Abstract: There is provided a method of profiling a tumour, the method comprising determining a relative proportion for each of 96 mutation types, wherein the 96 mutation types are defined as the six possible sequence changes C>A, C>G, C>T, T>A, T>C, or T>G in the context of each of four possible nucleotides (A, C, G, or T) at the position immediately 5? to the mutation and each of four possible nucleotides at the position immediately 3? to the mutation; assigning the tumour, using the determined relative proportion for each of the 96 mutation types, to at least one of eight clusters defined herein; and determining at least one tumour characteristic based on the assignment to a cluster.

Abstract: Biomarkers and methods for identifying circulating serum-based cfDNA sequences. The cfDNA sequences (PDcRAs) can be used to differentiate patient's suffering from Parkinson's disease (PD) from non-PD patients.

Abstract: Splice variants associated with neomorphic SF3B1 mutations are described herein. This application also relates to methods of detecting the described splice variants, and uses for diagnosing cancer, evaluating modulators of SF3B1, and methods of treating cancer associated with mutations in SF3B1.

Abstract: A double-stranded DNA biomarker derived from exosomes is useful in early diagnosis and preoperative evaluation of pheochromocytoma and paraganglioma, and applications thereof. The biomarker is genome double-stranded DNA fragment specifically derived from exosomes in blood serum of pheochromocytoma and paraganglioma patients. The double-stranded DNA can represent variations of RET, VHL, and HIF2A with high frequency of somatic cell mutation, and metastatic phenotype-related SDHB, which are susceptibility genes of PCCs and PGLs. The circulating exosome DNA in patient's peripheral blood contains 97% of the same chromosomal point mutation information as the tumor cells from which the DNA originated. There is evidence of the existence of double-stranded DNA in the serum exosomes of PCCs and PGLs. The double-stranded DNA can be used to identify mutations in tumor cells and provide a noninvasive molecular marker for the clinical diagnosis and preoperative evaluation of PCCs and PGLs.

Abstract: Dysregulated expression of microRNAs (miRNAs) has emerged as a hallmark feature in human cancers. Aspects of the disclosure relate to methods for selecting optimal therapy for a patient from several alternative treatment options. A major clinical challenge in cancer treatment is to identify the subset of patients who will benefit from a therapeutic regimen, both in metastatic and adjuvant settings. The number of anti-cancer drugs and multi-drug combinations has increased substantially in the past decade, however, treatments continue to be applied empirically using a trial-and-error approach. Here methods and compositions are provided to determine the optimal treatment option for gastric cancer patients.

Abstract: A process for analysing chromosome regions and interactions relating to breast cancer.

Abstract: The invention generally relates to methods and compositions for the prediction of therapeutic efficacy of cancer treatments and the prognosis of cancer. The invention discloses markers that are associated with favorable and unfavorable outcomes, respectively, in certain cancer treatments and are useful as prognostic markers for cancer. Methods involving these markers are disclosed for predicting cancer therapy benefit and prognosing clinical outcome for cancer patients.

Abstract: The invention features methods of identifying patients as being likely to respond to anti-VEGF therapy. Furthermore, in those patients identified as failing to include one or more of the above ophthalmic response markers, the invention features treatment with an EPO antagonist (e.g., alone, or in combination with a VEGF antagonist).

Abstract: This disclosure provides new genetic targets, diagnostic methods, and therapeutic treatment regimens for multiple autoimmune disorders, including pediatric autoimmune disorders that are co-inherited and genetically shared. The disclosure, for example, provides methods of diagnosing or determining a susceptibility for one or more autoimmune diseases and methods of determining treatment protocols for patients with one or more autoimmune diseases based on determining if the patients have genetic alterations in particular genes.

Abstract: A method of diagnosing prostatic diseases such as prostate cancer, prostatic hyperplasia, and the like through bacterial metagenomic analysis, and more particularly, to a method of diagnosing prostate cancer or prostatic hyperplasia by analyzing an increase or decrease in content of extracellular vesicles derived from specific bacteria through bacterial metagenomic analysis using a subject-derived sample. An extracellular vesicle secreted from a bacterium present in the environment can be absorbed into the body and directly affect the occurrence of inflammation and cancer, and prostatic diseases such as prostate cancer, prostatic hyperplasia, and the like is difficult to diagnose early on before any symptom appears, which makes efficient treatment difficult.

Abstract: The disclosure provides methods of identifying a human subject as a candidate for treating or inhibiting a liver disease by inhibiting HSD17B13. The disclosure also provides methods of treating a subject who is PNPLA3 Ile148Met+ by administering an inhibitor of HSD17B13. The disclosure also provides method of detecting a PNPLA3 Ile148Met variant and functional HSD17B13 in a subject. The disclosure also provides method of identifying a subject having a protective effect against liver disease. The disclosure also provides inhibitors of HSD17B13 for use in the treatment of a liver disease.

Abstract: The present invention relates to gene expression profiles for B-cell lymphoma. More specifically, the present invention relates to gene expression profiles for diagnosis, prognosis or therapy selection for an aggressive B-cell lymphoma.

Abstract: The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital analysis is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.

Abstract: The invention relates to methods for predicting the response of a patient with a malignant disease to immunotherapy with a pharmaceutical compound that is designed to inhibit an immunoregulatory effect of an immune checkpoint selected from cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and its ligands Cluster of differentiation 80 (CD80) and Cluster of Differentiation 86 (CD86). The methods are based on a DNA methylation analysis of the CTLA4 gene of cells of the malignant disease and/or T lymphocytes interacting with said cells of the malignant disease.

Abstract: The present description provides a cancer assay panel for targeted detection of cancer-specific methylation patterns. Further provided herein are methods of designing, making, and using the cancer assay panel for the diagnosis of cancer.

Abstract: The present invention is directed to an in vitro method of detecting cell free nucleic acids, preferably cell free DNA (cfDNA) in a body fluid sample from an individual or a patient, wherein the method comprises the step of accurately and sensitively determining the concentration of cell free nucleic acid in the sample and/or determining the concentration or amount of said cell free nucleic acid of a size range and/or the index of integrity or size fraction ratio (SFR) of said cell free nucleic acid and/or the determination of the presence of genetic polymorphisms (such as known Single Nucleotide Polymorphisms (SNPs) or mutations). The invention encompasses also a method to discriminate body fluid individuals where cfDNA are highly released by comparing the size profile obtained for at least one of three size ranges of cfDNA.

Abstract: A method for determining a hyperexcitability in a subject comprising detecting a repeat expansion of TTTCA, TTTTA, or a complementary sequence thereof in a nucleic acid sample from the subject.

Abstract: The present disclosure relates to a method for diagnosing Parkinson's disease in which the method includes measuring the expression level of Parkinson's disease-related genes from a subject's nasal mucus sample, a composition for diagnosing Parkinson's disease, and a kit including the same.

Abstract: Disclosed herein is a kit for diagnosing spinal muscular atrophy (SMA) in a human subject based on the copy numbers of exons 7 and 8 of SMN1 gene and the copy numbers of exons 7 and 8 of SMN2 gene in a DNA sample isolated from the human subject. Also disclosed herein are methods of diagnosing SMA by use of the present kit, and methods of treating SMA based on the diagnostic result.

Abstract: Disclosed herein are methods of detecting an altered gene expression levels in a subject suspected of having atopic dermatitis. Further described herein are methods of treating atopic dermatitis in a subject having an exhibiting an altered gene expression level.