Authors: Tünde Vágó, Péter Tóth, Tim Hague, Szilveszter Juhos

Introduction:
The 1000 Genomes Project (1KG) was the first large-scale sequencing project to obtain comparable whole genome sequences from diverse human populations. Previously we validated our HLA typing method using these datasets for Class-II and Class-II HLA genes for 3 fields accuracy. Furthermore, using family trio data it was concluded that our genotyping method can be used for genes other than HLA-A,B,C and HLA-DRB1,-DQB1. In this study we are presenting genotyping results obtained from 1KG dataset with different ethnical background considering most of the reference genes present in the IMGT/HLA database.

Methods And Materials:
Whole-exome FASTQ files from the 1KG data repository were pre-filtered for HLA typing; the filter discarded reads that were shorter than 75 basepairs or if the read was not mappable to the IMGT/HLA reference sequences. Generally, a few dozen thousand reads were retained for HLA typing. The algorithm produces 3 fields precision results for all the genes in the IMGT/HLA database.

Results:
The estimated diversity of genes studied is presented. Differences in ethnic groups can be found not only in highly polymorphic HLA genes, but also in other, more conserved loci.

Conclusion:
Estimating MHC genotype profile is possible from large-scale sequencing data, and deriving genotypes of MHC genes can provide valuable information about cohort diversity.

 

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