Abstract: Methods and compositions are provided for determining a subtype of Muscle Invasive Bladder Cancer (MIBC) in an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for MIBC. Also provided herein are methods and compositions for determining the response of an individual with a MIBC subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of lung adenocarcinoma (AD) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung adenocarcinoma. Also provided herein are methods and compositions for determining the response of an individual with an adenocarcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of lung squamous cell carcinoma (SQ) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung squamous cell carcinoma. Also provided herein are methods and compositions for determining the response of an individual with a squamous cell carcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of head and neck squamous cell carcinoma (HNSCC) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for HNSCC. Also provided herein are methods and compositions for determining the response of an individual with a HNSCC subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a pan-cancer clustering of cluster assignment (COCA) subtype of a cancer in an individual by detecting the expression level of at least one classifier biomarker selected from a group of classifier biomarkers for COCA subtypes. Also provided herein are methods and compositions for determining the response of an individual with a COCA subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining whether an adenocarcinoma or squamous cell carcinoma patient is likely to respond to PARP inhibitor treatment. Specifically, a method of assessing whether a patient's adenocarcinoma (AD) lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) or a patient's squamous cell carcinoma (SQ) is primitive, classical, secretory or basal is provided herein. The method entails detecting the levels of classifier biomarkers at the nucleic acid level, in an AD or SQ lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the AD lung cancer sample is classified as a TRU, PI, or PP AD sample or the SQ lung cancer sample is classified as primitive, classical, secretory or basal and a determination of whether the patient is likely to respond to PARP inhibitor treatment can be made.

Abstract: Methods and compositions are provided for determining a pan-cancer clustering of cluster assignment (COCA) subtype of a cancer in an individual by detecting the expression level of at least one classifier biomarker selected from a group of classifier biomarkers for COCA subtypes. Also provided herein are methods and compositions for determining the response of an individual with a COCA subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for the molecular subtyping of lung cancer samples. Specifically, a method of assessing whether a patient's adenocarcinoma lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) is provided herein. The method entails detecting the levels of the classifier biomarkers of Table 1-Table 6 or a subset thereof at the nucleic acid level, in a lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the lung cancer sample is classified as a TRU, PI, or PP sample.

Abstract: Methods and compositions are provided for the molecular subtyping of lung cancer samples. Specifically, a method of assessing whether a patient's adenocarcinoma lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) is provided herein. The method entails detecting the levels of the classifier biomarkers of Table 1-Table 6 or a subset thereof at the nucleic acid level, in a lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the lung cancer sample is classified as a TRU, PI, or PP sample.

Abstract: Methods and compositions are provided for determining TMB in a tumor sample using transcriptome profiling data. Also provided herein are methods and compositions for determining the response of an individual with a specific TMB to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a pan-cancer clustering of cluster assignment (COCA) subtype of a cancer in an individual by detecting the expression level of at least one classifier biomarker selected from a group of classifier biomarkers for COCA subtypes. Also provided herein are methods and compositions for determining the response of an individual with a COCA subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of lung squamous cell carcinoma (SQ) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung squamous cell carcinoma. Also provided herein are methods and compositions for determining the response of an individual with a squamous cell carcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of lung adenocarcinoma (AD) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung adenocarcinoma. Also provided herein are methods and compositions for determining the response of an individual with an adenocarcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of lung squamous cell carcinoma (SQ) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung squamous cell carcinoma. Also provided herein are methods and compositions for determining the response of an individual with a squamous cell carcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for the molecular subtyping of lung cancer samples. Specifically, a method of assessing whether a patient's adenocarcinoma lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) is provided herein. The method entails detecting the levels of the classifier biomarkers of Table 1-Table 6 or a subset thereof at the nucleic acid level, in a lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the lung cancer sample is classified as a TRU, PI, or PP sample.

Abstract: Methods are provided for determining a subtype of head and neck squamous cell carcinoma (HNSCC) of an individual by detecting the expression level of at least one subtype classifier selected from a group of genes that are relevant for determining HNSCC subtypes. Also provided herein are methods for determining a suitable treatment and predicting the overall survival and the likelihood of metastasis for the HNSCC patients according to their subtypes.

Abstract: Methods and compositions are provided for determining a subtype of lung adenocarcinoma (AD) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung adenocarcinoma. Also provided herein are methods and compositions for determining the response of an individual with an adenocarcinoma subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining a subtype of Muscle Invasive Bladder Cancer (MIBC) in an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for MIBC. Also provided herein are methods and compositions for determining the response of an individual with a MIBC subtype to a therapy such as immunotherapy.

Abstract: Methods and compositions are provided for determining whether an adenocarcinoma or squamous cell carcinoma patient is likely to respond to PARP inhibitor treatment. Specifically, a method of assessing whether a patient's adenocarcinoma (AD) lung cancer subtype is terminal respiratory unit (TRU), proximal inflammatory (PI), or proximal proliferative (PP) or a patient's squamous cell carcinoma (SQ) is primitive, classical, secretory or basal is provided herein. The method entails detecting the levels of classifier biomarkers at the nucleic acid level, in an AD or SQ lung cancer sample obtained from the patient. Based in part on the levels of the classifier biomarkers, the AD lung cancer sample is classified as a TRU, PI, or PP AD sample or the SQ lung cancer sample is classified as primitive, classical, secretory or basal and a determination of whether the patient is likely to respond to PARP inhibitor treatment can be made.

Abstract: Methods and compositions are provided for determining a subtype of head and neck squamous cell carcinoma (HNSCC) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for HNSCC. Also provided herein are methods and compositions for determining the response of an individual with a HNSCC subtype to a therapy such as immunotherapy.