Cargando…

Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Anukul, Nampeung, Jenjaroenpun, Piroon, Sirikul, Chonticha, Wankaew, Natnicha, Nimsamer, Pattaraporn, Roothumnong, Ekkapong, Pithukpakorn, Manop, Leetrakool, Nipapan, Wongsurawat, Thidathip
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326273/
https://www.ncbi.nlm.nih.gov/pubmed/37424729
http://dx.doi.org/10.3389/fgene.2023.1213457
_version_ 1785069388998639616
author Anukul, Nampeung
Jenjaroenpun, Piroon
Sirikul, Chonticha
Wankaew, Natnicha
Nimsamer, Pattaraporn
Roothumnong, Ekkapong
Pithukpakorn, Manop
Leetrakool, Nipapan
Wongsurawat, Thidathip
author_facet Anukul, Nampeung
Jenjaroenpun, Piroon
Sirikul, Chonticha
Wankaew, Natnicha
Nimsamer, Pattaraporn
Roothumnong, Ekkapong
Pithukpakorn, Manop
Leetrakool, Nipapan
Wongsurawat, Thidathip
author_sort Anukul, Nampeung
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10326273
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-103262732023-07-08 Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing Anukul, Nampeung Jenjaroenpun, Piroon Sirikul, Chonticha Wankaew, Natnicha Nimsamer, Pattaraporn Roothumnong, Ekkapong Pithukpakorn, Manop Leetrakool, Nipapan Wongsurawat, Thidathip Front Genet Genetics 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. Frontiers Media S.A. 2023-06-23 /pmc/articles/PMC10326273/ /pubmed/37424729 http://dx.doi.org/10.3389/fgene.2023.1213457 Text en Copyright © 2023 Anukul, Jenjaroenpun, Sirikul, Wankaew, Nimsamer, Roothumnong, Pithukpakorn, Leetrakool and Wongsurawat. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Anukul, Nampeung
Jenjaroenpun, Piroon
Sirikul, Chonticha
Wankaew, Natnicha
Nimsamer, Pattaraporn
Roothumnong, Ekkapong
Pithukpakorn, Manop
Leetrakool, Nipapan
Wongsurawat, Thidathip
Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
title Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
title_full Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
title_fullStr Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
title_full_unstemmed Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
title_short Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
title_sort ultrarapid and high-resolution hla class i typing using transposase-based nanopore sequencing applied in pharmacogenetic testing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326273/
https://www.ncbi.nlm.nih.gov/pubmed/37424729
http://dx.doi.org/10.3389/fgene.2023.1213457
work_keys_str_mv AT anukulnampeung ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT jenjaroenpunpiroon ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT sirikulchonticha ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT wankaewnatnicha ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT nimsamerpattaraporn ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT roothumnongekkapong ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT pithukpakornmanop ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT leetrakoolnipapan ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting
AT wongsurawatthidathip ultrarapidandhighresolutionhlaclassitypingusingtransposasebasednanoporesequencingappliedinpharmacogenetictesting