PMID- 31173929
OWN - NLM
STAT- MEDLINE
DCOM- 20200701
LR  - 20200901
IS  - 1943-7811 (Electronic)
IS  - 1525-1578 (Print)
IS  - 1525-1578 (Linking)
VI  - 21
IP  - 5
DP  - 2019 Sep
TI  - Resolving MiSeq-Generated Ambiguities in HLA-DPB1 Typing by Using the Oxford 
      Nanopore Technology.
PG  - 852-861
LID - S1525-1578(19)30068-6 [pii]
LID - 10.1016/j.jmoldx.2019.04.009 [doi]
AB  - The technical limitations of current next-generation sequencing technologies, 
      combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, 
      form the basis for the additional ambiguities encountered at an increasing rate 
      in clinical practice. HLA-DPB1 characterization, particularly, generates a 
      significant percentage of ambiguities (25.5%), posing a challenge for accurate 
      and unambiguous HLA-DPB1 genotyping. Phasing of exonic heterozygous positions 
      between exon 2 and all other downstream exons has been the major cause of 
      ambiguities. In this study, the Oxford Nanopore MinION, a third-generation 
      sequencing technology, was used to resolve the phasing. The accurate MiSeq 
      sequencing data, combined with the long reads obtained from the MinION platform, 
      allow for the resolution of the tested ambiguities.
CI  - Copyright (c) 2019 American Society for Investigative Pathology and the Association 
      for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
FAU - Duke, Jamie L
AU  - Duke JL
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
FAU - Mosbruger, Timothy L
AU  - Mosbruger TL
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
FAU - Ferriola, Deborah
AU  - Ferriola D
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
FAU - Chitnis, Nilesh
AU  - Chitnis N
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
FAU - Hu, Taishan
AU  - Hu T
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
FAU - Tairis, Nikolaos
AU  - Tairis N
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
FAU - Margolis, David J
AU  - Margolis DJ
AD  - Department of Dermatology, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, Pennsylvania; Departments of Dermatology and 
      Biostatistics and Epidemiology, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, Pennsylvania.
FAU - Monos, Dimitri S
AU  - Monos DS
AD  - Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, 
      Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of 
      Pathology and Laboratory Medicine, Perelman School of Medicine, University of 
      Pennsylvania, Philadelphia, Pennsylvania. Electronic address: 
      monosd@email.chop.edu.
LA  - eng
GR  - R01 AR070873/AR/NIAMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20190604
PL  - United States
TA  - J Mol Diagn
JT  - The Journal of molecular diagnostics : JMD
JID - 100893612
RN  - 0 (HLA-DP beta-Chains)
RN  - 0 (HLA-DPB1 antigen)
SB  - IM
MH  - Exons
MH  - Genetic Testing/*methods
MH  - HLA-DP beta-Chains/*genetics
MH  - High-Throughput Nucleotide Sequencing/*methods/*standards
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - *Nanopores
MH  - Sequence Analysis, DNA/*methods
PMC - PMC6734860
EDAT- 2019/06/08 06:00
MHDA- 2020/07/02 06:00
PMCR- 2020/09/01
CRDT- 2019/06/08 06:00
PHST- 2019/02/01 00:00 [received]
PHST- 2019/04/19 00:00 [revised]
PHST- 2019/04/30 00:00 [accepted]
PHST- 2019/06/08 06:00 [pubmed]
PHST- 2020/07/02 06:00 [medline]
PHST- 2019/06/08 06:00 [entrez]
PHST- 2020/09/01 00:00 [pmc-release]
AID - S1525-1578(19)30068-6 [pii]
AID - 10.1016/j.jmoldx.2019.04.009 [doi]
PST - ppublish
SO  - J Mol Diagn. 2019 Sep;21(5):852-861. doi: 10.1016/j.jmoldx.2019.04.009. Epub 2019 
      Jun 4.