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Results Found: 17
  • Comprehensive Genomic Characterization of Acral Melanoma

    Authors
    Sosman, Jeffrey
    Trent, Jeffrey
    Ariyan, Charlotte Eielson
    Liang, Winnie S.
    Description

    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...

    Subject
    Chromosome Aberrations
    Melanoma/genetics
    Melanoma/pathology
    Mutation
    Transcriptome
    Access Rights
    Application Required
  • Whole Exome Sequencing of Six Signet Ring/Plasmacytoid Variant Bladder Tumors

    Authors
    Solit, David
    Description

    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,...

    Subject
    DNA Mutational Analysis
    Mutation
    Plasmacytoma/genetics
    Urinary Bladder Neoplasms
    Access Rights
    Application Required
  • TMB and Immunotherapy (MSKCC, Nat Genet 2019): Genomic and survival data from 1661 tumor-normal pairs from 1661 patients with various cancer types sequenced with the MSK-IMPACT assay.

    Description

    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),...

    Subject
    DNA Mutational Analysis
    Immunotherapy
    Mutation
    Tumor Burden
    Access Rights
    Free to All
  • Gene expression analysis of primary mouse prostate organoid culture with overexpression of FOXA1

    Authors
    Adams, Elizabeth
    Sawyers, Charles L.
    Leslie, Christina
    Description

    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...

    Subject
    Chromatin
    Mutation
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Genomic analyses of primary mouse prostate organoid culture with overexpression of FOXA1

    Authors
    Adams, Elizabeth
    Sawyers, Charles L.
    Leslie, Christina
    Description

    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...

    Subject
    Chromatin
    Mutation
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Chromatin Landscape Analysis of primary mouse prostate organoid culture with overexpression of FOXA1

    Authors
    Adams, Elizabeth
    Sawyers, Charles L.
    Leslie, Christina
    Description

    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.

    Subject
    Chromatin
    Mutation
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy

    Authors
    Erho, Nicholas
    Crisan, Anamaria
    Vergara, Ismael A.
    Mitra, Anirban P.
    15 more author(s)...
    Description

    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...

    Subject
    Mutation
    Prostatectomy
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Integrative genomic profiling of human prostate cancer

    Authors
    Taylor, Barry Stephen
    Schultz, Nikolaus D.
    Hieronymus, Haley
    Sawyers, Charles L.
    Description

    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:...

    Subject
    Mutation
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Co-expression of genes with ERG in prostate cancers

    Authors
    Boormans, Joost L.
    Trapman , Jan
    Jenster, Guido
    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...

    Subject
    Mutation
    Prostatectomy
    Prostatic Neoplasms
    Transcriptional Regulator ERG
    Access Rights
    Free to All
  • Cancer associated SF3B1 hotspot mutations induce cryptic 3' splice site selection through use of a different branch point

    Authors
    Seiler, Michael
    Buonamici, Silvia
    Description

    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...

    Subject
    Mutation
    Nonsense Mediated mRNA Decay
    RNA Splicing
    Spliceosomes
    Access Rights
    Free to All