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
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shivangi.agarwal800
1 answer
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
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