Why there are 4 files for copy number variation (CNV) in TCGA database
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4.0 years ago
akij ▴ 100

In TCGA there are 4 files related to each case, for example this one

https://portal.gdc.cancer.gov/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.case_id%22,%22value%22:%5B%22001ad307-4ad3-4f1d-b2fc-efc032871c7e%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:%5B%22Copy%20Number%20Variation%22%5D%7D%7D%5D%7D&facetTab=cases

I don't completely understand why 4 files. Or I don't know how to interpret properly. Both tumor and normal sample has 2 files(grch38.seg.txt and nocnv.grch38.seg.txt). I understand that grch38.seg contain normally occurring CNVs and nocnv.grch38.seg contains tumor specific changes(CNA). What I don't understand is that why do we have 2 files for normal sample? Why normal samples have CNA?

CNV sequencing TCGA • 1.5k views
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Look at the file names,

ASPER_p_TCGA_b_306_308_146_NSP_GenomeWideSNP_6_C06_1365494.grch38.seg.txt ASPER_p_TCGA_b_306_308_146_NSP_GenomeWideSNP_6_C06_1365494.nocnv_grch38.seg.txt ASPER_p_TCGA_b_306_308_146_NSP_GenomeWideSNP_6_C07_1365544.grch38.seg.txt ASPER_p_TCGA_b_306_308_146_NSP_GenomeWideSNP_6_C07_1365544.nocnv_grch38.seg.txt

You can see two _C06_, two _C07_. I guess the data analysed from two different center. In either C06 or C07, it has two files, one file named with nocnv and the other without. In this condition, let's say one sample only has one CNV file.

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