MHC*IMP – Imputation of Alleles for Genes in the Major Histocompatibility Complex
David McG Squire, Allan Motyer, Richard Ahn, Joanne Nititham, Zhi-Ming Huang, Jorge R Oksenberg, John Foerster, Wilson Liao, Stephen Leslie
Cold Spring Harbor Laboratory
AbstractWe report the development of MHC*IMP, a method for imputing non-classical HLA and other genes in the human Major Histocompatibility Complex (MHC). We created a reference panel for 25 genes in the MHC using allele calls from Whole Genome Sequencing data, combined with SNP data for the same individuals. We used this to construct an allele imputation model, MHC*IMP, for each gene. Cross-validation showed that MHC*IMP performs very well, with allele prediction accuracy 93% or greater for all but two of the genes, and greater than 95% for all but four.