen miRNA kit 100 TB09.0550_v15 TB09.0550 CamFinal Tumour Qiagen miRNA kit 101 TB09.0606_v3 TB09.0606 CamFinal Low Tumour Qiagen miRNA kit 102 TB09.0706_v5 TB09.0706 CamFinal Tumour Qiagen miRNA kit 103 TB09.0720_v19 TB09.0720 CamFinal Tumour Qiagen miRNA kit 104 TB09.0721_v14 TB09.0721 CamFinal Low Tumour Qiagen miRNA kit 105 TB09.0721_v15 TB09.0721 CamFinal Low Tumour Qiagen miRNA kit 106 TB09.0725_v9 TB09.0725 CamFinal Tumour Qiagen miRNA kit 107 TB09.0774_v1 TB09.0774 CamFinal Stroma Qiagen miRNA kit 108 TB09.0774_v15 TB09.0774 CamFinal Low Tumour Qiagen miRNA kit 109 TB09.0850_v2 TB09.0850 CamFinal Low Tumour Qiagen miRNA kit 110 TB09.0962_v13 TB09.0962 CamFinal Tumour Qiagen miRNA kit 111 TB09.0962_v16 TB09.0962 CamFinal Tumour Qiagen miRNA kit 112 NP1 ICR_38 1208 Normal Trizol 113 NP10 ICR_47 309 Normal Trizol 114 NP11 ICR_50 309 Normal Trizol 115 NP12 ICR_58 309 Normal Trizol 116 NP14 ICR_35 309 Normal Trizol 117 NP15 ICR_65 309 Normal Trizol 118 NP16 ICR_69 309 Normal Trizol 119 NP17 ICR_51 509 Normal Trizol 120 NP18 ICR_66 509 Stroma Trizol 121 NP19 ICR_73 509 Stroma Trizol 122 NP2 ICR_37 1208 Normal Trizol 123 NP20 ICR_57 509 Normal Trizol 124 NP21 ICR_56 509 Stroma Trizol 125 NP4 ICR_47 1208 Normal Trizol 126 NP5 ICR_59 1208 Normal Trizol 127 NP8 ICR_34 309 Normal Trizol 128 NP9 ICR_54 309 Normal Trizol 129 PRC140 ICR_20 509 Low Tumour Trizol 130 PRC101 ICR_28 908 Tumour RNAeasyPlus 131 PRC102 ICR_44 908 Tumour Trizol 132 PRC103 ICR_34 908 Tumour RNAeasyPlus 133 PRC105 ICR_43 908 Tumour RNAeasyPlus 134 PRC106 ICR_54 908 Low Tumour RNAeasyPlus 135 PRC109 ICR_54 1008 Tumour Trizol 136 PRC10 ICR_49 507 Tumour Trizol 137 PRC110 ICR_22 1008 Tumour Trizol 138 PRC111 ICR_49 1008 Tumour Trizol 139 PRC112 ICR_49 1008 Normal Trizol 140 PRC113 ICR_60 1008 Tumour Trizol 141 PRC114 ICR_63 1008 Tumour Trizol 142 PRC115 ICR_41 1008 Tumour Trizol 143 PRC116 ICR_41 1008 Tumour Trizol 144 PRC117 ICR_17 1008 Tumour Trizol 145 PRC118 ICR_17 1008 Tumour Trizol 146 PRC119 ICR_50 1008 Tumour Trizol 147 PRC11 ICR_59 507 Tumour Trizol 148 PRC122 ICR_4 1008 Low Tumour Trizol 149 PRC123 ICR_17 1008 Low Tumour Trizo 150 PRC124 ICR_40 1008 Tumour Trizol 151 PRC125 ICR_61 1208 Tumour Trizol 152 PRC126 ICR_40 1208 Tumour Trizol 153 PRC127 ICR_48 1208 Tumour Trizol 154 PRC128 ICR_48 1208 Low Tumour Trizol 155 PRC129 ICR_55 1208 Tumour Trizol 156 PRC12 ICR_55 507 Tumour Trizol 157 PRC130 ICR_25 1208 Tumour Trizol 158 PRC133 ICR_58 309 Tumour Trizol 159 PRC134 ICR_35 309 Normal Trizol 160 PRC135 ICR_35 309 Tumour Trizol 161 PRC136 ICR_68 309 Tumour Trizol 162 PRC137 ICR_71 309 Tumour Trizol 163 PRC138 ICR_65 309 Tumour Trizol 164 PRC139 ICR_69 309 Tumour Trizol 165 PRC13 ICR_69 507 Tumour Trizol 166 PRC141 ICR_2 509 Tumour Trizol 167 PRC142 ICR_68 509 Normal Trizol 168 PRC143 ICR_67 509 Low Tumour Trizol 169 PRC144 ICR_73 509 Tumour Trizol 170 PRC145 ICR_57 509 Low Tumour Trizol 171 PRC146 ICR_45 ICRFinal Low Tumour Trizol 172 PRC147 ICR_56 ICRFinal Low Tumour Trizol 173 PRC148 ICR_70 ICRFinal Tumour Trizol 174 PRC149 ICR_70 ICRFinal Low Tumour Trizol 175 PRC14 ICR_39 507 Normal Trizol 176 PRC150 ICR_72 ICRFinal Tumour Trizol 177 PRC151 ICR_7 ICRFinal Tumour Trizol 178 PRC152 ICR_53 ICRFinal Low Tumour Trizol 179 PRC153 ICR_64 ICRFinal Tumour Trizol 180 PRC154 ICR_33 ICRFinal Tumour Trizol 181 PRC155 ICR_33 ICRFinal Tumour Trizol 182 PRC156 ICR_1 ICRFinal Tumour Trizol 183 PRC157 ICR_62 ICRFinal Tumour Trizol 184 PRC158 ICR_74 I CRFina Tumour Trizol 185 PRC159 ICR_8 ICRFinal Tumour Trizol 186 PRC15 ICR_80 507 Normal Trizol 187 PRC160 ICR_79 ICRFinal Tumour Trizol 188 PRC161 ICR_23 ICRFinal Tumour Trizol 189 PRC162 ICR_76 ICRFinal Tumour Trizol 190 PRC163 ICR_80 ICRFinal Tumour Trizol 191 PRC164 ICR_81 ICRFinal Tumour Trizol 192 PRC165 ICR_73 ICRFina Tumour Trizol 193 PRC166 ICR_3 ICRFinal Tumour Trizol 194 PRC167 ICR_36 ICRFinal Tumour Trizol 195 PRC168 ICR_19 ICRFinal Tumour Trizol 196 PRC169 ICR_78 ICRFinal Low Tumour Trizol 197 PRC16 ICR_77 507 Normal Trizol 198 PRC17 ICR_75 507 Low Tumour Trizol 199 PRC18 ICR_6 507 Tumour Trizol 200 PRC19 ICR_25 507 Low Tumour Trizol 201 PRC1 ICR_27 507 Tumour Trizol 202 PRC20 ICR_2 507 Low Tumour Trizol 203 PRC21 ICR_82 507 Low Tumour Trizol 204 PRC22 ICR_82 507 Normal Trizol 205 PRC23 ICR_24 507 Normal Trizol 206 PRC24 ICR_26 507 Tumour Trizol 207 PRC25 ICR_12 507 Tumour Trizo 208 PRC26 ICR_29 507 Low Tumour Trizol 209 PRC27 ICR_30 407 Tumour Trizol 210 PRC28 ICR_13 407 Low Tumour Trizol 211 PRC29 ICR_15 407 Low Tumour Trizol 212 PRC2 ICR_18 507 Low Tumour Trizol 213 PRC30 ICR_7 407 Tumour Trizol 214 PRC31 ICR_22 507 Low Tumour Trizol 215 PRC32 ICR_14 507 Low Tumour Trizol 216 PRC34 ICR_21 407 Normal Trizol 217 PRC35 ICR_5 407 Normal Trizol 218 PRC36 ICR_5 407 Low Tumour Trizol 219 PRC38 ICR_12 407 Low Tumour Trizol 220 PRC39 ICR_11 407 Low Tumour Trizol 221 PRC3 ICR_32 507 Tumour Trizol 222 PRC40 ICR_9 407 Tumour Trizol 223 PRC42 ICR_20 407 Low Tumour Trizol 224 PRC45 ICR_10 407 Normal Trizol 225 PRC4 ICR_14 507 Tumour Trizol 226 PRC5 ICR_16 507 Low Tumour Trizol 227 PRC6 ICR_23 507 Tumour Trizol 228 PRC7 ICR_10 507 Tumour Trizol 229 PRC8 ICR_23 507 Tumour Trizol 230 PRC9 ICR_31 507 Tumour Trizol 231 ST1 ICR_48 1208 Stroma Trizol 232 ST2 ICR_46 ICRFinal Stroma Trizol 233 ST3 ICR_52 ICRFinal Stroma Trizol 234 ST4 ICR_66 ICRFinal Stroma Trizol 235 ST5 ICR_76 ICRFinal Stroma Trizol Row Centre ERG_FISH_status Tumour_percentage Ethnicity 1 Cambridge 0 White - British 2 Cambridge 0 White - British 3 Cambridge 2N 75 White - British 4 Cambridge 2N 5 White - British 5 Cambridge 2N 10 White - British 6 Cambridge MixedEdel 33 White - British 7 Cambridge Edel 10 White - British 8 Cambridge Edel 30 White - British 9 Cambridge 0 White - British 10 Cambridge 2N 2 White - British 11 Cambridge 0 White - British 12 Cambridge 2N 0 White - British 13 Cambridge Esplit 0 14 Cambridge 3 White - British 15 Cambridge 0 White - British 16 Cambridge Esplit 30 White - British 17 Cambridge 2N 33 White - British 18 Cambridge Edel 75 Turkish 19 Cambridge 2N 50 White - British 20 Cambridge MixedEsplit 40 White - British 21 Cambridge 2N 36 White - British 22 Cambridge MixedPloidy 10 White - British 23 Cambridge 2N 0 White - British 24 Cambridge MixedPloidy 8 White - British 25 Cambridge 2N 45 White - British 26 Cambridge MixedRearrangement 15 White - British 27 Cambridge 2N 40 White - British 28 Cambridge 0 White - British 29 Cambridge MixedRearrangement 40 White - British 30 Cambridge MixedEdel 70 White - British 31 Cambridge Esplit 21 White - British 32 Cambridge 2N 33 White - British 33 Cambridge MixedEsplit 50 White - British 34 Cambridge 2N 0 White - British 35 Cambridge 2N 50 White - British 36 Cambridge Esplit 3 White - British 37 Cambridge Edel 18 White - British 38 Cambridge MixedPloidy 34 White - British 39 Cambridge Esplit 35 White - Other 40 Cambridge MixedRearrangement 5 White - British 41 Cambridge MixedEsplit 15 White - British 42 Cambridge MixedEsplit 15 White - British 43 Cambridge MixedPloidy 8 Black or Black British - Caribbean 44 Cambridge MixedRearrangement 20 White - Other 45 Cambridge Edel 40 White - British 46 Cambridge Edel 5 White - British 47 Cambridge 2N 0 White - British 48 Cambridge 2N 20 White - British 49 Cambridge 2N 0 White - British 50 Cambridge 2Edel 55 White - British 51 Cambridge MixedRearrangement 45 White - British 52 Cambridge 2N 23 White - British 53 Cambridge MixedPloidy 20 White - British 54 Cambridge 2N 45 White - British 55 Cambridge 2N 29 White - British 56 Cambridge MixedEsplit 38 White - British 57 Cambridge 2N 49 White - British 58 Cambridge MixedRearrangement 4 White - British 59 Cambridge 0 White - British 60 Cambridge 2N 30 White - British 61 Cambridge MixedRearrangement 48 White - British 62 Cambridge MixedEdel 78 White - British 63 Cambridge MixedEdel 78 White - British 64 Cambridge MixedEdel 50 White - British 65 Cambridge MixedRearrangement 10 White - British 66 Cambridge 2Esplit 10 White - British 67 Cambridge MixedRearrangement 20 White - British 68 Cambridge MixedRearrangement 30 White - British 69 Cambridge 2N 78 White - British 70 Cambridge 2N 40 White - British 71 Cambridge MixedRearrangement 48 White - British 72 Cambridge MixedRearrangement 50 White - British 73 Cambridge 2N 31 White - British 74 Cambridge 2Esplit 33 White - British 75 Cambridge MixedRearrangement 15 White - British 76 Cambridge MixedEsplit 56 White - British 77 Cambridge MixedRearrangement 30 White - British 78 Cambridge Edel 0 White - British 79 Cambridge White - British 80 Cambridge Edel 63 White - British 81 Cambridge MixedPloidy 28 White - British 82 Cambridge 2N 10 White - British 83 Cambridge MixedRearrangement 11 White - British 84 Cambridge Esplit 57 White - British 85 Cambridge 2N 4 White - British 86 Cambridge 2N 0 White - British 87 Cambridge MixedRearrangement 50 White - British 88 Cambridge 2N 25 White - British 89 Cambridge Esplit 65 White - British 90 Cambridge 2N 35 White - British 91 Cambridge 2N 70 White - British 92 Cambridge 2N 68 Black or Black British - Caribbean 93 Cambridge MixedPloidy 5 Black or Black British - Caribbean 94 Cambridge Edel 2 White - British 95 Cambridge 2N 65 White - British 96 Cambridge MixedPloidy 33 White - British 97 Cambridge MixedEsplit 8 White - British 98 Cambridge Edel 20 White - British 99 Cambridge 2N 50 White - British 100 Cambridge MixedEsplit 55 White - British 101 Cambridge MixedPloidy 18 White - British 102 Cambridge Esplit 54 White - British 103 Cambridge Edel 23 White - British 104 Cambridge MixedPloidy 10 White - British 105 Cambridge RG 3 White - British 106 Cambridge 2N 68 White - British 107 Cambridge Esplit 0 White - British 108 Cambridge 2N 10 White - British 109 Cambridge MixedEsplit 5 White - British 110 Cambridge MixedPloidy 23 White - British 111 Cambridge Esplit 75 White - British 112 ICR 2N 0 White - British 113 ICR 2N 0 White - British 114 ICR 2N 0 White - British 115 ICR 2N 0 White - British 116 ICR 2N 0 White - British 117 ICR 2N 0 White - British 118 ICR 2N 0 Black or Black British - African 119 ICR 2N 0 120 ICR 2N 0 White - British 121 ICR 2N 0 White - British 122 ICR 2N 0 White - British 123 ICR 2N 0 White - British 124 ICR 2N 0 White - British 125 ICR 3N 0 White - British 126 ICR 2N 0 White - British 127 ICR 2N 0 White - British 128 ICR 2N 0 White - Other 129 ICR Esplit 10 White - British 130 ICR Edel 40 White - British 131 ICR 2N 60 White - British 132 ICR 2N 20 White - British 133 ICR 2N 45 White - Other 134 ICR 2N 15 White - Other 135 ICR Edel 60 White - British 136 ICR Edel White - British 137 ICR 2Edel 55 White - British 138 ICR 2N 20 White - British 139 ICR 2N 0 White - Other 140 ICR 2N 70 White - British 141 ICR 2Esplit 40 White - British 142 ICR 2Esplit 30 White - British 143 ICR MixedRearrangement 50 White - British 144 ICR Esplit 20 White - British 145 ICR 2N 90 White - British 146 ICR Edel 30 White - British 147 ICR Edel 60 White - British 148 ICR Esplit 3 White - British 149 ICR 2N 5 150 ICR 2N 20 White - British 151 ICR 2N 45 152 ICR 2Edel 70 White - British 153 ICR Edel 50 White - British 154 ICR 2Esplit 15 White - British 155 ICR 2Esplit 70 White - British 156 ICR 85 White - British 157 ICR 2N 70 White - British 158 ICR MixedPloidy 90 White - British 159 ICR MixedPloidy 0 White - British 160 ICR 2Esplit 60 White - British 161 ICR MixedPloidy 70 White - British 162 ICR 2N 30 White - British 163 ICR 2N 60 Black or Black British - African 164 ICR 2N 70 Black or Black British - African 165 ICR 2Edel 25 White - British 166 ICR Edel 60 White - Other 167 ICR 2N 0 White - British 168 ICR Edel 5 White - British 169 ICR Edel 70 White - British 170 ICR NG 5 White - British 171 ICR 2N 2 White - British 172 ICR MixedEdel 5 White - British 173 ICR 2N 35 White - British 174 ICR MixedPloidy 5 White - British 175 ICR 2N 0 White - Other 176 ICR Esplit 30 White - British 177 ICR 2N 50 White - British 178 ICR 2N 15 White - British 179 ICR 2N 20 White - British 180 ICR MixedPloidy 65 181 ICR 2N 65 White - British 182 ICR Edel 50 White - Other 183 ICR 2N 85 White - British 184 ICR MixedPloidy 70 White - British 185 ICR 4N 40 White - Other 186 ICR 2N 0 White - British 187 ICR 2N 75 White - Other 188 ICR 2N 60 White - British 189 ICR Esplit 50 White - British 190 ICR 2N 50 White - British 191 ICR Esplit 40 White - Irish 192 ICR Edel 30 White - Other 193 ICR Edel 65 White - British 194 ICR Esplit 70 White - British 195 ICR Edel 70 White - British 196 ICR Esplit 10 White - British 197 ICR 0 White - British 198 ICR Esplit 10 White - British 199 ICR White - British 200 ICR 5 White - British 201 ICR Edel 45 White - British 202 ICR Esplit 15 203 ICR 2Esplit 15 204 ICR 0 White - British 205 ICR 0 White - British 206 ICR 2Edel 30 White - British 207 ICR Edel 35 White - British 208 ICR 2N 15 White - British 209 ICR 50 Black or Black British - Caribbean 210 ICR 5 White - British 211 ICR MixedPloidy 15 White - British 212 ICR Edel 10 White - Other 213 ICR Edel White - British 214 ICR 5 White - British 215 ICR 5 White - Other 216 ICR 2N 0 White - Irish 217 ICR Edel 0 White - Irish 218 ICR Edel 5 White - British 219 ICR Edel 15 White - British 220 ICR 10 White - British 221 ICR Edel 50 White - British 222 ICR Edel 70 White - British 223 ICR Edel 5 White - British 224 ICR 0 White - British 225 ICR 2Esplit 25 White - British 226 ICR Esplit 3 White - British 227 ICR 80 White - British 228 ICR 50 White - British 229 ICR 80 White - British 230 ICR 30 White - British 231 ICR Edel 0 White - British 232 ICR 2N 0 White - British 233 ICR 2N 0 White - British 234 ICR 2N 0 White - British 235 ICR 2N 0 White - Other Row Sample ID Age_at_Diagnosis Pathology_Stage Pathology_sub_stage PSA_pre_prostatectomy Gleason_Score 1 TB08.0234_v1 64 T2 b 5.80 3 + 5 2 TB08.0234_v3 64 T2 b 5.80 3 + 5 3 TB08.0262_v3 69 T3 a 8.30 3 + 4 4 TB08.0268_v3 56 T3 a 8.70 3 + 4 5 TB08.0271_v1 74 T2 x 15.40 3 + 4 6 TB08.0311_v2 69 T3 a 15.30 3 + 4 7 TB08.0311_v3 69 T3 a 15.30 3 + 4 8 TB08.0327_v1 57 T2 x 4.80 3 + 4 9 TB08.0341_v1 57 T2 x 5.10 3 + 4 10 TB08.0341_v5 57 T2 x 5.10 3 + 4 11 TB08.0359_v16 63 T2 a 9.90 3 + 4 12 TB08.0359_v2 63 T2 a 9.90 3 + 4 13 TB08.0368_v14 71 T3 b 4 + 3 14 TB08.0429_v7 72 T3 b 9.20 3 + 4 15 TB08.0489_v5 62 T3 a 5.30 4 + 3 16 TB08.0489_v13 62 T3 a 5.30 4 + 3 17 TB08.0501_v8 64 T3 a 20.50 3 + 4 18 TB08.0519_v14 55 T4 x 9.80 5 + 4 19 TB08.0533_v6 65 T3 a 5.80 3 + 4 20 TB08.0588_v1 55 T3 a 13.90 3 + 4 21 TB08.0589_v1 66 T4 x 5.17 5 + 4 22 TB08.0589_v2 66 T4 x 5.17 5 + 4 23 TB08.0589_v4 66 T4 x 5.17 5 + 4 24 TB08.0589_v5 66 T4 x 5.17 5 + 4 25 TB08.0598_v12 65 T2 x 8.80 3 + 4 26 TB08.0609_v11 66 T2 x 11.40 4 + 3 27 TB08.0667_v9 57 T2 x 7.80 3 + 3 28 TB08.0667_v6 57 T2 x 7.80 3 + 3 29 TB08.0689_v14 51 T2 x 8.80 3 + 3 30 TB08.0689_v15 51 T2 x 8.80 3 + 3 31 TB08.0689_v2 51 T2 x 8.80 3 + 3 32 TB08.0689_v8 51 T2 x 8.80 3 + 3 33 TB08.0691_v13 69 T3 a 9.40 3 + 4 34 TB08.0716_v18 64 T3 a 8.90 3 + 4 35 TB08.0719_v11 62 T2 x 6.50 3 + 3 36 TB08.0731_v13 59 T3 a 7.90 3 + 4 37 TB08.0816_v2 63 T3 a 10.40 3 + 4 38 TB08.0817_v14 62 T3 a 10.40 3 + 4 39 TB08.0848_v10 63 T3 a 4.90 4 + 3 40 TB08.0869_v4 58 T2 x 40.00 3 + 3 41 TB08.0869_v6 58 T2 x 40.00 3 + 3 42 TB08.0869_v7 58 T2 x 40.00 3 + 3 43 TB08.0870_v18 71 T3 b 8.20 3 + 4 44 TB08.0872_v2 63 T2 c 7.50 3 + 3 45 TB08.0877_v19 61 T2 x 8.70 3 + 3 46 TB08.0879_v11 62 T3 a 8.40 4 + 3 47 TB08.0884_v2 46 T2 x 2.40 3 + 4 48 TB08.0927_v5 59 T2 c 9.30 3 + 3 49 TB08.0943_v7 56 T3 a 3.40 3 + 4 50 TB08.0958_v12 42 T2 x 11.80 3 + 3 51 TB08.0958_v13 42 T2 x 11.80 3 + 3 52 TB08.0973_v9 68 T2 c 6.40 3 + 4 53 TB08.0978_v7 64 T3 a 12.00 3 + 4 54 TB08.0978_v8 64 T3 a 12.00 3 + 4 55 TB08.0978_v9 64 T3 a 12.00 3 + 4 56 TB08.0986_v2 56 T3 a 15.50 3 + 4 57 TB08.0987_v6 54 T3 a 12.00 3 + 4 58 TB08.0993_v12 66 T2 c 7.70 4 + 3 59 TB08.0997_v6 62 T3 a 7.00 4 + 3 60 TB08.0999_v11 67 T3 a 9.20 3 + 4 61 TB08.0999_v2 67 T3 a 9.20 3 + 4 62 TB08.1015_v10 63 T3 a 8.00 3 + 5 63 TB08.1015_v11 63 T3 a 8.00 3 + 5 64 TB08.1015_v9 63 T3 a 8.00 3 + 5 65 TB08.1019_v1 59 T3 a 5.00 3 + 4 66 TB08.1019_v14 59 T3 a 5.00 3 + 4 67 TB08.1019_v15 59 T3 a 5.00 3 + 4 68 TB08.1019_v2 59 T3 a 5.00 3 + 4 69 TB08.1026_v17 61 T3 a 8.40 3 + 4 70 TB08.1044_v7 71 T3 a 7.90 3 + 4 71 TB08.1053_v5 71 T3 a 17.00 3 + 4 72 TB08.1063_v16 67 T3 a 5.80 4 + 3 73 TB08.1063_v8 67 T3 a 5.80 4 + 3 74 TB08.1083_v3 64 T3 a 7.30 3 + 3 75 TB08.1116_v2 61 T3 a 6.00 3 + 4 76 TB08.1116_v3 61 T3 a 6.00 3 + 4 77 TB08.1116_v9 61 T3 a 6.00 3 + 4 78 TB08.1159_v2 56 T2 a 7.90 3 + 3 79 TB08.0601_v16 66 T2 x 8.28 3 + 3 80 TB09.0217_v16 63 T3 a 11.50 3 + 4 81 TB09.0217_v7 63 T3 a 11.50 3 + 4 82 TB09.0219_v13 62 T3 a 17.30 3 + 4 83 TB09.0219_v2 62 T3 a 17.30 3 + 4 84 TB09.0219_v21 62 T3 a 17.30 3 + 4 85 TB09.0219_v8 62 T3 a 17.30 3 + 4 86 TB09.0238_v12 66 T3 a 9.60 3 + 4 87 TB09.0238_v18 66 T3 a 9.60 3 + 4 88 TB09.0238_v5 66 T3 a 9.60 3 + 4 89 TB09.0272_v6 62 T3 a 12.00 3 + 4 90 TB09.0272_v7 62 T3 a 12.00 3 + 4 91 TB09.0295_v2 64 T3 b 22.60 3 + 4 92 TB09.0413_v11 48 T3 a 5.30 4 + 3 93 TB09.0413_v8 48 T3 a 5.30 4 + 3 94 TB09.0443_v3 41 T3 a 16.20 3 + 4 95 TB09.0443_v8 41 T3 a 16.20 3 + 4 96 TB09.0448_v8 70 T2 c 4.68 3 + 4 97 TB09.0462_v7 56 T3 a 5.80 3 + 4 98 TB09.0471_v11 54 T2 c 5.80 3 + 3 99 TB09.0504_v4 60 T2 a 5.10 3 + 5 100 TB09.0550_v15 47 T3 a 11.50 3 + 4 101 TB09.0606_v3 64 T3 b 10.00 4 + 5 102 TB09.0706_v5 63 T3 a 7.30 3 + 4 103 TB09.0720_v19 67 T2 x 8.90 3 + 3 104 TB09.0721_v14 58 T2 c 4.00 3 + 3 105 TB09.0721_v15 58 T2 c 4.00 3 + 3 106 TB09.0725_v9 64 T2 x 10.70 3 + 4 107 TB09.0774_v1 64 T2 c 6.40 3 + 4 108 TB09.0774_v15 64 T2 c 6.40 3 + 4 109 TB09.0850_v2 21 T3 a 5.70 3 + 4 110 TB09.0962_v13 65 T2 x 6.20 3 + 3 111 TB09.0962_v16 65 T2 x 6.20 3 + 3 112 NP1 66 T2 a 9.80 3 + 3 113 NP10 60 T3 b 15.00 4 + 3 114 NP11 61 T2 c 6.90 3 + 4 115 NP12 65 T2 c 7.40 4 + 3 116 NP14 72 T2 x 11.10 3 + 4 117 NP15 64 T2 c 6.10 3 + 4 118 NP16 53 T2 c 11.10 3 + 3 119 NP17 58 T2 c 4.70 3 + 4 120 NP18 60 T2 c 16.90 3 + 4 121 NP19 60 T3 b 8.00 4 + 5 122 NP2 53 T3 a 3 + 4 123 NP20 68 T2 c 7.10 3 + 4 124 NP21 66 T2 c 6.10 3 + 4 125 NP4 60 T3 b 15.00 4 + 3 126 NP5 61 T2 c 3.10 3 + 3 127 NP8 59 T2 c 7.70 3 + 4 128 NP9 62 T2 c 7.60 3 + 5 129 PRC140 71 T2 b 6.30 4 + 3 130 PRC101 55 T2 c 4.75 3 + 4 131 PRC102 59 T2 c 7.70 3 + 4 132 PRC103 61 T2 c 4.00 3 + 4 133 PRC105 62 T2 c 7.60 3 + 5 134 PRC106 62 T2 c 7.60 3 + 5 135 PRC109 62 T3 b 12.40 3 + 4 136 PRC10 58 T2 c 6.60 3 + 3 137 PRC110 62 T3 b 12.40 3 + 4 138 PRC111 62 T3 b 12.40 3 + 4 139 PRC112 68 T2 c 6.40 3 + 4 140 PRC113 49 T2 c 8.90 3 + 4 141 PRC114 40 T2 c 8.40 3 + 4 142 PRC115 40 T2 c 8.40 3 + 4 143 PRC116 61 T2 c 7.90 3 + 4 144 PRC117 61 T2 c 7.90 3 + 4 145 PRC118 61 T2 c 6.90 3 + 4 146 PRC119 61 T2 c 3.10 3 + 3 147 PRC11 58 T2 x 4.10 3 + 3 148 PRC122 61 T2 c 7.90 3 + 4 149 PRC123 55 T3 a 3.30 3 + 4 150 PRC124 61 T3 a 6.40 3 + 4 151 PRC125 55 T3 a 3.30 3 + 4 152 PRC126 72 T3 b 4 + 5 153 PRC127 72 T3 b 4 + 5 154 PRC128 70 T3 a 4.70 4 + 3 155 PRC129 70 T3 a 4.70 4 + 3 156 PRC12 63 T3 a 13.70 4 + 3 157 PRC130 65 T2 c 7.40 4 + 3 158 PRC133 72 T2 x 11.10 3 + 4 159 PRC134 72 T2 x 11.10 3 + 4 160 PRC135 71 T2 b 6.30 4 + 3 161 PRC136 51 T2 c 8.90 4 + 3 162 PRC137 64 T2 c 6.10 3 + 4 163 PRC138 53 T2 c 11.10 3 + 3 164 PRC139 53 T2 c 11.10 3 + 3 165 PRC13 63 T3 b 13.00 4 + 3 166 PRC141 64 T2 c 15.20 3 + 4 167 PRC142 60 T3 b 8.00 4 + 5 168 PRC143 68 T2 c 7.10 3 + 4 169 PRC144 61 T2 c 7.80 3 + 4 170 PRC145 66 T2 c 6.10 3 + 4 171 PRC146 63 T2 c 5.60 3 + 4 172 PRC147 63 T2 c 5.60 3 + 4 173 PRC148 66 T2 c 6.70 3 + 4 174 PRC149 63 T2 c 11.50 4 + 3 175 PRC14 53 T2 x 8.00 3 + 3 176 PRC150 50 T2 c 4.40 3 + 4 177 PRC151 56 T3 a 7.70 3 + 4 178 PRC152 58 T2 c 9.60 3 + 3 179 PRC153 58 T2 c 9.60 3 + 3 180 PRC154 69 T2 c 4.53 3 + 4 181 PRC155 61 T2 c 7.50 3 + 3 182 PRC156 50 T3 a 3.60 3 + 4 183 PRC157 56 T1 c 10.50 3 + 3 184 PRC158 55 T3 a 7.00 4 + 5 185 PRC159 60 T3 a 5.40 4 + 3 186 PRC15 50 T3 b 16.20 3 + 4 187 PRC160 64 T3 b 7.20 4 + 3 188 PRC161 55 T3 a 7.00 4 + 5 189 PRC162 56 T3 b 9.28 3 + 4 190 PRC163 60 T3 b 8.00 4 + 5 191 PRC164 62 T2 c 17.40 3 + 4 192 PRC165 64 T2 c 12.90 3 + 4 193 PRC166 55 T2 c 12.40 3 + 4 194 PRC167 64 T3 a 3.80 3 + 4 195 PRC168 59 T2 c 8.70 3 + 3 196 PRC169 70 T2 c 8.10 3 + 4 197 PRC16 67 T3 a 16.00 3 + 3 198 PRC17 49 T3 b 7.50 3 + 4 199 PRC18 63 T3 b 13.00 4 + 3 200 PRC19 65 T3 b 9.70 4 + 3 201 PRC1 61 T2 c 9.30 3 + 3 202 PRC20 65 T2 x 9.80 3 + 4 203 PRC21 65 T2 x 9.80 3 + 4 204 PRC22 57 T2 c 7.10 3 + 4 205 PRC23 69 T2 x 5.60 3 + 4 206 PRC24 56 T2 a 7.90 3 + 3 207 PRC25 58 T2 c 5.60 3 + 3 208 PRC26 52 T2 c 3.40 3 + 3 209 PRC27 56 T3 b 8.00 3 + 3 210 PRC28 48 T2 c 3.70 3 + 3 211 PRC29 64 T2 x 5.60 3 + 4 212 PRC2 53 T2 x 8.00 3 + 3 213 PRC30 58 T2 x 4.10 3 + 3 214 PRC31 56 T2 a 12.80 3 + 3 215 PRC32 52 T2 x 6.10 3 + 3 216 PRC34 56 T2 x 4.50 3 + 3 217 PRC35 56 T2 x 4.50 3 + 3 218 PRC36 56 T2 a 7.90 3 + 3 219 PRC38 55 T2 c 5.70 3 + 3 220 PRC39 62 T3 b 22.30 3 + 4 221 PRC3 50 T3 b 16.20 3 + 4 222 PRC40 61 T2 c 9.30 3 + 3 223 PRC42 68 T2 x 9.80 3 + 3 224 PRC45 56 T2 a 12.80 3 + 3 225 PRC4 54 T3 a 11.40 3 + 3 226 PRC5 41 T2 x 4.00 3 + 3 227 PRC6 67 T3 a 16.00 3 + 3 228 PRC7 68 T2 x 9.80 3 + 3 229 PRC8 67 T3 a 16.00 3 + 3 230 PRC9 67 T2 c 13.90 4 + 5 231 ST1 72 T3 b 4 + 5 232 ST2 63 T2 b 4.78 3 + 4 233 ST3 63 T2 c 5.00 3 + 3 234 ST4 60 T2 c 16.90 3 + 4 235 ST5 64 T3 b 7.20 4 + 3 Row Margins Extra_Capsular_Extension BCR_FreeTime_months BCR_Event ICGC_category 1 negative margins N 66.00 FALSE normal 2 negative margins N 66.00 FALSE normal 3 Positive circumferential Y 65.00 FALSE cat_1 4 Positive circumferential Y 59.00 FALSE cat_1 5 Negative N 73.00 FALSE cat_2 6 Positive base Y 64.00 FALSE cat_2 7 Positive base Y 64.00 FALSE cat_2 8 Negative N 64.00 FALSE cat_1 9 negative margins N 6.00 TRUE normal 10 negative margins N 6.00 TRUE cat_1 11 positive Apex margin N 2.00 TRUE normal 12 positive Apex margin N 2.00 TRUE cat_1 13 positive apex & Y 34.00 FALSE unknown circumferential margin 14 positive circumferential Y 3.00 FALSE normal margin 15 negative margins Y 49.00 FALSE normal 16 negative margins Y 49.00 FALSE cat_2 17 Negative Y 76.00 FALSE cat_3 18 positive apex cat_3 19 negative margins Y 62.00 FALSE cat_1 20 Negative Y 55.00 TRUE cat_2 21 Positive base Y 2.00 TRUE cat_3 22 Positive base Y 2.00 TRUE cat_3 23 Positive base Y 2.00 TRUE cat_3 24 Positive base Y 2.00 TRUE cat_3 25 negative margins N 61.00 FALSE cat_1 26 Negative N 34.00 FALSE cat_2 27 negative margins N 42.00 FALSE cat_1 28 negative margins N 42.00 FALSE normal 29 Negative N 60.00 FALSE cat_1 30 Negative N 60.00 FALSE cat_1 31 Negative N 60.00 FALSE cat_1 32 Negative N 60.00 FALSE cat_1 33 Negative Y 8.00 TRUE cat_1 34 negative margins Y 60.00 FALSE cat_1 35 positive circumferential N 60.00 FALSE cat_1 margin 36 Negative Y 61.00 FALSE cat_1 37 negative margins Y 60.00 FALSE cat_2 38 Negative Y 24.00 TRUE cat_2 39 negative margins Y 55.00 FALSE cat_2 40 Negative N 19.00 TRUE cat_3 41 Negative N 19.00 TRUE cat_3 42 Negative N 19.00 TRUE cat_3 43 Negative Y 1.00 TRUE cat_1 44 Negative N 56.00 FALSE cat_1 45 Negative N 49.00 FALSE cat_1 46 Negative Y 60.00 FALSE cat_2 47 negative margins N 61.00 FALSE cat_1 48 positive Apex margin N 59.00 FALSE cat_1 49 positive base margin Y 53.00 FALSE cat_1 50 Negative N 43.00 FALSE cat_2 51 Negative N 43.00 FALSE cat_2 52 negative margins N 58.00 FALSE cat_1 53 Negative Y 58.00 FALSE cat_2 54 Negative Y 58.00 FALSE cat_2 55 Negative Y 58.00 FALSE cat_2 56 Positive base Y 58.00 FALSE cat_2 57 positive circumferential Y 58.00 FALSE cat_2 margin 58 Negative N 60.00 FALSE cat_2 59 positive Apex margin Y 58.00 FALSE normal 60 Negative Y 52.00 FALSE cat_1 61 Negative Y 52.00 FALSE cat_1 62 Negative Y 12.00 TRUE cat_3 63 Negative Y 12.00 TRUE cat_3 64 Negative Y 12.00 TRUE cat_3 65 Negative Y 68.00 FALSE cat_1 66 Negative Y 68.00 FALSE cat_1 67 Negative Y 68.00 FALSE cat_1 68 Negative Y 68.00 FALSE cat_1 69 negative margins Y 57.00 TRUE cat_1 70 Positive base & Y 59.00 FALSE cat_1 circumferential 71 Negative Y 57.00 FALSE cat_2 72 Positive base & Y 38.00 TRUE cat_2 circumferential 73 Positive base & Y 38.00 TRUE cat_2 circumferential 74 negative margins Y 57.00 FALSE cat_1 75 Negative Y 42.00 FALSE cat_1 76 Negative Y 42.00 FALSE cat_1 77 Negative Y 42.00 FALSE cat_1 78 negative margins N 56.00 FALSE cat_1 79 negative margins N 68.00 FALSE normal 80 Positive base Y 12.00 TRUE cat_2 81 Positive base Y 12.00 TRUE cat_2 82 Negative Y 16.00 TRUE cat_2 83 Negative Y 16.00 TRUE cat_2 84 Negative Y 16.00 TRUE cat_2 85 Negative Y 16.00 TRUE cat_2 86 Negative Y 54.00 FALSE cat_1 87 Negative Y 54.00 FALSE cat_1 88 Negative Y 54.00 FALSE cat_1 89 Negative Y 58.00 FALSE cat_2 90 Negative Y 58.00 FALSE cat_2 91 positive apex cat_3 92 Negative Y 45.00 TRUE cat_2 93 Negative Y 45.00 TRUE cat_2 94 Negative Y 51.00 FALSE cat_2 95 Negative Y 51.00 FALSE cat_2 96 Negative N 19.00 TRUE cat_1 97 Negative Y 57.00 FALSE cat_1 98 negative margins N 54.00 FALSE cat_1 99 Negative N 51.00 FALSE cat_3 100 Negative Y 51.00 FALSE cat_2 101 Negative Y 15.00 TRUE cat_3 102 Negative Y 17.00 TRUE cat_1 103 negative margins N 50.00 FALSE cat_1 104 Negative N 10.00 TRUE cat_1 105 Negative N 10.00 TRUE cat_1 106 negative margins N 49.00 FALSE cat_2 107 Negative N 49.00 FALSE cat_1 108 Negative N 49.00 FALSE cat_1 109 Negative Y 56.00 FALSE cat_1 110 Negative N 48.00 FALSE cat_1 111 Negative N 48.00 FALSE cat_1 112 Negative No 95.00 FALSE cat_1 113 Positive circumferential Unknown 55.00 FALSE normal 114 Negative No 72.00 FALSE normal 115 Negative No 15.00 TRUE normal 116 Positive circumferential Unknown 59.00 FALSE normal 117 Positive apex No 51.00 FALSE normal 118 Negative No 48.00 FALSE normal 119 Positive circumferential No 60.00 FALSE cat_1 120 Positive circumferential No 69.00 FALSE normal 121 Positive circumferential Yes 6.00 TRUE cat_3 122 Positive circumferential Yes 76.00 FALSE unknown 123 Negative No 61.00 FALSE normal 124 No 63.00 FALSE normal 125 Positive circumferential Unknown 55.00 FALSE cat_2 126 Negative No 68.00 FALSE cat_1 127 Negative No 55.00 FALSE normal 128 Negative Unknown 68.00 FALSE normal 129 Negative No 57.00 FALSE cat_2 130 Negative Unknown 64.00 FALSE cat_1 131 Negative No 55.00 FALSE cat_1 132 Negative No 72.00 FALSE cat_1 133 Negative Unknown 68.00 FALSE cat_3 134 Negative Unknown 68.00 FALSE cat_3 135 Positive apex & No 47.00 FALSE cat_2 circumferential 136 Unknown 3.00 TRUE cat_1 137 Positive apex & No 47.00 FALSE cat_2 circumferential 138 Positive apex & No 47.00 FALSE cat_2 circumferential 139 Positive apex No 39.00 FALSE cat_1 140 Negative No 43.00 FALSE cat_1 141 Negative No 16.00 FALSE cat_1 142 Negative No 16.00 FALSE cat_1 143 Negative Unknown 69.00 FALSE cat_1 144 Negative Unknown 69.00 FALSE cat_1 145 Negative No 72.00 FALSE cat_1 146 Negative No 68.00 FALSE cat_1 147 Positive circumferential No 93.00 FALSE cat_1 148 Negative Unknown 69.00 FALSE cat_1 149 Positive complex Yes 71.00 FALSE cat_2 150 Negative No 49.00 FALSE cat_1 151 Positive complex Yes 71.00 FALSE cat_2 152 Positive apex & Yes 56.00 TRUE unknown circumferential & base 153 Positive apex & Yes 56.00 TRUE unknown circumferential & base 154 Positive circumferential Yes 60.00 FALSE cat_3 155 Positive circumferential Yes 60.00 FALSE cat_3 156 Positive circumferential Yes 26.00 TRUE cat_3 157 Negative No 15.00 TRUE cat_2 158 Positive circumferential Unknown 59.00 FALSE cat_2 159 Positive circumferential Unknown 59.00 FALSE cat_2 160 Negative No 57.00 FALSE cat_2 161 Positive circumferential No 60.00 FALSE cat_2 162 Positive apex No 51.00 FALSE cat_1 163 Negative No 48.00 FALSE cat_2 164 Negative No 48.00 FALSE cat_2 165 Positive complex Unknown 9.00 TRUE cat_2 166 Positive circumferential No 27.00 FALSE cat_2 167 Positive circumferential Yes 6.00 TRUE cat_3 168 Negative No 61.00 FALSE cat_1 169 Negative No 23.00 TRUE cat_1 170 No 63.00 FALSE cat_1 171 Negative No 55.00 FALSE cat_1 172 Negative No 55.00 FALSE cat_1 173 Positive apex No 66.00 FALSE cat_1 174 Negative No 53.00 FALSE cat_2 175 Unknown 108.00 FALSE normal 176 Negative No 61.00 FALSE cat_1 177 Negative Yes 54.00 FALSE cat_2 178 Negative No 72.00 FALSE cat_1 179 Negative No 72.00 FALSE cat_1 180 Positive apex No 7.00 TRUE cat_1 181 Negative Unknown 70.00 FALSE cat_1 182 Yes 44.00 FALSE cat_2 183 Negative No 34.00 FALSE cat_2 184 Positive circumferential Yes 44.00 TRUE cat_3 185 Negative Yes 32.00 FALSE cat_3 186 Positive apex & Unknown 4.00 TRUE normal circumferential 187 Negative No 34.00 FALSE cat_2 188 Positive circumferential Yes 44.00 TRUE cat_3 189 Negative Unknown 15.00 TRUE cat_1 190 Positive circumferential Yes 6.00 TRUE cat_3 191 Negative No 65.00 FALSE cat_2 192 Unknown 9.00 TRUE cat_2 193 Positive circumferential No 73.00 FALSE cat_2 194 Negative Yes 67.00 FALSE cat_2 195 Negative No 39.00 FALSE cat_1 196 Negative No 32.00 FALSE cat_1 197 Positive complex Yes 66.00 TRUE normal 198 Positive apex & Unknown 17.00 TRUE cat_1 circumferential 199 Positive complex Unknown 9.00 TRUE cat_2 200 Positive complex Unknown 45.00 TRUE cat_2 201 Negative No 110.00 FALSE cat_1 202 56.00 FALSE cat_1 203 56.00 FALSE cat_1 204 Positive apex No 83.00 FALSE cat_1 205 Positive circumferential Unknown 80.00 FALSE cat_1 206 Positive complex No 92.00 FALSE cat_1 207 Positive apex & No 19.00 TRUE cat_1 circumferential 208 Negative No 94.00 FALSE cat_1 209 Positive complex No 98.00 FALSE cat_1 210 Positive complex Unknown 31.00 TRUE cat_1 211 Positive complex Unknown 90.00 FALSE cat_1 212 Unknown 108.00 FALSE cat_1 213 Positive circumferential No 93.00 FALSE cat_1 214 Negative No 108.00 FALSE cat_2 215 Positive complex No 91.00 FALSE cat_1 216 Positive apex & Unknown 129.00 FALSE cat_1 circumferential 217 Positive apex & Unknown 129.00 FALSE cat_1 circumferential 218 Positive complex No 92.00 FALSE cat_1 219 Positive base Unknown 89.00 FALSE cat_1 220 Positive apex No 84.00 FALSE cat_3 221 Positive apex & Unknown 4.00 TRUE cat_2 circumferential 222 Negative No 110.00 FALSE cat_1 223 Positive circumferential Unknown 39.00 TRUE cat_1 224 Negative No 108.00 FALSE cat_2 225 Negative Yes 123.00 FALSE cat_2 226 Negative Unknown 74.00 FALSE cat_1 227 Positive complex Yes 66.00 TRUE cat_2 228 Positive circumferential Unknown 39.00 TRUE cat_1 229 Positive complex Yes 66.00 TRUE cat_2 230 Negative No 11.00 TRUE cat_3 231 Positive apex & Yes 56.00 TRUE unknown circumferential & base 232 Positive circumferential No 67.00 FALSE cat_1 233 Negative No 60.00 FALSE cat_1 234 Positive circumferential No 69.00 FALSE cat_2 235 Negative No 34.00 FALSE normal

REFERENCES

  • 1. D'Amico, A. V., Moul, J., Carroll, P. R. & Sun, L. Cancer-specific mortality after surgery or radiation for patients with clinically localized prostate cancer managed during the prostate-specific antigen era. J. Clin. Oncol. 21, 2163-2172 (2003).
  • 2. Buyyounouski, M. K., Pickles, T. & Kestin, L. L. Validating the interval to biochemical failure for the identification of potentially lethal prostate cancer. J. Clin. Oncol. 30, 1857-1863 (2012).
  • 3. Draisma, G. et al. Lead time and overdiagnosis in prostate-specific antigen screening: importance of methods and context. J. Natl. Cancer Inst. 101, 374-383 (2009).
  • 4. Etzioni, R., Gulati, R., Mallinger, L. & Mandelblatt, J. Influence of study features and methods on overdiagnosis estimates in breast and prostate cancer screening. Ann. Intern. Med. 158, 831-838 (2013).
  • 5. Sorlie, T. et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl. Acad. Sci. U.S.A. 100, 8418-8423 (2003).
  • 6. Taylor, B. S. et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22 (2010).
  • 7. Ross-Adams, H. et al. Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study. EBioMedicine 2, 1133-1144 (2015).
  • 8. Carrivick, L. et al. Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques. J R Soc Interface 3, 367-381 (2006).
  • 9. Glinsky, G. V., Glinskii, A. B., Stephenson, A. J., Hoffman, R. M. & Gerald, W. L. Gene expression profiling predicts clinical outcome of prostate cancer. J. Clin. Invest. 113, 913-923 (2004).
  • 10. Erho, N. et al. Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy. PLoS ONE 8, e66855 (2013).
  • 11. Cuzick, J. et al. Prognostic value of an RNA expression signature derived from cell cycle proliferation genes in patients with prostate cancer: a retrospective study. Lancet Oncol. 12, 245-255 (2011).
  • 12. Ramos-Montoya, A. et al. HES6 drives a critical AR transcriptional programme to induce castration-resistant prostate cancer through activation of an E2F1-mediated cell cycle network. EMBO Molecular Medicine n/a-n/a (2014). doi:10.1002/emmm.201303581
  • 13. Tomlins, S. A. et al. Characterization of 1577 primary prostate cancers reveals novel biological and clinicopathologic insights into molecular subtypes. Eur. Urol. 68, 555-567 (2015).
  • 14. You, S. et al. Integrated classification of prostate cancer reveals a novel luminal subtype with poor outcome. Cancer Res. (2016). doi:10.1158/0008-5472.CAN-16-0902
  • 15. Blei, D. M., Ng, A. Y. & Jordan, M. I. Latent dirichlet allocation. the Journal of machine Learning research (2003).
  • 16. Boutros, P. C. et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat. Genet. (2015). doi:10.1038/ng.3315
  • 17. Clark, J. et al. Complex patterns of ETS gene alteration arise during cancer development in the human prostate. Oncogene 27, 1993-2003 (2008).
  • 18. Cooper, C. S. et al. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat. Genet. 47, 367-372 (2015).
  • 19. Svensson, M. A. et al. Testing mutual exclusivity of ETS rearranged prostate cancer. Lab. Invest. 91, 404-412 (2011).
  • 20. Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell 163, 1011-1025 (2015).
  • 21. Olmos, D. et al. Prognostic value of blood mRNA expression signatures in castration-resistant prostate cancer: a prospective, two-stage study. Lancet Oncol. 13, 1114-1124 (2012).
  • 22. Klein, E. A., Yousefi, K., Haddad, Z., Choeurng, V. & Buerki, C. A genomic classifier improves prediction of metastatic disease within 5 years after surgery in node-negative high-risk prostate cancer patients managed by . . . Eur. Urol. (2015).
  • 23. Stephenson, A. J. et al. Integration of gene expression profiling and clinical variables to predict prostate carcinoma recurrence after radical prostatectomy. Cancer 104, 290-298 (2005).
  • 24. Ramaswamy, S., Ross, K. N., Lander, E. S. & Golub, T. R. A molecular signature of metastasis in primary solid tumors. Nat. Genet. 33, 49-54 (2003).
  • 25. Klein, E. A. et al. A 17-gene assay to predict prostate cancer aggressiveness in the context of Gleason grade heterogeneity, tumor multifocality, and biopsy undersampling. Eur. Urol 66, 550-560 (2014).
  • 26. Tomlins, S. A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644-648 (2005).
  • 27. Weischenfeldt, J. et al. Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 123, 159-170 (2013).
  • 28. Park, K. et al. TMPRSS2: ERG Gene Fusion Predicts Subsequent Detection of Prostate Cancer in Patients With High-Grade Prostatic Intraepithelial Neoplasia. J. Clin. Oncol 32, 206-211 (2014).
  • 29. Friedl, P., Locker, J., Sahai, E. & Segall, J. E. Classifying collective cancer cell invasion. Nat. Cell Biol. 14, 777-783 (2012).
  • 30. Schröder, F. H. et al. Screening and prostate cancer mortality: results of the European Randomised Study of Screening for Prostate Cancer (ERSPC) at 13 years of follow-up. Lancet 384, 2027-2035 (2014).
  • 31. Warren, A. Y. et al. Method for sampling tissue for research which preserves pathological data in radical prostatectomy. Prostate 73, 194-202 (2013).
  • 32. Jhavar, S. et al. Detection of TMPRSS2-ERG translocations in human prostate cancer by expression profiling using GeneChip Human Exon 1.0 ST arrays. J Mol Diagn 10, 50-57 (2008).
  • 33. Irizarry, R. A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264 (2003).
  • 34. Johnson, W. E., Li, C. & Rabinovic, A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics (2007).
  • 35. Rogers, S., Girolami, M., Campbell, C. & Breitling, R. The latent process decomposition of cDNA microarray data sets. IEEE/ACM Trans Comput Biol Bioinform 2, 143-156 (2005).
  • 36. Ritchie, M. E. et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
  • 37. Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. Journal of statistical software (2010).
  • 38. Breiman, L. Random forests. Machine learning (2001).
  • 39. Liaw, A. & Wiener, M. Classification and regression by randomForest. R news (2002).

We gratefully acknowledge the support of the Institute of Cancer Research and also the University of Cambridge for supplying the CancerMap data.

Claims

1. A method of classifying cancer or predicting cancer progression, comprising:

a. determining the expression status of a plurality of genes in a sample obtained from the patient to provide a patient expression profile;
b. conducting a statistical Bayesian clustering analysis or other clustering analysis on the patient expression profile and a reference dataset for the same plurality of genes from different patients;
c. optionally repeating the analysis step b) multiple times; and
d. classifying the cancer or predicting cancer progression.

2. The method of claim 1, wherein step b) is repeated at least 2, at least 3, at least 5, at least 20 times, at least 50 times or at least 100 times.

3. The method of claim 2, wherein a different random seed is used for each clustering analysis.

4. The method of any preceding claim, wherein determining the expression status of the plurality of genes comprises determining the level of expression of the plurality of genes.

5. The method of any preceding claim, wherein the expression status is determined for at least 50, at least 100, at least 200 or most preferably at least 500.

6. The method of any preceding claim, further comprising normalising the patent expression profile to the reference dataset prior to conducting the statistical analysis.

7. The method of any preceding claim, where the genes of step a) are selected from the genes listed in Table 1.

8. The method of any preceding claim, wherein step a) comprises determining the expression status of at least 20, at least 50, at least 100, at least 200, at least 500 genes or at least 1000 genes.

9. The method of any preceding claim, wherein step a) comprises determining the expression status of at least 100 genes selected from Table 1.

10. The method of any preceding claim, wherein step a) comprises determining the expression status of all 500 genes selected from Table 1.

11. The method of any preceding claim further comprising a step of selecting a sub-set of genes whose expression status has been determined for statistical analysis.

12. The method of claim 11, wherein the expression status of the each of the genes in the subset of genes is known to vary across cancer patient samples.

13. The method of any preceding claim, further comprising assigning a unique label to the patient expression profile prior to statistical analysis.

14. The method of any preceding claim, wherein step d) comprises determining the DESNT status of the patient cancer sample.

15. The method of any preceding claim, wherein step d) comprises determining the DESNT status of the patient cancer sample.

16. The method of any preceding claim, wherein the DESNT status of each of the expression profiles in the reference dataset is known.

17. The method of any preceding claim, wherein the patient expression profile is combined with at least 2 reference datasets prior to statistical analysis.

18. The method of any preceding claim, wherein the statistical analysis is LPD analysis.

19. The method of claim 18, wherein the LPD analysis organises individual patient expression profiles into groups.

20. The method of claim 19, wherein organising individual patient expression profiles into groups comprises, for each expression profile, using the LDP analysis to determine the contribution (pi) of each group to the overall expression profile for each patient expression profile.

21. The method of claim 20, wherein a patient expression profile is assigned to an individual group according to the group that contributes the most to the overall expression profile.

22. The method of claim 20 or claim 21, wherein cancer progression in the patient is predicted according to the contribution (pi value) of the DESNT process to the overall expression profile.

23. The method of claim 22, wherein DESNT cancer is predicted when the contribution of the DESNT process to the overall expression profile is greater than the contribution of any other single process to the overall expression profile.

24. The method of claim 22, wherein DESNT cancer is predicted according to the contribution of the DESNT process to the overall expression profile and according to the stage of the patient's tumour, the Gleason score of the patient and/or PSA score of the patient.

25. The method of claim 22, wherein DESNT cancer is predicted when the pi value for the DESNT process for the patient cancer sample is at least 0.1, at least 0.2, at least 0.3, at least 0.4 or at least 0.5.

26. The method of claim 19, wherein the groups are assigned either DESNT or a non-DESNT status.

27. The method of claim 26, wherein only group is assigned DESNT status.

28. The method of claim 27, wherein the patient cancer is classified as aggressive or cancer progression is predicted when the patient sample groups with DESNT cancers from the reference dataset or datasets.

29. The method of claim 27, wherein the statistical analysis is carried out multiple times and the patient cancer is classified as aggressive or cancer progression is predicted when the patient sample groups with DESNT cancers from the reference dataset or datasets in at least 60% of runs of the statistical analysis.

30. The method of any preceding claim, wherein the cancer is prostate cancer.

31. A method of classifying cancer or predicting cancer progression, comprising:

a. providing a reference dataset wherein the cancer progression status of each patient sample in the dataset is known;
b. selecting from this dataset a plurality of genes, wherein the plurality of genes comprises at least 5, at least 10, at least 20, at least 30, at least 40 or at least genes selected from the group listed in Table 2 or at least 5, at least 10, at least 15 or at least 20 genes selected from the group listed in Table 3;
c. optionally: i. determining the expression status of at least 1 further, different, gene in the patient sample as a control, wherein the control gene is not a gene listed in Table 2 or Table 3; and ii. determining the relative levels of expression of the plurality of genes and of the control gene(s);
d. using the expression status of those selected genes to apply a supervised machine learning algorithm on the dataset to obtain a predictor for cancer progression;
e. determining the expression status of the same plurality of genes in a sample obtained from the patient to provide a patient expression profile;
f. optionally normalising the patient expression profile to the reference dataset; and
g. applying the predictor to the patient expression profile to classify the cancer, or to predict cancer progression.

32. The method of claim 31, wherein the plurality of genes comprises at least 5, at least 10, at least 20, at least 30, at least 40 or at least 45 genes selected from the group listed in Table 2.

33. The method of claim 31, wherein the plurality of genes comprises at least 5, at least 10, at least 15 or at least 20 genes selected from the group listed in Table 3.

34. The method of any one of claims 31 to 33, wherein determining the relative levels of expression comprises determining a ratio of expression for each pair of genes in the patient dataset and the reference dataset.

35. The method of any one of claims 31 to 34, wherein the machine learning algorithm is a random forest analysis.

36. The method of any one of claims 31 to 35, wherein the cancer progression status of each patient sample in the dataset is known according to the DESNT status of the cancer.

37. The method of any one of claims 31 to 36, wherein the DESNT status of the cancer has been previously determined using an analysis involving LPD.

38. The method of claim 37, the DESNT status of the cancer has been previously determined using a method according to any one of claims 1 to 23.

39. The method according to any one of claims 31 to 36, wherein classifying the cancer or predicting cancer progression comprises determining the DESNT status of the cancer.

40. The method of any one of claims 31 to 39, wherein the at least 1 control gene is a gene listed in Table 6 or Table 7.

41. The method of any one of claims 31 to 40, wherein expression status of at least 2 control genes is determined.

42. A method of classifying cancer or predicting cancer progression, comprising:

a. providing a reference dataset wherein the cancer progression status of each patient sample in the dataset is known (for example as determined by LPD analysis);
b. selecting from this dataset of a plurality of genes;
c. using the expression status of those selected genes to apply a supervised machine learning algorithm on the dataset to obtain a predictor for cancer progression;
d. determining the expression status of the same plurality of genes in a sample obtained from the patient to provide a patient expression profile;
e. optionally normalising the patient expression profile to the reference dataset; and
f. applying the predictor to the patient expression profile to classify the cancer, or to predict cancer progression.

43. The method of claim 42, wherein the cancer progression status of each patient sample in the dataset is known according to the DESNT status of the cancer.

44. The method of claim 42 or 43, wherein the DESNT status of the cancer has been previously determined using an analysis involving LPD.

45. The method of claim 44, the DESNT status of the cancer has been previously determined using a method according to any one of claims 1 to 23.

46. The method according to any one of claims 42 to 45, wherein the supervised machine learning algorithm is a random forest analysis.

47. The method according to any one of claims 42 to 46, wherein classifying the cancer or predicting cancer progression comprises determining the DESNT status of the cancer.

48. A method according to any one of claims 42 to 47, wherein at least 10, at least 20, at least 30, at least 40 or at least 50 genes are selected in step b).

49. A method according to any one of claims 42 to 48, wherein the genes selected in step b) are downregulated in cancers that will or have progressed.

50. A method according to any one of claims 42 to 49, wherein the genes selected in step b) comprise at least 5, at least 10, at least 15, at least 20, at least 30, at least 40, or all 45 genes listed in Table 2.

51. A method of classifying cancer or predicting cancer progression, comprising:

a. providing one or more reference datasets where the cancer progression status of each patient sample in the datasets is known (for example as determined by LPD analysis);
b. selecting from this dataset a plurality of genes whose expression statuses are known to vary between cancer that has or will progress and cancer that does not or will not progress;
c. applying a LASSO logistic regression model analysis on the selected genes to identify a subset of the selected genes that predict cancer progression;
d. using the expression status of this subset of selected genes to apply a supervised machine learning algorithm on the dataset to obtain a predictor for DESNT cancers;
e. determining the expression status of the subset of selected genes in a sample obtained from the patient to provide a patient expression profile;
f. optionally normalising the patient expression profile to the reference dataset(s); and
g. applying the predictor to the patient expression profile to classify the cancer or predict cancer progression.

52. The method of claim 51, wherein the cancer progression status of each patient sample in the dataset is known according to the DESNT status of the cancer.

53. The method of claim 51 or 52, wherein the DESNT status of the cancer has been previously determined using an analysis involving LPD.

54. The method of claim 53, wherein the DESNT status of the cancer has been previously determined using a method according to any one of claims 1 to 23.

55. The method of any one of claims 51 to 54, wherein the plurality of genes is at least 100, at least 200, at least 300, at least 400, at least 500 or at least 1000 genes listed in Table 4.

56. The method of any one of claims 51 to 55, wherein the genes predict cancer progression according to the DESNT status of the cancer.

57. The method of any one of claims 51 to 56, wherein the supervised machine learning algorithm is a random forest analysis.

58. The method according to any one of claims 51 to 57, wherein classifying the cancer or predicting cancer progression comprises determining the DESNT status of the cancer.

59. A method according to any preceding claim, wherein the cancer is prostate cancer.

60. A method according to any preceding claim, wherein the sample is a urine sample, a semen sample, a prostatic exudate sample, or any sample containing macromolecules or cells originating in the prostate, a whole blood sample, a serum sample, saliva, or a biopsy.

61. The method of claim 60, wherein the sample is a prostate biopsy, prostatectomy or TURP sample.

62. A method according to any preceding claim, further comprising obtaining a sample from a patient.

63. A method according to any preceding claim, wherein the method is carried out on at least 2, at least 3, at least 3 or at least 5 samples.

64. A method according to claim 63, wherein the method is conducted on the multiple patient samples concurrently.

65. A method according to claim 63, wherein the method is conducting on the multiple patient samples simultaneously.

66. A method according to any preceding claim wherein the dataset or datasets comprise a plurality or tumour or patient expression profiles.

67. The method of claim 66, wherein the datasets each comprise at least 20, at least 50, at least 100, at least 200, at least 300, at least 400 or at least 500 patient or tumour expression profiles.

68. The method of claim 66 or claim 67, wherein the patient or tumour expression profiles comprise information on the expression status of at least 10, at least 40, at least 100, at least 500, at least 1000, at least 1500, at least 2000, at least 5000 or at least 10000 genes.

69. The method of claim 66 or 67, wherein the patient or tumour expression profiles comprise information on the levels of expression of at least 10, at least 40, at least 100, at least 500, at least 1000, at least 1500, at least 2000, at least 5000 or at least 10000 genes.

70. A method of treating cancer, comprising administering a treatment to a patient that has undergone a diagnosis according to the method of any one of claims 1 to 69.

71. The method of claim 70, comprising:

a. providing a patient sample;
b. predicting cancer progression according to method as defined in any one of claims 1 to 69; and
c. administering to the patient a treatment for cancer if cancer progression is predicted, detected or suspected according to the results of the prediction in step b).

72. A method of diagnosing cancer, comprising predicting cancer progression according to a method as defined in any one of claims 1 to 69.

73. A computer apparatus configured to perform a method according to any one of claims 1 to 72.

74. A computer readable medium programmed to perform a method according to any one of claims 1 to 72.

75. A biomarker panel, comprising at least 5, at least 10, at least 20, at least 30, at least or all 45 genes listed in Table 2.

76. The biomarker panel of claim 75, comprising at least 40 genes listed in Table 2.

77. The biomarker panel of claim 75, comprising all 45 genes listed in Table 2.

78. A biomarker panel, comprising at least 5, at least 10, at least 15 or all 20 genes listed in Table 3.

79. The biomarker panel of claim 78, comprising at least 15 genes listed in Table 3.

80. The biomarker panel of claim 78, comprising all 20 genes listed in Table 3.

81. A biomarker panel, comprising at least 10, or at least 15, at least 20, at least 50, at least 100, at least 200, at least 300, at least 400 or all 500 genes listed in Table 1.

82. The biomarker panel of claim 81, comprising at least 400 genes listed in Table 1.

83. The biomarker panel of claim 81, comprising all 500 genes listed in Table 1.

84. A biomarker panel, comprising at least 5, at least 10, at least 20, at least 30 or all 35 genes listed in Table 5.

85. The biomarker panel of claim 84, comprising at least 30 genes listed in Table 5.

86. The biomarker panel of claim 84, comprising all 37 genes listed in Table 5.

87. A biomarker panel prepared by a method according to any one of claims 1 to 69.

88. A biomarker panel according to any one of claims 75 to 87 for use in diagnosing cancer or for use in predicting cancer progression.

89. Use of a biomarker panel according to any one of claims 75 to 87 in a method of diagnosing or prognosing cancer, a method of predicting cancer progression, or a method of classifying cancer.

90. A method of diagnosing or prognosing cancer, or a method of predicting cancer progression, or a method of classifying cancer, comprising determining the level of expression or expression status of the genes in any one of biomarker panels 75 to 87.

91. The method of claim 90, further comprising comparing the level of expression or expression status of the measured biomarkers with one or more reference genes.

92. The method of claim 91, wherein the one or more reference genes is/are a housekeeping gene(s).

93. The method of claim 92, wherein the housekeeping genes is/are selected from the genes in Table 6 or Table 7.

94. The method of claim 93, wherein comparing the level of expression or expressions status of the measured biomarkers.

95. The method of claim 94, wherein the biomarker panel comprises at least at least 5, at least 10, at least 20, at least 30, at least 40 or all 45 genes listed in Table 2, or comprises least 5, at least 10, at least 20, at least 30 or all 35 genes listed in Table 5, and comparing the levels of expression or expression status with a reference comprises comparing with the level of expression or expression status of the same gene or genes in a sample from a healthy patient or a patient that does not have cancer that has or will progress.

96. The method of any one of claims 90 to 95, wherein the level of expression or expression status of the genes is done using a sample obtained from the patient.

97. The method of claim 90, wherein the method comprises conducting a statistical analysis according to a method as defined in any one of claims 1 to 69.

98. A kit comprising means for detecting the level of expression or expression status of at least 5 genes from a biomarker panel as defined in any one of claims 75 to 87.

99. The kit of claim 98, comprising means for detecting the level of expression or expression status of all the genes in a biomarker panel as defined in any one of claims 75 to 87.

100. The kit of claim 98 or claim 99, further comprising means for detecting the level of expression or expression status of one or more control or reference genes.

101. A kit of any one of claims 98 to 100, further comprising instructions for use.

102. A kit of any one of claims 98 to 101, further comprising a computer readable medium as defined in claim 74.

103. A biosensor configured to detect the level of expression or expressions status of at least 5 genes from a biomarker panel as defined in any one of claims 75 to 87.

104. The biosensor of claim 103, wherein the biosensor is configured to detect the level of expression or expression status of all the genes in a biomarker panel as defined in any one of claims 75 to 87.

105. The biosensor of claim 103 or 104, wherein the biosensor is further configured to detect the level of expression or expression status of one or more control or reference genes.

106. The biosensor of any one of claims 103 to 105, wherein the biosensor is a microarray.

107. The kit of any one of claims 98 to 102 comprising a biosensor as defined in any one of claims 103 to 106.

Patent History
Publication number: 20230349000
Type: Application
Filed: Jul 5, 2023
Publication Date: Nov 2, 2023
Inventors: Bogdan-Alexandru Luca (Norfolk), Vincent Moultion (Norfolk), Daniel Simon Brewer (Norfolk), Colin Stephen Cooper (Norfolk)
Application Number: 18/347,074
Classifications
International Classification: C12Q 1/6886 (20060101);