TCGA sample identifiers in BRCA copy number data? TCGA-G9-6371-01A-11D-1784-02_BC1NP2ACXX---TCGA-G9-6371-10A-01D-1784-02_BC1NP2ACXX---Segment.tsv

Question

[jamesdalg]

I'm trying to derive the exact sample IDs from BRCA copy number data and match them up with the supplementary tables provided by the author. Does anyone know the exact format of the copy number data filename and it's meaning? https://portal.gdc.cancer.gov/legacy-archive/files/eae79eca-4b64-45df-9ce9-e1e074ec3080

The supplementary table I'm looking at is table 1, found here: https://www.nature.com/articles/nature11412#supplementary-information Within this file are several lines that give a "Complete TCGA ID" with some information that I'm interested in about the sample, including ER, PR, and HER status(e.g. "TCGA-A2-A0T2").

Answer 1

[jamesdalg]

I've found the answer: TCGA-G9-6371 is the sample identifier for this particular one. Every sample listed in the GDC archive matches a line in supplemental table 1 if one simply takes the first six alphanumeric characters after TCGA.