I am not sure if we can consider cancer genotypes with reference allele and alternate allele to be technically correct. I also read somewhere that since there is no defined ploidy in cancer genomes and considering variantions in the major read counts and minor read counts also due to anueploidy and CNVs, we can't say there is actual reference allele and alternate allele. I am a bit confused with this. Could someone please clarify?
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written
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MAPK
2 answers
It doesn't matter what the ploidy is. You can have one, two or more alleles for a given gene. If the allele is identical to the reference one, that's the reference allele; if not, the alternate. In cancer, however, it may be more interesting to report whether alleles are somatic mutations or not compared to the individual's genotype, and not compared to the human genome reference.
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abascalfederico
To add to the other answer, generally, you're only reporting somatic mutations in cancer, so you'll talk about the 'variant allele', which may or not have a variant allele frequency near 50% (depending on ploidy, CN, etc)
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