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  • CNV from TCGA level 3

    Hi all!
    I am looking for CNV public profiles for the TCGA data to use as a reference.
    Do you know if there are TCGA level 3 copy number profiles that available for more than GBM, OV and LUSC?

    For example: BRCA, COAD, HNSC etc.

    i found here that only these are availble..
    The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that sequenced and molecularly characterized over 11,000 cases of primary cancer samples. Learn more about how the program transformed the cancer research community and beyond.


    Thanks,
    Pap

  • #2
    There are many snp6 copy number level 3 files for many TCGA diseases.

    Comment


    • #3
      Originally posted by Richard Finney View Post
      There are many snp6 copy number level 3 files for many TCGA diseases.
      Thanks! but i need the Copy number alterations for aggregated/segmented regions, per sample, and not the SNP data..

      Comment


      • #4
        Copy number can be guestimated from SNP6 data.

        See this post ...


        Example file from
        The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that sequenced and molecularly characterized over 11,000 cases of primary cancer samples. Learn more about how the program transformed the cancer research community and beyond.


        It looks like this ...
        Sample Chromosome Start End Num_Probes Segment_Mean
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 3218610 59982831 30896 0.005
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 59983689 59983731 2-1.8298
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 59987818 247813706 97244 4e-04
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 484222 85332445 48655 0.0055
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 85332460 85333406 2-1.9034
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 85333976 242476062 81598 0.0048
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 3 2212571 197538677 105526 3e-04
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 4 1053934 188762240 101844 6e-04
        AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 5 914233 41791600 24110 0.0018

        Comment


        • #5
          Hi! great! i think...

          What i understand from this format is that if the "Segment_Mean" negative, there is assuming for "loss", and if its possitive assuming for "gain".
          If i will (2^Segment_Mean)*2 i will get the actual CN.

          Am i right?

          BTW, what is the difference between the *hg19.seg.txt file and *nocnv_hg19.seg.txt file?
          i can see the "no" in the name, but both looks like CN files......

          Thanks!!

          Comment

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