PMID- 37424729
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230718
IS  - 1664-8021 (Print)
IS  - 1664-8021 (Electronic)
IS  - 1664-8021 (Linking)
VI  - 14
DP  - 2023
TI  - Ultrarapid and high-resolution HLA class I typing using transposase-based 
      nanopore sequencing applied in pharmacogenetic testing.
PG  - 1213457
LID - 10.3389/fgene.2023.1213457 [doi]
LID - 1213457
AB  - Nanopore sequencing has been examined as a method for rapid and high-resolution 
      human leukocyte antigen (HLA) typing in recent years. We aimed to apply 
      ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug 
      hypersensitivity, including HLA-A*31:01, HLA-B*15:02, and HLA-C*08:01. Most 
      studies have used the Oxford Nanopore Ligation Sequencing kit for HLA typing, 
      which requires several enzymatic reactions and remains relatively expensive, even 
      when the samples are multiplexed. Here, we used the Oxford Nanopore Rapid 
      Barcoding kit, which is transposase-based, with library preparation taking less 
      than 1 h of hands-on time and requiring minimal reagents. Twenty DNA samples were 
      genotyped for HLA-A, -B, and -C; 11 samples were from individuals of different 
      ethnicity and nine were from Thai individuals. Two primer sets, a commercial set 
      and a published set, were used to amplify the HLA-A, -B, and -C genes. HLA-typing 
      tools that used different algorithms were applied and compared. We found that 
      without using several third-party reagents, the transposase-based method reduced 
      the hands-on time from approximately 9 h to 4 h, making this a viable approach 
      for obtaining same-day results from 2 to 24 samples. However, an imbalance in the 
      PCR amplification of different haplotypes could affect the accuracy of typing 
      results. This work demonstrates the ability of transposase-based sequencing to 
      report 3-field HLA alleles and its potential for race- and population-independent 
      testing at considerably decreased time and cost.
CI  - Copyright (c) 2023 Anukul, Jenjaroenpun, Sirikul, Wankaew, Nimsamer, Roothumnong, 
      Pithukpakorn, Leetrakool and Wongsurawat.
FAU - Anukul, Nampeung
AU  - Anukul N
AD  - Division of Transfusion Science, Department of Medical Technology, Faculty of 
      Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.
FAU - Jenjaroenpun, Piroon
AU  - Jenjaroenpun P
AD  - Division of Medical Bioinformatics, Research and Innovation Department, Faculty 
      of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
AD  - Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol 
      University, Bangkok, Thailand.
FAU - Sirikul, Chonticha
AU  - Sirikul C
AD  - Division of Transfusion Science, Department of Medical Technology, Faculty of 
      Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.
FAU - Wankaew, Natnicha
AU  - Wankaew N
AD  - Division of Medical Bioinformatics, Research and Innovation Department, Faculty 
      of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
AD  - Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol 
      University, Bangkok, Thailand.
FAU - Nimsamer, Pattaraporn
AU  - Nimsamer P
AD  - Division of Medical Bioinformatics, Research and Innovation Department, Faculty 
      of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
AD  - Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol 
      University, Bangkok, Thailand.
FAU - Roothumnong, Ekkapong
AU  - Roothumnong E
AD  - Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj 
      Hospital, Mahidol University, Bangkok, Thailand.
FAU - Pithukpakorn, Manop
AU  - Pithukpakorn M
AD  - Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj 
      Hospital, Mahidol University, Bangkok, Thailand.
AD  - Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, 
      Bangkok, Thailand.
FAU - Leetrakool, Nipapan
AU  - Leetrakool N
AD  - Blood Bank Section, Maharaj Nakorn Chiang Mai Hospital, Faculty of Medicines, 
      Chiang Mai University, Chiang Mai, Thailand.
FAU - Wongsurawat, Thidathip
AU  - Wongsurawat T
AD  - Division of Medical Bioinformatics, Research and Innovation Department, Faculty 
      of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
AD  - Siriraj Long-read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Mahidol 
      University, Bangkok, Thailand.
AD  - Department of Biomedical Informatics, College of Medicine, University of Arkansas 
      for Medical Sciences, Little Rock, AR, United States.
LA  - eng
PT  - Journal Article
DEP - 20230623
PL  - Switzerland
TA  - Front Genet
JT  - Frontiers in genetics
JID - 101560621
PMC - PMC10326273
OTO - NOTNLM
OT  - ADR
OT  - HLA-B*15:02
OT  - Thai
OT  - human leukocyte antigen
OT  - long-read sequencing
OT  - nanopore
OT  - pharmacogenomics
OT  - turnaround time
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2023/07/10 06:42
MHDA- 2023/07/10 06:43
PMCR- 2023/06/23
CRDT- 2023/07/10 04:47
PHST- 2023/04/28 00:00 [received]
PHST- 2023/06/06 00:00 [accepted]
PHST- 2023/07/10 06:43 [medline]
PHST- 2023/07/10 06:42 [pubmed]
PHST- 2023/07/10 04:47 [entrez]
PHST- 2023/06/23 00:00 [pmc-release]
AID - 1213457 [pii]
AID - 10.3389/fgene.2023.1213457 [doi]
PST - epublish
SO  - Front Genet. 2023 Jun 23;14:1213457. doi: 10.3389/fgene.2023.1213457. eCollection 
      2023.