Abstract: Disclosed herein are methods of treating an individual having a cancer, of treating or identifying an individual having cancer for a treatment, or stratifying individuals having a cancer for a treatment based on a tumor mutational burden (TMB) score or a TMB score and a microsatellite instability assessment.

Abstract: Provided herein are ABL1 fusion nucleic acid molecules and polypeptides, methods related to detecting ABL1 fusion nucleic acid molecules and polypeptides in cancer, as well as methods of treatment and uses related thereto. Detection of an ABL1 fusion nucleic acid molecule or polypeptide can be used to identify individuals that may benefit from treatment with an anti-cancer therapy.

Abstract: Provided herein are anaplastic lymphoma kinase (ALK) fusion nucleic acid molecules and polypeptides, methods related to detecting ALK fusion nucleic acid molecules and polypeptides in cancer, as well as methods of treatment and uses related thereto. Detection of an ALK fusion nucleic acid molecule or polypeptide can be used to identify individuals that may benefit from treatment with an anti-cancer therapy.

Abstract: Novel mutant ESR1 molecules and uses are disclosed.

Abstract: Methods for predicting gene alteration states in tissue samples based on analysis of pathology images are described. The methods may comprise, e.g., receiving a plurality of image patches derived from at least one slide image, where each image patch is associated with a tissue phenotype classification label; identifying a set of tumor region image patches based on the tissue phenotype classification label for each image patch of the plurality; identifying buffer region image patches from the plurality of image patches based on the identified set of tumor region patches and a proximity relationship; inputting the tumor region and buffer region image patches into a gene alteration state classification model configured to predict a gene alteration state based on image features identified in the tumor region and buffer region image patches; and outputting a prediction of at least one gene alteration state for the tissue sample.

Abstract: Provided herein are methods related to treating or delaying progression of osteosarcoma in an individual. In some embodiments, the methods comprise detecting an FGFR1-MTSS1 or TACC1-FGFR1 gene fusion in one or more samples from an individual having a cancer; and administering to the individual an effective amount of a treatment that comprises an anti-cancer agent.

Abstract: Methods for predicting an origin of an alteration of a sample are described. The methods may comprise, for example, receiving, using one or more processors, sequence read data associated with the sample, selecting, using the one or more processors, a plurality of reads from the sequence read data based on the alteration, determining, using the one or more processors, at least one feature characterizing the selected plurality of reads, inputting, using the one or more processors, the at least one feature into a statistical model, generating, using the one or more processors, a score indicative of the origin of the alteration by the statistical model, and predicting, using the one or more processors, the origin of the alteration in the sample by comparing the score and one or more predefined thresholds.

Abstract: Provided herein are kinase fusion nucleic acid molecules and polypeptides, methods related to detecting kinase fusion nucleic acid molecules and polypeptides in cancer, as well as methods of treatment and uses related thereto. Detection of a kinase fusion nucleic acid molecule or the fusion polypeptide encoded by the fusion nucleic acid molecule can be used to identify individuals that may benefit from treatment with an anti-cancer therapy.

Abstract: Methods for detecting a deficient DNA repair mechanism and/or evaluating microsatellite instability in a sample from a subject are described. The disclosed methods comprise analyzing nucleic acid sequence data for a plurality of microsatellite loci to calculate a microsatellite instability (MSI) score for the sample from a ratio of the number of microsatellite loci that exhibit variant alleles to the total number of microsatellite loci that meet, e.g., a minimum sequencing coverage requirement. The MSI score is compared a first threshold and, m some cases, to a second threshold to assign a status of high microsatellite instability?(MSI-H), microsatellite stable (MSS), or equivocal microsatellite instability (MSI-E) for the sample.

Abstract: Methods and compositions for treating cholangiocarcinoma.

Abstract: Methods for selecting an anti-cancer therapy for or treating a subject having cancer with an anti-cancer therapy comprising determining risk scores that predict the likelihood of response to the treatment are described. The methods may comprise, for example, obtaining genomic data comprising aneuploidy status or loss of heterozygosity data for one or more subgenomic intervals in a sample from the subject; analyzing the genomic data for the subject using a model configured to receive genomic data comprising aneuploidy status or loss of heterozygosity data for the one or more identified subgenomic intervals in the subject and output a risk score for the subject, wherein the risk score predicts the subject's response to a selected treatment. Also described are biomarkers for specific diseases (e.g., metastatic pancreatic cancer) and methods for treating subjects having cancer based on the determined risk scores.

Abstract: Provided are systems and methods for capturing outcome information associated with various cancer treatments. The system facilitates capture and analysis of cancer treatment information and associated outcome information. The treatment and outcome information can include genomic analysis and information on treatment of different cancers. The system can store and analyze any one or more of: tumor type, genomic alterations (e.g., genes and associated alterations, gene sequence mutations, alterations, amplifications, deletions, etc.), and treatment data (including, for example, treatments targeted to specific genes and/or genomic alterations). Users of the outcome system can supply and use the treatment and outcome information to facilitate diagnosis and therapy decisions. User interfaces within the system can be configured to allow users to easily locate outcome information associated with particular treatments of tumors having certain genomic alterations.

Abstract: The present disclosure provides biomarkers associated with response to a treatment in individuals having prostate cancer, as well as to methods of diagnosis, assessment, and treatment of prostate cancer.

Abstract: A method implemented by one or more processors includes segmenting an image into a plurality of patches grouping the plurality of patches into at least one bag of patches, and inputting the at least one bag of patches into a machine-learning model trained to generate a prediction of an image class label based on the at least one bag of patches. The machine-learning model includes a first layer trained to generate one or more feature maps based on the at least one bag of patches, a second layer trained to normalize the one or more feature maps utilizing a set of batch normalization parameters determined from the at least one bag of patches to generate one or more normalized feature maps, and a third layer trained to generate the prediction of the image class label based at least in part on the one or more normalized feature maps.

Abstract: Disclosed herein are methods and systems for determining an origin of viral sequence reads detected in a sample (e.g., a liquid biopsy sample) from an individual. The sample may contain cfDNA fragments of varying fragment lengths. Embodiments of the present disclosure can receive sequence read data associated with the sample, which may be a liquid biopsy sample. The sequence read data can be used to determine if one or more viral sequence reads are detected in the sample. If the viral sequence reads are detected, the system can determine one or more fragmentomic features based on the sequence read data. The system can then generate an output indicative of the origin of the viral sequence reads by inputting the fragmentomic features into a statistical model including, for example, a trained machine-learning model. Based on the output, the system can then determine whether the viral sequence reads originate from a tumor.

Abstract: Methods for determining a variant frequency in a test sample from a subject, and methods for labeling sequencing reads as having or not having a variant are described herein. Exemplary methods include generating a reference match score and a variant match score by aligning sequencing reads to a corresponding variant sequence and a corresponding reference sequence, and labeling the sequencing read as having or not having the variant based on the determined match scores. Also described herein are methods monitoring disease progression and methods of treating a subject having a disease. Further described are devices and systems for implementing such methods.

Abstract: Provided herein are methods related to detecting loss of heterozygosity (LOH) of one or more human leukocyte antigen (HLA) genes and/or tumor mutational burden (TMB), as well as methods of treatment and uses related thereto. Detection of LOH of one or more HLA genes and/or TMB can be used to identify individuals that may benefit from treatment with an immune checkpoint inhibitor.

Abstract: Novel RET fusion molecules and uses are disclosed.

Abstract: The present disclosure provides methods of detecting analytes such as RNA and/or DNA, extracting analytes such as RNA and/or DNA, improving library construction for nucleic acid sequencing, and reducing the level of embedding agent in analyte samples such as RNA and/or DNA samples that are extracted from embedded samples such as paraffin-embedded samples.

Abstract: Provided herein are methods related to detecting genetic and epigenetic information in a single workflow, as well as methods of treatment, uses, systems, and computer readable storage media related thereto. These methods allow, e.g., for detection of genetic variants and epigenetic modifications (e.g., methylation level) in a single workflow and/or from a single sample (e.g., a DNA sample).