What are the terms for reference allele and alternate alleles in cancer?
2
0
Entering edit mode
9.0 years ago
MAPK ★ 2.1k

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?

cancer Sequencing • 11k views
ADD COMMENT
1
Entering edit mode
9.0 years ago
abascalfederico ★ 1.2k

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.

ADD COMMENT
0
Entering edit mode

Thanks!

ADD REPLY
1
Entering edit mode
9.0 years ago

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)

ADD COMMENT

Login before adding your answer.

Traffic: 814 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6