Journal
NUCLEIC ACIDS RESEARCH
Volume 41, Issue 14, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt481
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Funding
- Department of Pathology and Immunology, Washington University School of Medicine
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Department of Health and Human Services [HHSN272200900018C]
- NIAID [HHSN272200900018C]
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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.
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