High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.

ABSTRACT: Genetic variation at the Human Leucocyte Antigen (HLA) genes is associated with many autoimmune and infectious disease phenotypes, is an important element of the immunological distinction between self and non-self, and shapes immune epitope repertoires. Determining the allelic state of the HLA genes (HLA typing) as a by-product of standard whole-genome sequencing data would therefore be highly desirable and enable the immunogenetic characterization of samples in currently ongoing population sequencing projects. Extensive hyperpolymorphism and sequence similarity between the HLA genes, however, pose problems for accurate read mapping and make HLA type inference from whole-genome sequencing data a challenging problem. We describe how to address these challenges in a Population Reference Grap

SUBMITTER: Dilthey AT 

PROVIDER: S-EPMC5085092 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature