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2 hours ago by

To my understanding, one needs the B-allele frequencies for allele-specific copy number. To get those, you usually use germline SNPs for the following reason:

"In this context, the b allele is the non-reference allele observed in a germline heterozygous SNP, i.e. in the normal/control sample. Since the tumor cells' DNA originally derived from normal cells' DNA, most of these SNPs will also be present in the tumor sample. But due to allele-specific copy number alterations, loss of heterozygosity or allelic imbalance, the allelic frequency of these SNPs may be different in the tumor, and that's evidence that one (or both) of the germline copies was gained or lost during tumor evolution."

However, is there anything wrong with using somatic SNVs as well? Somatic SNVs are confirmed heterozygous sites that should give the same insight into frequencies of the non-reference allele, right?

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