Hi, I'm a beginner in analyzing NGS data. This is my first time reading a paper. However I'm confused about the concept "Allelic ratio"
My question is: why the y-values (Allelic ratio) in the figure below are all between 0.2 and 0.8. Can "Allelic ratio" equal 1 in normal cells?
Figure legend: "Allelic ratio data of heterozygous loci in the normal genome are centered around 0.5, which represents the presence of two alleles". It's figure 1a in this paper.
Here is how I think about "Allelic ratio":
So, I think the ratio should be about 1 for a SNP genotype AA; 0.5 for AB; 0 for BB. But few points in this figure have a ratio more than 0.8 or less than 0.2, I'm confused about it.
Thank you for your help.
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written
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Cheng Guo •
heterozygous loci in the normal genome
So, they are only reporting those loci that are heterozygous in the normal. If it had 5/0 alleles, then it would not qualify as heterozygous.
For the SAME loci, they report also ratio for the tumour, and that goes between 0 and 1 as there could be some Loss of Heterozygosity (LOH)
Thanks for your answer. How did they know that loci is "heterozygous"? I mean did they get it from a database or simply filtering locis with allelic ratio in 0.2-0.8?
It depends. Different algorithms use different aproaches. The paper is about LOH and monoallelic expression, so they only care about those loci where the normal is heterozygous. There should be roughly as many (I think) where it is homozygous for non reference. But those are not informative forl LOH.
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