PMID- 32595056
OWN - NLM
STAT- MEDLINE
DCOM- 20210609
LR  - 20211109
IS  - 1879-1166 (Electronic)
IS  - 0198-8859 (Print)
IS  - 0198-8859 (Linking)
VI  - 81
IP  - 8
DP  - 2020 Aug
TI  - Utilizing nanopore sequencing technology for the rapid and comprehensive 
      characterization of eleven HLA loci; addressing the need for deceased donor 
      expedited HLA typing.
PG  - 413-422
LID - S0198-8859(20)30339-6 [pii]
LID - 10.1016/j.humimm.2020.06.004 [doi]
AB  - The comprehensive characterization of human leukocyte antigen (HLA) genomic 
      sequences remains a challenging problem. Despite the significant advantages of 
      next-generation sequencing (NGS) in the field of Immunogenetics, there has yet to 
      be a single solution for unambiguous, accurate, simple, cost-effective, and 
      timely genotyping necessary for all clinical applications. This report 
      demonstrates the benefits of nanopore sequencing introduced by Oxford Nanopore 
      Technologies (ONT) for HLA genotyping. Samples (n = 120) previously characterized 
      at high-resolution three-field (HR-3F) for 11 loci were assessed using ONT 
      sequencing paired to a single-plex PCR protocol (Holotype) and to two multiplex 
      protocols OmniType (Omixon) and NGSgo(R)-MX6-1 (GenDx). The results demonstrate the 
      potential of nanopore sequencing for delivering accurate HR-3F typing with a 
      simple, rapid, and cost-effective protocol. The protocol is applicable to 
      time-sensitive applications, such as deceased donor typings, enabling better 
      assessments of compatibility and epitope analysis. The technology also allows 
      significantly shorter turnaround time for multiple samples at a lower cost. 
      Overall, the nanopore technology appears to offer a significant advancement over 
      current next-generation sequencing platforms as a single solution for all HLA 
      genotyping needs.
CI  - Copyright (c) 2020 The Authors. Published by Elsevier Inc. All rights reserved.
FAU - Mosbruger, Timothy L
AU  - Mosbruger TL
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Dinou, Amalia
AU  - Dinou A
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Duke, Jamie L
AU  - Duke JL
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Ferriola, Deborah
AU  - Ferriola D
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Mehler, Hilary
AU  - Mehler H
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Pagkrati, Ioanna
AU  - Pagkrati I
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Damianos, Georgios
AU  - Damianos G
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Mbunwe, Eric
AU  - Mbunwe E
AD  - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, PA, USA.
FAU - Sarmady, Mahdi
AU  - Sarmady M
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory 
      Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 
      PA, USA.
FAU - Lyratzakis, Ioannis
AU  - Lyratzakis I
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA.
FAU - Tishkoff, Sarah A
AU  - Tishkoff SA
AD  - Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 
      Philadelphia, PA, USA.
FAU - Dinh, Anh
AU  - Dinh A
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory 
      Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 
      PA, USA.
FAU - Monos, Dimitri S
AU  - Monos DS
AD  - Department of Pathology and Laboratory Medicine, Children's Hospital of 
      Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory 
      Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 
      PA, USA. Electronic address: monosd@email.chop.edu.
LA  - eng
GR  - R01 DK104339/DK/NIDDK NIH HHS/United States
GR  - R35 GM134957/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20200625
PL  - United States
TA  - Hum Immunol
JT  - Human immunology
JID - 8010936
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Genomics/methods
MH  - Genotyping Techniques/*methods
MH  - HLA Antigens/*genetics
MH  - High-Throughput Nucleotide Sequencing/methods
MH  - Histocompatibility Testing/methods
MH  - Humans
MH  - Nanopore Sequencing/*methods
MH  - Sequence Analysis, DNA/methods
MH  - Tissue Donors
PMC - PMC7870017
MID - NIHMS1608877
OTO - NOTNLM
OT  - HLA genotyping
OT  - Human Leukocyte Antigens
OT  - NGS
OT  - Oxford Nanopore sequencing
OT  - Transplantation
COIS- Disclosures D.S. Monos is a consultant to, and owns options in Omixon. D.S. 
      Monos, D. Ferriola and J.L. Duke receive royalties from Omixon. The other authors 
      of this manuscript have no conflicts of interest to disclose.
EDAT- 2020/07/01 06:00
MHDA- 2021/06/10 06:00
PMCR- 2021/02/08
CRDT- 2020/06/30 06:00
PHST- 2020/04/29 00:00 [received]
PHST- 2020/06/03 00:00 [revised]
PHST- 2020/06/03 00:00 [accepted]
PHST- 2020/07/01 06:00 [pubmed]
PHST- 2021/06/10 06:00 [medline]
PHST- 2020/06/30 06:00 [entrez]
PHST- 2021/02/08 00:00 [pmc-release]
AID - S0198-8859(20)30339-6 [pii]
AID - 10.1016/j.humimm.2020.06.004 [doi]
PST - ppublish
SO  - Hum Immunol. 2020 Aug;81(8):413-422. doi: 10.1016/j.humimm.2020.06.004. Epub 2020 
      Jun 25.