Empirical evaluations of analytical issues arising from predicting HLA alleles using multiple SNPs.

Publication Type:

Journal Article


BMC genetics, Volume 12, p.39 (2011)


2011, Center-Authored Paper, Clinical Research Division, Genomics Core Facility, Public Health Sciences Division, Research Trials Office Core Facility - Biostatistics Service, Shared Resources


Numerous immune-mediated diseases have been associated with the class I and II HLA genes located within the major histocompatibility complex (MHC) consisting of highly polymorphic alleles encoded by the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci. Genotyping for HLA alleles is complex and relatively expensive. Recent studies have demonstrated the feasibility of predicting HLA alleles, using MHC SNPs inside and outside of HLA that are typically included in SNP arrays and are commonly available in genome-wide association studies (GWAS). We have recently described a novel method that is complementary to the previous methods, for accurately predicting HLA alleles using unphased flanking SNPs genotypes. In this manuscript, we address several practical issues relevant to the application of this methodology.