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PoisonAlien / TCGAmutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
MIT License
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Request for additional metadata: Capture Kit #16

Open selkamand opened 10 months ago

selkamand commented 10 months ago

Hi,

Just wondering about feasibility of adding additional sample metadata, for example which capture kit was used?

Reason we care about capture kit:

Capture kit biases have led to false negative mutation calls in multiple TCGA cohorts. Variability in the capture kits used can contribute to inter-cohort TMB variation. More importantly, there are some genes that may be mutated in a sample, but whose mutation you will/won't see because of the specific capture kit that was used. See Wang et al. 2018 for details

PoisonAlien commented 10 months ago

Hi,

This information for early tcga studies is hard to obtain. This is also why one should use MC3 mafs which have been harmonized for such biases. This point is also mentioned in the discussions section of the MC3 paper