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HLA Typing pp 163-176 | Cite as

Imputation-Based HLA Typing with SNPs in GWAS Studies

  • Xiuwen ZhengEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

SNP-based imputation approaches for human leukocyte antigen (HLA) typing take advantage of the extended haplotype structure within the major histocompatibility complex (MHC) to predict classical HLA alleles using dense SNP genotypes, such as those available on chip panels of genome-wide association study (GWAS). These methods enable HLA analyses of classical alleles on existing SNP datasets genotyped in GWAS studies at no extra cost. Here, I describe the workflow of HIBAG, an imputation method with attribute bagging, for obtaining a sample’s HLA class I and II genotypes of two-field resolution using SNP data. Two examples are provided to illustrate with a publicly available HLA and SNP dataset: genotype imputation with pre-fit classifiers in GWAS, and model training to build a new classifier.

Keywords

HLA MHC Imputation SNP GWAS HIBAG 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of BiostatisticsUniversity of WashingtonSeattleUSA

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