Correcting variant allele fraction using tumor purity (experimentally measured)
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4 months ago
Luca Beltrame ▴ 220

I have a set of tumor samples with a known somatic mutation that is likely clonal (it is part of the etiology of this tumor type), with a given tumor fraction.

Recently, the clinical part of this project sent me the data on the approximate tumor purity of each sample, calculated by their anatomopathologists. So in this case I would like to do the opposite than what it is normally done: use the experimental purity measurement to correct or verify the variant allele fractions calculated by the variant caller, starting with the clonal mutation as a guide.

Has anyone ever done this?

variant calling sequencing cancer SNP next-gen • 184 views

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