PMID- 20603174
OWN - NLM
STAT- MEDLINE
DCOM- 20110405
LR  - 20100917
IS  - 1879-1166 (Electronic)
IS  - 0198-8859 (Linking)
VI  - 71
IP  - 10
DP  - 2010 Oct
TI  - Next-generation sequencing: the solution for high-resolution, unambiguous human 
      leukocyte antigen typing.
PG  - 1033-42
LID - 10.1016/j.humimm.2010.06.016 [doi]
AB  - Human leukocyte antigen (HLA) typing has been a challenge for more than 50 years. 
      Current methods (Sanger sequencing, sequence-specific primers [SSP], 
      sequence-specific oligonucleotide probes [SSOP]) continue to generate ambiguities 
      that are time-consuming and expensive to resolve. However, next-generation 
      sequencing (NGS) overcomes ambiguity through the combination of clonal 
      amplification, which provides on-phase sequence and a high level of parallelism, 
      whereby millions of sequencing reads are produced enabling an expansion of the 
      HLA regions sequenced. We explored HLA typing using NGS through a three-step 
      process. First, HLA-A, -B, -C, -DRB1, and -DQB1 were amplified with long-range 
      PCR. Subsequently, amplicons were sequenced using the 454 GS-FLX platform. 
      Finally, sequencing data were analyzed with Assign-NG software. In a single 
      experiment, four individual samples and two mixtures were sequenced producing >75 
      Mb of sequence from >300,000 individual sequence reads (average length, 244 b). 
      The reads were aligned and covered 100% of the regions amplified. Allele 
      assignment was 100% concordant with the known HLA alleles of our samples. Our 
      results suggest this method can be a useful tool for complete genomic 
      characterization of new HLA alleles and for completion of sequence for existing, 
      partially sequenced alleles. NGS can provide complete, unambiguous, 
      high-resolution HLA typing; however, further evaluation is needed to explore the 
      feasibility of its routine use.
CI  - 2010 American Society for Histocompatibility and Immunogenetics. Published by 
      Elsevier Inc. All rights reserved.
FAU - Lind, C
AU  - Lind C
AD  - Department of Pathology and Laboratory Medicine, The Children's Hospital of 
      Philadelphia, Philadelphia, Pennsylvania, USA.
FAU - Ferriola, D
AU  - Ferriola D
FAU - Mackiewicz, K
AU  - Mackiewicz K
FAU - Heron, S
AU  - Heron S
FAU - Rogers, M
AU  - Rogers M
FAU - Slavich, L
AU  - Slavich L
FAU - Walker, R
AU  - Walker R
FAU - Hsiao, T
AU  - Hsiao T
FAU - McLaughlin, L
AU  - McLaughlin L
FAU - D'Arcy, M
AU  - D'Arcy M
FAU - Gai, X
AU  - Gai X
FAU - Goodridge, D
AU  - Goodridge D
FAU - Sayer, D
AU  - Sayer D
FAU - Monos, D
AU  - Monos D
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20100805
PL  - United States
TA  - Hum Immunol
JT  - Human immunology
JID - 8010936
RN  - 0 (DNA Primers)
SB  - IM
MH  - DNA Primers
MH  - Diagnostic Errors/prevention & control
MH  - Feasibility Studies
MH  - Histocompatibility Testing/methods/*trends
MH  - Humans
MH  - Polymerase Chain Reaction
MH  - Reproducibility of Results
MH  - Sensitivity and Specificity
MH  - *Sequence Analysis, DNA/methods
EDAT- 2010/07/07 06:00
MHDA- 2011/04/06 06:00
CRDT- 2010/07/07 06:00
PHST- 2010/03/24 00:00 [received]
PHST- 2010/06/15 00:00 [revised]
PHST- 2010/06/22 00:00 [accepted]
PHST- 2010/07/07 06:00 [entrez]
PHST- 2010/07/07 06:00 [pubmed]
PHST- 2011/04/06 06:00 [medline]
AID - S0198-8859(10)00159-X [pii]
AID - 10.1016/j.humimm.2010.06.016 [doi]
PST - ppublish
SO  - Hum Immunol. 2010 Oct;71(10):1033-42. doi: 10.1016/j.humimm.2010.06.016. Epub 
      2010 Aug 5.