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2015 Breast Cancer Challenge

    Table of contents
    1. 1. Progress
    2. 2. Tasks
    3. 3. Data

    For details see https://www.synapse.org

    Progress

    • Requested access to all data sets - gribskov 20 Jul 2015
    • Requests approved by Purdue and forwarded to DACs - gribskov 28 July 2015
    • CGEMS data approved - gribskov 28 July 2015

    Tasks

    • Need to get annotation for HumanHap550v1.1 chip, i.e., what is the chromosome location and gene location of each gene?
    • reference genome 36.3 for humanhap550v1.1

    Data

    • CGEMS - /depot/mgribsko/data/challenge/CGEMS_breast_cancer
      make sure you have read the data use agreement
      • example of genotype data
        tar files have names like 
        phg000032.v1.CGEMS_BreastCancer.genotype-calls-indfmt.HumanHap550v1.c1.GRU.set1.tar.gz,
        I extracted one individual to .../Genotypefiles/set1/CGEMS_BreastCancer.CG-B01-04463.CS-B01-00529.ind
      • example of marker information, see
        .../GenotypeFiles/phg000032.CGEM.illumina_550k.v1.marker-info.txt 
      • example of phenotype data, see for example .../PhenotypeFiles/phs000147.v3.pht000663.v3.p1.c1.CGEMS_Breast_Cancer_Subject_Phenotypes.GRU.txt
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    Files 4

    FileSizeDateAttached by 
     CGEMS_data_use_agreement.pdf
    PLEASE READ - data use agreement
    130.63 kB08:24, 30 Jul 2015gribskovActions
     CGEMS_individual_genotype.sample.txt
    example of individual genotype
    2.5 kB08:47, 30 Jul 2015gribskovActions
     CGEMS_marker_info.sample.txt
    example of marker information
    6.64 kB08:47, 30 Jul 2015gribskovActions
     CGEMS_subject_phenotype_example.txt
    example of subject phenotype
    2.28 kB08:47, 30 Jul 2015gribskovActions
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