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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| creator | Baek, In-Cheol Choi, Eun-Jeong Shin, Dong-Hwan Kim, Hyoung-Jae Choi, Haeyoun Kim, Tai-Gyu |
| 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.sup.® HLA v2 kit, Illumina MiSeqDx platform system, and Assign.sup.[TM] for TruSight.sup.[TM] 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: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (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. |
| doi_str_mv | 10.1371/journal.pone.0253619 |
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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.sup.® HLA v2 kit, Illumina MiSeqDx platform system, and Assign.sup.[TM] for TruSight.sup.[TM] 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: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0253619</identifier><identifier>PMID: 34153078</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Alleles ; Ambiguity ; Analysis ; Antigens ; Biology and Life Sciences ; Computer and Information Sciences ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; DQA1 protein ; Drafting software ; Drb1 protein ; Engineering and Technology ; Funding ; Gene amplification ; Gene frequency ; Genetic aspects ; Haplotypes ; Hematopoietic stem cells ; Histocompatibility antigen HLA ; Histocompatibility antigens ; HLA histocompatibility antigens ; Homogeneity ; Leukocytes ; Medical schools ; Medicine ; Medicine and Health Sciences ; Methodology ; Methods ; Microbiology ; Minority & ethnic groups ; Morbidity ; Next-generation sequencing ; Nucleotide sequencing ; People and Places ; Population ; Population genetics ; Research and analysis methods ; Sample preparation ; Software ; Stem cell transplantation ; Stem cells ; Tissue typing ; Transplantation ; Transplants & implants</subject><ispartof>PloS one, 2021-06, Vol.16 (6), p.e0253619-e0253619</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Baek et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Baek et al 2021 Baek et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c669t-cbed238100422be870b57b4aa5fb349d8d52e283d14b839ff220bf93ab6ab79a3</citedby><cites>FETCH-LOGICAL-c669t-cbed238100422be870b57b4aa5fb349d8d52e283d14b839ff220bf93ab6ab79a3</cites><orcidid>0000-0002-2226-2138</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216545/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8216545/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids></links><search><contributor>Augusto, Danillo G</contributor><creatorcontrib>Baek, In-Cheol</creatorcontrib><creatorcontrib>Choi, Eun-Jeong</creatorcontrib><creatorcontrib>Shin, Dong-Hwan</creatorcontrib><creatorcontrib>Kim, Hyoung-Jae</creatorcontrib><creatorcontrib>Choi, Haeyoun</creatorcontrib><creatorcontrib>Kim, Tai-Gyu</creatorcontrib><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><title>PloS one</title><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.sup.® HLA v2 kit, Illumina MiSeqDx platform system, and Assign.sup.[TM] for TruSight.sup.[TM] 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: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (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.</description><subject>Alleles</subject><subject>Ambiguity</subject><subject>Analysis</subject><subject>Antigens</subject><subject>Biology and Life Sciences</subject><subject>Computer and Information Sciences</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>DQA1 protein</subject><subject>Drafting software</subject><subject>Drb1 protein</subject><subject>Engineering and Technology</subject><subject>Funding</subject><subject>Gene amplification</subject><subject>Gene frequency</subject><subject>Genetic aspects</subject><subject>Haplotypes</subject><subject>Hematopoietic stem cells</subject><subject>Histocompatibility antigen HLA</subject><subject>Histocompatibility antigens</subject><subject>HLA histocompatibility antigens</subject><subject>Homogeneity</subject><subject>Leukocytes</subject><subject>Medical schools</subject><subject>Medicine</subject><subject>Medicine and Health Sciences</subject><subject>Methodology</subject><subject>Methods</subject><subject>Microbiology</subject><subject>Minority & ethnic groups</subject><subject>Morbidity</subject><subject>Next-generation sequencing</subject><subject>Nucleotide sequencing</subject><subject>People and Places</subject><subject>Population</subject><subject>Population genetics</subject><subject>Research and analysis methods</subject><subject>Sample preparation</subject><subject>Software</subject><subject>Stem cell transplantation</subject><subject>Stem cells</subject><subject>Tissue typing</subject><subject>Transplantation</subject><subject>Transplants & 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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><author>Baek, In-Cheol ; Choi, Eun-Jeong ; Shin, Dong-Hwan ; Kim, Hyoung-Jae ; Choi, Haeyoun ; Kim, Tai-Gyu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c669t-cbed238100422be870b57b4aa5fb349d8d52e283d14b839ff220bf93ab6ab79a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Alleles</topic><topic>Ambiguity</topic><topic>Analysis</topic><topic>Antigens</topic><topic>Biology and Life Sciences</topic><topic>Computer and Information Sciences</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>DQA1 protein</topic><topic>Drafting software</topic><topic>Drb1 protein</topic><topic>Engineering and Technology</topic><topic>Funding</topic><topic>Gene amplification</topic><topic>Gene frequency</topic><topic>Genetic aspects</topic><topic>Haplotypes</topic><topic>Hematopoietic stem cells</topic><topic>Histocompatibility antigen HLA</topic><topic>Histocompatibility antigens</topic><topic>HLA histocompatibility antigens</topic><topic>Homogeneity</topic><topic>Leukocytes</topic><topic>Medical schools</topic><topic>Medicine</topic><topic>Medicine and Health Sciences</topic><topic>Methodology</topic><topic>Methods</topic><topic>Microbiology</topic><topic>Minority & ethnic groups</topic><topic>Morbidity</topic><topic>Next-generation sequencing</topic><topic>Nucleotide sequencing</topic><topic>People and Places</topic><topic>Population</topic><topic>Population genetics</topic><topic>Research and analysis methods</topic><topic>Sample preparation</topic><topic>Software</topic><topic>Stem cell transplantation</topic><topic>Stem cells</topic><topic>Tissue typing</topic><topic>Transplantation</topic><topic>Transplants & 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Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Baek, In-Cheol</au><au>Choi, Eun-Jeong</au><au>Shin, Dong-Hwan</au><au>Kim, Hyoung-Jae</au><au>Choi, Haeyoun</au><au>Kim, Tai-Gyu</au><au>Augusto, Danillo G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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</atitle><jtitle>PloS one</jtitle><date>2021-06-21</date><risdate>2021</risdate><volume>16</volume><issue>6</issue><spage>e0253619</spage><epage>e0253619</epage><pages>e0253619-e0253619</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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.sup.® HLA v2 kit, Illumina MiSeqDx platform system, and Assign.sup.[TM] for TruSight.sup.[TM] 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: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (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.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34153078</pmid><doi>10.1371/journal.pone.0253619</doi><tpages>e0253619</tpages><orcidid>https://orcid.org/0000-0002-2226-2138</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2021-06, Vol.16 (6), p.e0253619-e0253619 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2543679857 |
| source | DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Alleles Ambiguity Analysis Antigens Biology and Life Sciences Computer and Information Sciences Deoxyribonucleic acid DNA DNA sequencing DQA1 protein Drafting software Drb1 protein Engineering and Technology Funding Gene amplification Gene frequency Genetic aspects Haplotypes Hematopoietic stem cells Histocompatibility antigen HLA Histocompatibility antigens HLA histocompatibility antigens Homogeneity Leukocytes Medical schools Medicine Medicine and Health Sciences Methodology Methods Microbiology Minority & ethnic groups Morbidity Next-generation sequencing Nucleotide sequencing People and Places Population Population genetics Research and analysis methods Sample preparation Software Stem cell transplantation Stem cells Tissue typing Transplantation Transplants & implants |
| 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 |
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