PMID- 26880737
OWN - NLM
STAT- MEDLINE
DCOM- 20161213
LR  - 20211203
IS  - 2059-2310 (Electronic)
IS  - 2059-2302 (Linking)
VI  - 87
IP  - 3
DP  - 2016 Mar
TI  - Determining performance characteristics of an NGS-based HLA typing method for 
      clinical applications.
PG  - 141-52
LID - 10.1111/tan.12736 [doi]
AB  - This study presents performance specifications of an in-house developed human 
      leukocyte antigen (HLA) typing assay using next-generation sequencing (NGS) on 
      the Illumina MiSeq platform. A total of 253 samples, previously characterized for 
      HLA-A, -B, -C, -DRB1 and -DQB1 were included in this study, which were typed at 
      high-resolution using a combination of Sanger sequencing, sequence-specific 
      primer (SSP) and sequence-specific oligonucleotide probe (SSOP) technologies and 
      recorded at the two-field level. Samples were selected with alleles that cover a 
      high percentage of HLA specificities in each of five different race/ethnic 
      groups: European, African-American, Asian Pacific Islander, Hispanic and Native 
      American. Sequencing data were analyzed by two software programs, Omixon's target 
      and GenDx's NGSengine. A number of metrics including allele balance, sensitivity, 
      specificity, precision, accuracy and remaining ambiguity were assessed. Data 
      analyzed by the two software systems are shown independently. The majority of 
      alleles were identical in the exonic sequences (third field) with both programs 
      for HLA-A, -B, -C and -DQB1 in 97.7% of allele determinations. Among the 
      remaining discrepant genotype calls at least one of the analysis programs agreed 
      with the reference typing. Upon additional manual analysis 100% of the 2530 
      alleles were concordant with the reference HLA genotypes; the remaining 
      ambiguities did not exceed 0.8%. The results demonstrate the feasibility and 
      significant benefit of HLA typing by NGS as this technology is highly accurate, 
      eliminates virtually all ambiguities, provides complete sequencing information 
      for the length of the HLA gene and forms the basis for utilizing a single 
      methodology for HLA typing in the immunogenetics labs.
CI  - (c) 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
FAU - Duke, J L
AU  - Duke JL
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Lind, C
AU  - Lind C
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Mackiewicz, K
AU  - Mackiewicz K
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Ferriola, D
AU  - Ferriola D
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Papazoglou, A
AU  - Papazoglou A
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Gasiewski, A
AU  - Gasiewski A
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Heron, S
AU  - Heron S
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Huynh, A
AU  - Huynh A
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - McLaughlin, L
AU  - McLaughlin L
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Rogers, M
AU  - Rogers M
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Slavich, L
AU  - Slavich L
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Walker, R
AU  - Walker R
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
FAU - Monos, D S
AU  - Monos DS
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The 
      Children's Hospital of Philadelphia, Philadelphia, PA, USA.
AD  - Department of Pathology and Laboratory Medicine, Perelman School of Medicine, 
      University of Pennsylvania, Philadelphia, PA, USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20160216
PL  - England
TA  - HLA
JT  - HLA
JID - 101675570
RN  - 0 (DNA Primers)
RN  - 0 (DNA Probes)
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Alleles
MH  - DNA Primers/chemical synthesis
MH  - DNA Probes/chemical synthesis
MH  - *Genotype
MH  - HLA Antigens/*classification/*genetics/immunology
MH  - High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Testing/instrumentation/*methods/standards
MH  - Humans
MH  - Polymerase Chain Reaction
MH  - Racial Groups
MH  - Sensitivity and Specificity
MH  - Sequence Analysis, DNA
MH  - Software
OTO - NOTNLM
OT  - MiSeq
OT  - human leukocyte antigen genotyping
OT  - next-generation sequencing
EDAT- 2016/02/18 06:00
MHDA- 2016/12/15 06:00
CRDT- 2016/02/17 06:00
PHST- 2015/07/27 00:00 [received]
PHST- 2015/12/03 00:00 [revised]
PHST- 2016/01/04 00:00 [accepted]
PHST- 2016/02/17 06:00 [entrez]
PHST- 2016/02/18 06:00 [pubmed]
PHST- 2016/12/15 06:00 [medline]
AID - 10.1111/tan.12736 [doi]
PST - ppublish
SO  - HLA. 2016 Mar;87(3):141-52. doi: 10.1111/tan.12736. Epub 2016 Feb 16.