Question: HLA analysis using SNP2HLA
gravatar for bioinf
2.2 years ago by
bioinf20 wrote:


I have run snp2hla in my dataset and got the imputed results. But I am unable to interpret it. The softwares website also does not have sufficient information. Could anyone help me on this. Thanks in advance.

next-gen • 736 views
ADD COMMENTlink modified 14 months ago by Charles Warden7.6k • written 2.2 years ago by bioinf20

You should show your output to get help :)

ADD REPLYlink written 2.2 years ago by Titus910
gravatar for jyoti.khadake
14 months ago by
jyoti.khadake20 wrote:

The output has P or A against the haplotype which indicates either presence or absence of haplotype

ADD COMMENTlink written 14 months ago by jyoti.khadake20
gravatar for Charles Warden
14 months ago by
Charles Warden7.6k
Duarte, CA
Charles Warden7.6k wrote:

I would have to couple check the output files on my home computer, but I think there should be a way to define your top 2 haplotypes.

For example, I have these comparisons with different HLA programs for my own genome data (underneath the huge "23andMe versus Genes for Good" Venn Diagram):

For example, concordance was generally better for my HLA-A, HLA-B, HLA-C genes.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Charles Warden7.6k

Hi Charles, Soumya mentioned in his Nature Genetics paper 2012. 2767 SNPs were selected to tag the entire MHC. Where I can find the list for these 2767 SNPs. Thanks.

ADD REPLYlink written 13 months ago by Shicheng Guo8.1k

That is a good question - I am not entirely sure (which sites are most informative for the SNP chip imputation, or which ones are used in that paper).

With the NGS data, you'd probably want a specific HLA reference with the HLA haplotypes (rather than a more typical genome alignment).

If you look up HLA-A on the UCSC Genome Browser, you get a lot of alternative chromosome coordinates. I don't remember seeing those as often on SNP chip data, but perhaps you could look in the range of variants for the overall HLA region on chr6?

I'll double-check where I see a dip in my Veritas WGS data when I get home (since I believe they provided a filtered bam per chromosome, instead of raw .fastq files). So, perhaps this can be revised, but maybe sites within chr6:32,390,512-33,117,623 (on hg19) could be of interest?

Update: My Veritas WGS data has a dip from chr6:28,478,344-33,451,189 (for reads that weren't aligned to the canonical chromosomes, and not having unaligned reads to test for re-alignment). That is a larger region than I originally guessed. I suspect there are also regions mapped to other areas (possibly with homology to the alternate HLA chromosomes), but this was the most clear to me.

ADD REPLYlink modified 13 months ago • written 13 months ago by Charles Warden7.6k
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