Question: (Closed) What'S "Allelic Ratio"? Can It Equal 1 In Normal Cells?
3
gravatar for Cheng Guo
8.0 years ago by
Cheng Guo30
China
Cheng Guo30 wrote:

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 1a, apollo
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":
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.

next-gen • 6.1k views
ADD COMMENTlink modified 8.0 years ago by Stefano Berri4.1k • written 8.0 years ago by Cheng Guo30
6
gravatar for Stefano Berri
8.0 years ago by
Stefano Berri4.1k
Cambridge, UK
Stefano Berri4.1k wrote:

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)

ADD COMMENTlink written 8.0 years ago by Stefano Berri4.1k

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?

ADD REPLYlink written 8.0 years ago by Cheng Guo30
4

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.

ADD REPLYlink written 8.0 years ago by Stefano Berri4.1k
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