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PMID: 21244689 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't

Next-generation sequencing for HLA typing of class I loci.

BMC genomics ·Vol. 12 ·2011-01-18 ·Pages 42

Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, DePristo MA, Henn MR, Lennon NJ, de Bakker PI

Abstract

Comprehensive sequence characterization across the MHC is important for successful organ transplantation and genetic association studies. To this end, we have developed an automated sample preparation, molecular barcoding and multiplexing protocol for the amplification and sequence-determination of class I HLA loci. We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus. We have benchmarked our protocol with 270 HapMap individuals from four worldwide populations with 96.4% accuracy at 4-digit resolution. A variation of this initial protocol, more suitable for large sample sizes, in which molecular barcodes are added during PCR rather than library construction, was tested on 95 HapMap individuals with 98.6% accuracy at 4-digit resolution. Next-generation sequencing on the 454 FLX Titanium platform is a reliable, efficient, and scalable technology for HLA typing.

MeSH Terms
Genes, MHC Class I/genetics Histocompatibility Testing/methods Humans Polymerase Chain Reaction Sequence Analysis, DNA/methods
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Erlich Rachel L
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Jia Xiaoming
Anderson Scott
Banks Eric
Gao Xiaojiang
Carrington Mary
Gupta Namrata
DePristo Mark A
Henn Matthew R
Lennon Niall J
de Bakker Paul I W
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-12-42
Published
2011-01-18
Epub
2011-00-18
Pages
42
Language
English
Region
England
NLM ID
100965258
PMCID
PMC3033818
Subset
IM
Grants
NIAID NIH HHS · P30 AI060354 · United States
Intramural NIH HHS · United States
PHS HHS · HHSN26120080001E · United States
External Links
PubMed source DOI: 10.1186/1471-2164-12-42 PMC Full Text View journal details
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