PMID- 23748956
OWN - NLM
STAT- MEDLINE
DCOM- 20131104
LR  - 20211021
IS  - 1362-4962 (Electronic)
IS  - 0305-1048 (Print)
IS  - 0305-1048 (Linking)
VI  - 41
IP  - 14
DP  - 2013 Aug
TI  - ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.
PG  - e142
LID - 10.1093/nar/gkt481 [doi]
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.
FAU - Liu, Chang
AU  - Liu C
AD  - Department of Pathology and Immunology, Washington University School of Medicine, 
      St. Louis, MO 63110, USA.
FAU - Yang, Xiao
AU  - Yang X
FAU - Duffy, Brian
AU  - Duffy B
FAU - Mohanakumar, Thalachallour
AU  - Mohanakumar T
FAU - Mitra, Robi D
AU  - Mitra RD
FAU - Zody, Michael C
AU  - Zody MC
FAU - Pfeifer, John D
AU  - Pfeifer JD
LA  - eng
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20130608
PL  - England
TA  - Nucleic Acids Res
JT  - Nucleic acids research
JID - 0411011
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - *Exome
MH  - HLA Antigens/classification/*genetics
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Sequence Analysis, DNA/*methods
MH  - *Software
PMC - PMC3737559
EDAT- 2013/06/12 06:00
MHDA- 2013/11/05 06:00
PMCR- 2013/06/08
CRDT- 2013/06/11 06:00
PHST- 2013/06/11 06:00 [entrez]
PHST- 2013/06/12 06:00 [pubmed]
PHST- 2013/11/05 06:00 [medline]
PHST- 2013/06/08 00:00 [pmc-release]
AID - gkt481 [pii]
AID - 10.1093/nar/gkt481 [doi]
PST - ppublish
SO  - Nucleic Acids Res. 2013 Aug;41(14):e142. doi: 10.1093/nar/gkt481. Epub 2013 Jun 
      8.