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How can I conduct a secondary analysis of HLA gene genomic variation across different geographic and ethnic populations, such as American, European, South Asian, and Mongolian populations?

I want to investigate the genomic variation of HLA gene across the different population of different regions in the world.

data genomic analysis
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updated by dthorbur dthorbur • written by backupdata • backupdata

Should be straightforward. You can either use REST API from ENSEMBL to request the diversity within each genomic region for a given population. Or, you can download the vcf file from 1000 genomes and do it yourself locally.

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written by manaswwm manaswwm

I agree with the other commenter that there is a lot of good public data out there that shouldn't be too hard to get with a little know how. That said, HLA is a notoriously difficult region to accurately genotype due to the extremely high sequence and copy number polymorphism. If you are looking for genotypes rather than raw variation, you'll likely need to be very cautious with what data you accept.

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written by dthorbur dthorbur

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