Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants?

For instance, rs4349859 is a known HLAB27 SNP.

If I can find rs4349859 in the patient's VCF file, could I say he is HLAB27+ ?

  • 1
    $\begingroup$ What do you mean "test" it? VCF files normally don't have nucleotide sequences (well, they have the variant, but that isn't what you normally need). If you want to check whether a patient has the antigen, you should probably be looking at protein data, not DNA. Please edit your question and clarify what you are trying to do. $\endgroup$
    – terdon
    Dec 12, 2017 at 11:46

1 Answer 1


Some papers claim that you can do HLA typing from exome sequencing data. I have not validated this myself. I also guess it depends on capture. Nonetheless, I don't think you can type HLA with VCF generated with a standard pipeline, which is not specifically designed for HLA. Current variant callers won't work on HLA genes due to their high diversity. Also in general, there are thousands of HLA-B alleles. In most cases, you can't find the allele by looking at only one SNP.

No, you can't check if the patient has HLA-B27 only from VCF. There might be a hope if you get raw reads and run a proper HLA typing tool designed for such data.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.