SNP-HLA Reference Consortium (SHLARC): HLA and SNP data sharing for promoting MHC-centric analyses in genomics.

Genetic Epidemiology
Nicolas VincePierre-Antoine Gourraud

Abstract

Genome-wide associations studies have repeatedly identified the major histocompatibility complex genomic region (6p21.3) as key in immune pathologies. Researchers have also aimed to extend the biological interpretation of associations by focusing directly on human leukocyte antigen (HLA) polymorphisms and their combination as haplotypes. To circumvent the effort and high costs of HLA typing, statistical solutions have been developed to infer HLA alleles from single-nucleotide polymorphism (SNP) genotyping data. Though HLA imputation methods have been developed, no unified effort has yet been undertaken to share large and diverse imputation models, or to improve methods. By training the HIBAG software on SNP + HLA data generated by the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) to create reference panels, we highlighted the importance of (a) the number of individuals in reference panels, with a twofold increase in accuracy (from 10 to 100 individuals) and (b) the number of SNPs, with a 1.5-fold increase in accuracy (from 500 to 24,504 SNPs). Results showed improved accuracy with CAAPA compared to the African American models available in HIBAG, highlighting the need for precise population-matc...Continue Reading

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Citations

Aug 27, 2021·Genetics and Molecular Biology·Vitor R C AguiarMaria Luiza Petzl-Erler

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Methods Mentioned

BETA
genotyping

Software Mentioned

Easy
SHLARC
HLA Genotype Imputation with Attribute Bagging ( HIBAG ) R pac...
HLA
HIBAG

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