title: ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.
abstract: Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing. This novel approach should be broadly applicable to research and clinical laboratories.
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
authors.forename: Brian
authors.initials: B
authors.lastname: Duffy
authors.forename: Thalachallour
authors.initials: T
authors.lastname: Mohanakumar
authors.forename: Robi D
authors.initials: RD
authors.lastname: Mitra
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.forename: John D
authors.initials: JD
authors.lastname: Pfeifer
mesh_terms: D000483:Alleles; D059472:Exome; D006680:HLA Antigens / Q000145:classification / Q000235:genetics*; D006650:Histocompatibility Testing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D006680:HLA Antigens