Query regarding TCGA samples

Question

[shivangi.agarwal800]

Hi

I want to look into the mutation profile of tumor samples obtained from TCGA. Looking deep into the sample barcodes, I found that the analyte codes of different samples are different, for e.g.

Here is three sample ids from same study, but there analyte is different.

TCGA-A7-A0DB-01A-11D-A272-09

TCGA-A7-A0DB-01A-11W-A019-09

TCGA-A2-A04Y-01A-21W-A050-09

One is from DNA (D) and other from Whole Genome Amplification (WGA) produced using Repli-G (Qiagen) DNA (W). So, if I want to look into their mutation profile, which one should I consider, D or W or both. Kindly suggest.

With regards

Shivangi

Answer 1

[Kevin Blighe]

The scientist in me would be curious enough to use all 3 and look to see what is different between each. From my experience in the wet-lab, whole genome amplification can introduce bias into a sample, relating wholly or in part to copy number variants. My preference, therefore, would be the un-amplified sample.

Kevin