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HLA typing analysis with plink or any other method?

Hi, I have a set of HLA variants from a case control study annotated in tabulated files. I thought of analyzing them with plink and after a hard work, I tried to convert my raw data to plink supporting file formats. (.lgen,.map and .fam). Thought everything went smooth, but when I tried to run my data with plink I get,

ERROR: Locus rs1050517 has >2 alleles:
       individual 1060 106 has genotype [ G C ]
       but we've already seen [ G ] and [ A ]

Since HLA variants contains multiple alleles, this phenomena is possible but I didn't know plink only accepts SNPs if and only if they have two alleles. Am I missing something here? Or could you specify me a better tool to do some HLA variant analysis.

Thanks a lot in advance.

hla plink
• 4,965 views • link
updated by Ram Ram • written by nilakshafreezon nilakshafreezon

Have you had a look at SNP2HLA?

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updated by Ram Ram • written by krobasky • krobasky

Seems interesting. I will take a closer look. But not sure whether It can be used in the analysis except for missing allele imputation. Thanks :)

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updated by Ram Ram • written by nilakshafreezon nilakshafreezon

1 answer

Standard genetic association tools aren't well suited for HLA. I would use R to do a statistical test to check if any allele was present in an excess of cases or controls (I would do this at varying levels of resolution). You would have to do some research on the appropriate tests to use. AFIAK there are no existing tools for HLA association tests.

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written by Katie D'Aco Katie D'Aco

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