TY - JOUR
T1 - ATHLATES
T2 - Accurate typing of human leukocyte antigen through exome sequencing
AU - Liu, Chang
AU - Yang, Xiao
AU - Duffy, Brian
AU - Mohanakumar, Thalachallour
AU - Mitra, Robi D.
AU - Zody, Michael C.
AU - Pfeifer, John D.
N1 - Funding Information:
Laboratory and Genomic Medicine Director discretionary fund from the Department of Pathology and Immunology, Washington University School of Medicine, and in part by Federal funds from the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Department of Health and Human Services [contract no.: HHSN272200900018C]. Funding for open access charge: Department of Pathology and Immunology, Washington University School of Medicine and NIAID [HHSN272200900018C].
PY - 2013/8
Y1 - 2013/8
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84881511328&partnerID=8YFLogxK
U2 - 10.1093/nar/gkt481
DO - 10.1093/nar/gkt481
M3 - Article
C2 - 23748956
AN - SCOPUS:84881511328
SN - 0305-1048
VL - 41
SP - e142
JO - Nucleic acids research
JF - Nucleic acids research
IS - 14
ER -