PMID- 32302780
OWN - NLM
STAT- MEDLINE
DCOM- 20210719
LR  - 20210719
IS  - 1943-7811 (Electronic)
IS  - 1525-1578 (Linking)
VI  - 22
IP  - 7
DP  - 2020 Jul
TI  - Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I 
      Typing in Routine Diagnostics.
PG  - 912-919
LID - S1525-1578(20)30091-X [pii]
LID - 10.1016/j.jmoldx.2020.04.001 [doi]
AB  - Matching of human leukocyte antigen (HLA) gene polymorphisms by high-resolution 
      DNA sequence analysis is the gold standard for determining compatibility between 
      patient and donor for hematopoietic stem cell transplantation. Single-molecule 
      sequencing (PacBio or MinION) is a newest (third) generation sequencing approach. 
      MinION is a nanopore sequencing platform, which provides long targeted DNA 
      sequences. The long reads provide unambiguous phasing, but the initial high error 
      profile prevented its use in high-impact applications, such as HLA typing for HLA 
      matching of donor and recipient in the transplantation setting. Ongoing 
      developments on instrumentation and basecalling software have improved the 
      per-base accuracy of 1D(2) nanopore reads tremendously. In the current study, two 
      validation panels of samples covering 70 of the 71 known HLA class I allele 
      groups were used to compare third field sequences obtained by MinION, with Sanger 
      sequence-based typing showing a 100% concordance between both data sets. In 
      addition, the first validation panel was used to set the acceptance criteria for 
      the use of MinION in a routine setting. The acceptance criteria were subsequently 
      confirmed with the second validation panel. In summary, the present study 
      describes validation and implementation of nanopore sequencing HLA class I typing 
      method and illustrates that nanopore sequencing technology has advanced to a 
      point where it can be used in routine diagnostics with high accuracy.
CI  - Copyright (c) 2020 Association for Molecular Pathology and American Society for 
      Investigative Pathology. Published by Elsevier Inc. All rights reserved.
FAU - Matern, Benedict M
AU  - Matern BM
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands.
FAU - Olieslagers, Timo I
AU  - Olieslagers TI
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands.
FAU - Groeneweg, Mathijs
AU  - Groeneweg M
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands.
FAU - Duygu, Burcu
AU  - Duygu B
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands.
FAU - Wieten, Lotte
AU  - Wieten L
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands.
FAU - Tilanus, Marcel G J
AU  - Tilanus MGJ
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands.
FAU - Voorter, Christina E M
AU  - Voorter CEM
AD  - Transplantation Immunology, Tissue Typing Laboratory, Maastricht University 
      Medical Center, Maastricht, the Netherlands. Electronic address: 
      c.voorter@mumc.nl.
LA  - eng
PT  - Journal Article
PT  - Validation Study
DEP - 20200414
PL  - United States
TA  - J Mol Diagn
JT  - The Journal of molecular diagnostics : JMD
JID - 100893612
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class I)
SB  - IM
MH  - Alleles
MH  - Base Sequence
MH  - Data Accuracy
MH  - Diagnostic Tests, Routine/*methods
MH  - Genetic Testing/methods
MH  - HLA Antigens/*genetics
MH  - High-Throughput Nucleotide Sequencing/methods
MH  - Histocompatibility Antigens Class I/*genetics
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - Nanopore Sequencing/*methods
MH  - Nanopores
MH  - Polymorphism, Single Nucleotide
MH  - Reproducibility of Results
MH  - Sequence Analysis, DNA/methods
MH  - Software
EDAT- 2020/04/18 06:00
MHDA- 2021/07/20 06:00
CRDT- 2020/04/18 06:00
PHST- 2020/01/10 00:00 [received]
PHST- 2020/03/03 00:00 [revised]
PHST- 2020/04/02 00:00 [accepted]
PHST- 2020/04/18 06:00 [pubmed]
PHST- 2021/07/20 06:00 [medline]
PHST- 2020/04/18 06:00 [entrez]
AID - S1525-1578(20)30091-X [pii]
AID - 10.1016/j.jmoldx.2020.04.001 [doi]
PST - ppublish
SO  - J Mol Diagn. 2020 Jul;22(7):912-919. doi: 10.1016/j.jmoldx.2020.04.001. Epub 2020 
      Apr 14.