Allele specific expression analysis using human cell line

Question

[Susmita Mandal]

Hello everybody,

I am going to do allele specific expression analysis onto human genome. Previously I had done ASE on mouse genome successfully as the SNP data of the mouse strains were available and parental genomes were created using that. But in human's case that's not possible. So i'm not sure how to go about it. For the human cell line I have SNP0.6 Array CEL file and feature intensity info csv file as well as the RNA seq data of the human cell line. Does anyone has any idea how to do allele specific analysis for human genomes?

Thanks in advance Susmita

Answer 1

[nsmi8446]

You will need the parental genomes unfortunately. Without the parental genomes you will not be able to determine which allele comes from the mother and which allele comes from the father.

[Susmita Mandal]

What if I just need to know which genes are monoallelic and biallelic, then also?

[nsmi8446]

Yes, let's say the mother has the following genotype: T / T and the father has the same genotype: T / T. Their offspring will all have the genotype T / T. How would you be able to tell whether the T came from only the mother or only the father?

[Susmita Mandal]

Yes I agree. So let's say I have the SNP data of the human cell line that I'm working on. But I don't know the parental origins. Then?

[nsmi8446]

Then I don't think you can do it. In this scenario you have the following genotypes of the mother: ? / ? and father: ? / ?

You will have the genotype of your sample (let's say A / G) but you will not be able to figure out which allele came from which parent and if allele specific expression is present or absent.

[Susmita Mandal]

But I will know if it is monoallelic or biallelic right?

[nsmi8446]

You would know it's not monoallelic in the example above because the sample is heterozygous at this site. One allele would come from the mother (A) and the other allele (G) would come from the father. This site would be bi-allelic.

[Susmita Mandal]

So if i look at heterozygous sites only, I'll know if it's mono or bi.

[nsmi8446]

All heterozygous sites will be bi-allelic.

[a.zore2]

Hi, I have the child RNA seq data obtained from LCL. I have the genotype data of the mother and the father. Can you please tell me if there are any tools that I can use to determine the allele-specific mapping and also be able to avoid reference biases. Awaiting a reply. Thank You advance.

[Susmita Mandal]

Hi, You can use SNPsplit if you have the parental SNP data. Or you can make a vcf file containing positions that are heterozygous, i.e; one from paternal and another from maternal, and then using that vcf file, do variant calling with HaplotypeCaller of GATK. You can use VarScan2 also for that matter. Let me know if you need more help.

[a.zore2]

Thanks a lot. I'll try these suggestions.