<p>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.</p>

<p>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.</p>

CC BY-SA 3.0
2017-12-12T15:17:48.430Z
2017-12-12T15:17:48.430Z
user172818
<p>Is it possible to check if patient has the HLAB27 antigen by comparing his exome stored in VCF with all known HLAB27 variants?</p>

<p>For instance, rs4349859 is a <a href="http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=6:31397510-31398510;source=dbSNP;v=rs4349859;vdb=variation;vf=2732890" rel="nofollow noreferrer">known</a> HLAB27 SNP.</p>

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

CC BY-SA 3.0
2017-12-12T11:46:52.753Z
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.
terdon
<vcf><exome>
Is it possible to check if a patient has the HLA-B27 antigen from his exome stored in a VCF file
# Is it possible to check if a patient has the HLA-B27 antigen from his exome stored in a VCF file

(Asked by: username_0 on 2017-12-12)

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](http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=6:31397510-31398510;source=dbSNP;v=rs4349859;vdb=variation;vf=2732890) HLAB27 SNP.

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

**Tags:** vcf, exome
> **Comments:**
> **username_1**: 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.  

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## 1 answers

### Answer by username_2 on 2017-12-12. Score: 2 | Accepted answer

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.


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