Question: What are the terms for reference allele and alternate alleles in cancer?
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gravatar for MAPK
3.4 years ago by
MAPK1.4k
United States
MAPK1.4k wrote:

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 • 3.7k views
ADD COMMENTlink modified 3.4 years ago by Chris Miller20k • written 3.4 years ago by MAPK1.4k
1
gravatar for abascalfederico
3.4 years ago by
abascalfederico1.1k
Spain
abascalfederico1.1k wrote:

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 COMMENTlink written 3.4 years ago by abascalfederico1.1k

Thanks!

 

ADD REPLYlink written 3.4 years ago by MAPK1.4k
1
gravatar for Chris Miller
3.4 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

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 COMMENTlink written 3.4 years ago by Chris Miller20k
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