PMID- 21299525
OWN - NLM
STAT- MEDLINE
DCOM- 20110610
LR  - 20211020
IS  - 1399-0039 (Electronic)
IS  - 0001-2815 (Print)
IS  - 0001-2815 (Linking)
VI  - 77
IP  - 3
DP  - 2011 Mar
TI  - A multi-site study using high-resolution HLA genotyping by next generation 
      sequencing.
PG  - 206-17
LID - 10.1111/j.1399-0039.2010.01606.x [doi]
AB  - The high degree of polymorphism at human leukocyte antigen (HLA) class I and 
      class II loci makes high-resolution HLA typing challenging. Current typing 
      methods, including Sanger sequencing, yield ambiguous typing results because of 
      incomplete genomic coverage and inability to set phase for HLA allele 
      determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation 
      sequencing system coupled with conexio atf software can provide very 
      high-resolution HLA genotyping. High-throughput genotyping can be achieved by use 
      of primers with multiplex identifier (MID) tags to allow pooling of the amplicons 
      generated from different individuals prior to sequencing. We have conducted a 
      double-blind study in which eight laboratory sites performed amplicon sequencing 
      using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, 
      -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single 
      sequencing run. The average sequence read length was 250 base pairs and the 
      average number of sequence reads per amplicon was 672, providing confidence in 
      the allele assignments. Of the 1280 genotypes considered, assignment was possible 
      in 95% of the cases. Failure to assign genotypes was the result of researcher 
      procedural error or the presence of a novel allele rather than a failure of 
      sequencing technology. Concordance with known genotypes, in cases where 
      assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with 
      overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS 
      FLX platform and CONEXIO ATF software allows reliable identification of HLA 
      genotypes at high resolution.
CI  - (c) 2011 John Wiley & Sons A/S.
FAU - Holcomb, C L
AU  - Holcomb CL
AD  - Roche Molecular Systems Inc. (RMS), Pleasanton, CA 94588, USA.
FAU - Hoglund, B
AU  - Hoglund B
FAU - Anderson, M W
AU  - Anderson MW
FAU - Blake, L A
AU  - Blake LA
FAU - Bohme, I
AU  - Bohme I
FAU - Egholm, M
AU  - Egholm M
FAU - Ferriola, D
AU  - Ferriola D
FAU - Gabriel, C
AU  - Gabriel C
FAU - Gelber, S E
AU  - Gelber SE
FAU - Goodridge, D
AU  - Goodridge D
FAU - Hawbecker, S
AU  - Hawbecker S
FAU - Klein, R
AU  - Klein R
FAU - Ladner, M
AU  - Ladner M
FAU - Lind, C
AU  - Lind C
FAU - Monos, D
AU  - Monos D
FAU - Pando, M J
AU  - Pando MJ
FAU - Proll, J
AU  - Proll J
FAU - Sayer, D C
AU  - Sayer DC
FAU - Schmitz-Agheguian, G
AU  - Schmitz-Agheguian G
FAU - Simen, B B
AU  - Simen BB
FAU - Thiele, B
AU  - Thiele B
FAU - Trachtenberg, E A
AU  - Trachtenberg EA
FAU - Tyan, D B
AU  - Tyan DB
FAU - Wassmuth, R
AU  - Wassmuth R
FAU - White, S
AU  - White S
FAU - Erlich, H A
AU  - Erlich HA
LA  - eng
GR  - U01 AI067068/AI/NIAID NIH HHS/United States
GR  - AI067068/AI/NIAID NIH HHS/United States
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PL  - England
TA  - Tissue Antigens
JT  - Tissue antigens
JID - 0331072
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Base Sequence
MH  - Double-Blind Method
MH  - Family Characteristics
MH  - Genotype
MH  - HLA Antigens/analysis/*genetics
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Humans
MH  - Models, Biological
MH  - Molecular Sequence Data
MH  - Multicenter Studies as Topic
MH  - Sequence Analysis, DNA/methods/*trends
MH  - Software
PMC - PMC4205124
MID - NIHMS254845
EDAT- 2011/02/09 06:00
MHDA- 2011/06/11 06:00
PMCR- 2014/10/21
CRDT- 2011/02/09 06:00
PHST- 2011/02/09 06:00 [entrez]
PHST- 2011/02/09 06:00 [pubmed]
PHST- 2011/06/11 06:00 [medline]
PHST- 2014/10/21 00:00 [pmc-release]
AID - 10.1111/j.1399-0039.2010.01606.x [doi]
PST - ppublish
SO  - Tissue Antigens. 2011 Mar;77(3):206-17. doi: 10.1111/j.1399-0039.2010.01606.x.