From the dbGaP study description: "In this study, we performed paired tumor/normal long insert whole genome and exome sequencing and tumor RNA sequencing on primary or metastatic acral melanoma tumors collected from 34 patients. Patients were enrolled from either Vanderbilt University or the Memorial Sloan-Kettering Cancer Center. We report an integrated analysis of DNA and RNA sequencing data to...

In this study, six plasmacytoid bladder cancers were analyzed by whole exome sequencing. The results show loss of the CDH1 gene in every sample and correlate with E-cadherin loss of expression by immunohistochemistry. A separate validation cohort of plasmacytoid samples showed loss of E-cadherin expression by CDH1 mutation or promoter hypermethylation. The data includes information about the study,...

This dataset contains summary data visualizations and clinical data from a broad sampling of 1,661 samples of across multiple cancer types showing tumor mutational load and survival following immunotherapy from 1,661 patients. The data was gathered utilizing the MSK-IMPACT targeted sequencing test. The clinical data includes tumor type (based on the opensource OncoTree ontology developed at MSK),...

Summary from the GEO: "Gene expression analysis of primary mouse prostate organoid culture with overexpression of FOXA1 Examination by genotypes and days elapsed prepared in 3 replicates." The study associated with the dataset further explains FOXA1 and how it connects to the dataset: "Mutations in the transcription factor FOXA1 define a unique subset of prostate cancers but the functional consequences...

Summary from the GEO: "Mutations in the FOXA1 transcription factor define a unique subset of prostate cancers but the functional consequences of these mutations and whether they confer gain or loss of function is unknown. By annotating the FOXA1 mutation landscape from 3086 human prostate cancers, we define two hotspots in the forkhead domain: Wing2 (~50% of all mutations) and R219 (~5%), a highly...

Summary from the GEO: "Chromatin Landscape Analysis of primary mouse prostate organoid culture with overexpression of FOXA1. Examination by genotypes and days elapsed prepared in 3 replicates." This dataset depicts mutations in the FOXA1 gene, which define a unique subset of prostate cancers.

Summary from the GEO: "Clinicopathologic features and biochemical recurrence are sensitive, but not specific, predictors of metastatic disease and lethal prostate cancer. We hypothesize that a genomic expression signature detected in the primary tumor represents true biological potential of aggressive disease and provides improved prediction of early prostate cancer metastasis. Methods: A nested...

GEO SuperSeries of expression profiling of prostatic neoplasms. This SuperSeries is composed of the SubSeries GSE21034, GSE21035, and GSM525577. Each one concerns measuring prostate cancer genomes and different arrays of expression data, including DNA copy number, mRNA and microRNA. The prostate tumor samples originated from 218 patients. Each dataset in the SubSeries share the same description:...

Summary from the GEO: "ERG overexpression is the most frequent molecular alteration in prostate cancer. We analyzed different stages of prostate cancer to identify genes that were coexpressed with ERG overexpression. In primary prostate tumors, it was shown that TDRD1 expression was the strongest correlated gene with ERG overexpression and we suggest TDRD1 as a direct ERG target gene. 48 Prostate...

Summary from GEO: "Recurrent mutations in the spliceosome are observed in several human cancers but their functional and therapeutic significance remain elusive. SF3B1, the most frequently mutated component of the spliceosome in cancer, is involved in the recognition of the branch point sequence (BPS) during selection of the 3’ splice site (ss) in RNA splicing. Here, we report that common and tumor-specific...