Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.

Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performe...

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Autores principales:	In-Cheol Baek, Eun-Jeong Choi, Dong-Hwan Shin, Hyoung-Jae Kim, Haeyoun Choi, Tai-Gyu Kim
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5f6f7268a9b14dccaa9b611ce90cd9bb
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spelling	oai:doaj.org-article:5f6f7268a9b14dccaa9b611ce90cd9bb2021-12-02T20:10:18ZAllele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.1932-620310.1371/journal.pone.0253619https://doaj.org/article/5f6f7268a9b14dccaa9b611ce90cd9bb2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253619https://doaj.org/toc/1932-6203Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performed using next generation DNA sequencing with long-range PCR, TruSight® HLA v2 kit, Illumina MiSeqDx platform system, and Assign™ for TruSight™ HLA software. Haplotype frequencies were calculated using the PyPop software. Direct counting methods were used to investigate the association with DRB1 for samples with only one copy of a particular secondary DRB locus. We compared these allele types with the ambiguous allele combinations of the IPD-IMGT/HLA database. We identified 20, 40, 26, 31, 19, 16, 4, and 16 alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, respectively. The number of HLA-DRB3/4/5 alleles was 4, 5, and 3, respectively. The haplotype frequencies of most common haplotypes were as follows: A33:03:01-B44:03:01-C14:03-DRB113:02:01-DQB106:04:01-DPB104:01:01 (2.89%), A33:03:01-B44:03:01-C14:03 (4.91%), DRB108:03:02-DQA101:03:01-DQB106:01:01-DPA102:02:02-DPB105:01:01 (5.41%), DRB104:05:01-DRB401:03:01 (12.72%), DQA101:03:01-DQB106:01:01 (13.01%), and DPA102:02:02-DPB105:01:01 (30.83%). In samples with only one copy of a specific secondary DRB locus, we examined its association with DRB1. We, thus, resolved 10 allele ambiguities in HLA-B, -C (each exon 2+3), -DRB1, -DQB1, -DQA1, and -DPB1 (each exon 2) of the IPD-IMGT/HLA database. Korean population was geographically close to Japanese and Han Chinese populations in the genetic distances by multidimensional scaling (MDS) plots. The information obtained by HLA typing of the 11 extended loci by next generation sequencing may be useful for more exact diagnostic tests on various transplantations and the genetic population relationship studies in South Koreans.In-Cheol BaekEun-Jeong ChoiDong-Hwan ShinHyoung-Jae KimHaeyoun ChoiTai-Gyu KimPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 6, p e0253619 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q In-Cheol Baek Eun-Jeong Choi Dong-Hwan Shin Hyoung-Jae Kim Haeyoun Choi Tai-Gyu Kim Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.
description	Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performed using next generation DNA sequencing with long-range PCR, TruSight® HLA v2 kit, Illumina MiSeqDx platform system, and Assign™ for TruSight™ HLA software. Haplotype frequencies were calculated using the PyPop software. Direct counting methods were used to investigate the association with DRB1 for samples with only one copy of a particular secondary DRB locus. We compared these allele types with the ambiguous allele combinations of the IPD-IMGT/HLA database. We identified 20, 40, 26, 31, 19, 16, 4, and 16 alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, respectively. The number of HLA-DRB3/4/5 alleles was 4, 5, and 3, respectively. The haplotype frequencies of most common haplotypes were as follows: A33:03:01-B44:03:01-C14:03-DRB113:02:01-DQB106:04:01-DPB104:01:01 (2.89%), A33:03:01-B44:03:01-C14:03 (4.91%), DRB108:03:02-DQA101:03:01-DQB106:01:01-DPA102:02:02-DPB105:01:01 (5.41%), DRB104:05:01-DRB401:03:01 (12.72%), DQA101:03:01-DQB106:01:01 (13.01%), and DPA102:02:02-DPB105:01:01 (30.83%). In samples with only one copy of a specific secondary DRB locus, we examined its association with DRB1. We, thus, resolved 10 allele ambiguities in HLA-B, -C (each exon 2+3), -DRB1, -DQB1, -DQA1, and -DPB1 (each exon 2) of the IPD-IMGT/HLA database. Korean population was geographically close to Japanese and Han Chinese populations in the genetic distances by multidimensional scaling (MDS) plots. The information obtained by HLA typing of the 11 extended loci by next generation sequencing may be useful for more exact diagnostic tests on various transplantations and the genetic population relationship studies in South Koreans.
format	article
author	In-Cheol Baek Eun-Jeong Choi Dong-Hwan Shin Hyoung-Jae Kim Haeyoun Choi Tai-Gyu Kim
author_facet	In-Cheol Baek Eun-Jeong Choi Dong-Hwan Shin Hyoung-Jae Kim Haeyoun Choi Tai-Gyu Kim
author_sort	In-Cheol Baek
title	Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.
title_short	Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.
title_full	Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.
title_fullStr	Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.
title_full_unstemmed	Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.
title_sort	allele and haplotype frequencies of human leukocyte antigen-a, -b, -c, -drb1, -drb3/4/5, -dqa1, -dqb1, -dpa1, and -dpb1 by next generation sequencing-based typing in koreans in south korea.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/5f6f7268a9b14dccaa9b611ce90cd9bb
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Allele and haplotype frequencies of human leukocyte antigen-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 by next generation sequencing-based typing in Koreans in South Korea.

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