Allele Polymorphism and Haplotype Diversity of HLA-A, -B and -DRB1 Loci in Sequence-Based Typing for Chinese Uyghur Ethnic Group

Hdl Handle:
http://hdl.handle.net/10675.2/607
Title:
Allele Polymorphism and Haplotype Diversity of HLA-A, -B and -DRB1 Loci in Sequence-Based Typing for Chinese Uyghur Ethnic Group
Authors:
Deng, Ya-jun; Ye, Shi-hui; Yan, Jiang-wei; Yang, Guang; Wang, Hong-dan; Qin, Hai-xia; Huang, Qi-zhao; Zhang, Jing-Jing; Shen, Chun-mei; Zhu, Bo-feng
Abstract:
Background: Previous studies indicate that the frequency distributions of HLA alleles and haplotypes vary from one ethnic group to another or between the members of the same ethnic group living in different geographic areas. It is necessary and meaningful to study the high-resolution allelic and haplotypic distributions of HLA loci in different groups.; Methodology/Principal Findings: High-resolution HLA typing for the Uyghur ethnic minority group using polymerase chain reaction-sequence-based-typing method was first reported. HLA-A, -B and -DRB1 allelic distributions were determined in 104 unrelated healthy Uyghur individuals and haplotypic frequencies and linkage disequilibrium parameters for HLA loci were estimated using the maximum-likelihood method. A total of 35 HLA-A, 51 HLA-B and 33 HLA-DRB1 alleles were identified at the four-digit level in the population. High frequency alleles were HLA-A*1101 (13.46%), A*0201 (12.50%), A*0301 (10.10%); HLA-B*5101(8.17%), B*3501(6.73%), B*5001 (6.25%); HLA-DRB1*0701 (16.35%), DRB1*1501 (8.65%) and DRB1*0301 (7.69%). The two-locus haplotypes at the highest frequency were HLA-A*3001-B*1302 (2.88%), A*2402-B*5101 (2.86%); HLA-B*5001-DRB1*0701 (4.14%) and B*0702-DRB1*1501 (3.37%). The three-locus haplotype at the highest frequency was HLA-A*3001-B*1302-DRB1*0701(2.40%). Significantly high linkage disequilibrium was observed in six two-locus haplotypes, with their corresponding relative linkage disequilibrium parameters equal to 1. Neighbor-joining phylogenetic tree between the Uyghur group and other previously reported populations was constructed on the basis of standard genetic distances among the populations calculated using the four-digit sequence-level allelic frequencies at HLA-A, HLA-B and HLA-DRB1 loci. The phylogenetic analyses reveal that the Uyghur group belongs to the northwestern Chinese populations and is most closely related to the Xibe group, and then to Kirgiz, Hui, Mongolian and Northern Han.; Conclusions/Significance: The present findings could be useful to elucidate the genetic background of the population and to provide valuable data for HLA matching in clinical bone marrow transplantation, HLA-linked disease-association studies, population genetics, human identification and paternity tests in forensic sciences.
Citation:
PLoS One. 2010 Nov 4; 5(11):e13458
Issue Date:
4-Nov-2010
URI:
http://hdl.handle.net/10675.2/607
DOI:
10.1371/journal.pone.0013458
PubMed ID:
21079793
PubMed Central ID:
PMC2973946
Type:
Article
ISSN:
1932-6203
Appears in Collections:
Vascular Biology Center: Faculty Research and Publication

Full metadata record

DC FieldValue Language
dc.contributor.authorDeng, Ya-jun-
dc.contributor.authorYe, Shi-hui-
dc.contributor.authorYan, Jiang-wei-
dc.contributor.authorYang, Guang-
dc.contributor.authorWang, Hong-dan-
dc.contributor.authorQin, Hai-xia-
dc.contributor.authorHuang, Qi-zhao-
dc.contributor.authorZhang, Jing-Jing-
dc.contributor.authorShen, Chun-meien_US
dc.contributor.authorZhu, Bo-fengen_US
dc.date.accessioned2012-10-26T16:26:51Z-
dc.date.available2012-10-26T16:26:51Z-
dc.date.issued2010-11-04en_US
dc.identifier.citationPLoS One. 2010 Nov 4; 5(11):e13458en_US
dc.identifier.issn1932-6203en_US
dc.identifier.pmid21079793en_US
dc.identifier.doi10.1371/journal.pone.0013458en_US
dc.identifier.urihttp://hdl.handle.net/10675.2/607-
dc.description.abstractBackground: Previous studies indicate that the frequency distributions of HLA alleles and haplotypes vary from one ethnic group to another or between the members of the same ethnic group living in different geographic areas. It is necessary and meaningful to study the high-resolution allelic and haplotypic distributions of HLA loci in different groups.en_US
dc.description.abstractMethodology/Principal Findings: High-resolution HLA typing for the Uyghur ethnic minority group using polymerase chain reaction-sequence-based-typing method was first reported. HLA-A, -B and -DRB1 allelic distributions were determined in 104 unrelated healthy Uyghur individuals and haplotypic frequencies and linkage disequilibrium parameters for HLA loci were estimated using the maximum-likelihood method. A total of 35 HLA-A, 51 HLA-B and 33 HLA-DRB1 alleles were identified at the four-digit level in the population. High frequency alleles were HLA-A*1101 (13.46%), A*0201 (12.50%), A*0301 (10.10%); HLA-B*5101(8.17%), B*3501(6.73%), B*5001 (6.25%); HLA-DRB1*0701 (16.35%), DRB1*1501 (8.65%) and DRB1*0301 (7.69%). The two-locus haplotypes at the highest frequency were HLA-A*3001-B*1302 (2.88%), A*2402-B*5101 (2.86%); HLA-B*5001-DRB1*0701 (4.14%) and B*0702-DRB1*1501 (3.37%). The three-locus haplotype at the highest frequency was HLA-A*3001-B*1302-DRB1*0701(2.40%). Significantly high linkage disequilibrium was observed in six two-locus haplotypes, with their corresponding relative linkage disequilibrium parameters equal to 1. Neighbor-joining phylogenetic tree between the Uyghur group and other previously reported populations was constructed on the basis of standard genetic distances among the populations calculated using the four-digit sequence-level allelic frequencies at HLA-A, HLA-B and HLA-DRB1 loci. The phylogenetic analyses reveal that the Uyghur group belongs to the northwestern Chinese populations and is most closely related to the Xibe group, and then to Kirgiz, Hui, Mongolian and Northern Han.en_US
dc.description.abstractConclusions/Significance: The present findings could be useful to elucidate the genetic background of the population and to provide valuable data for HLA matching in clinical bone marrow transplantation, HLA-linked disease-association studies, population genetics, human identification and paternity tests in forensic sciences.en_US
dc.rightsShen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.subjectResearch Articleen_US
dc.subjectGenetics and Genomics/Population Geneticsen_US
dc.subjectImmunology/Genetics of the Immune Systemen_US
dc.subjectEvolutionary Biology/Human Evolutionen_US
dc.subject.meshAllelesen_US
dc.subject.meshAsian Continental Ancestry Groupen_US
dc.subject.meshChinaen_US
dc.subject.meshGene Frequencyen_US
dc.subject.meshGenetic Variationen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHLA-A Antigensen_US
dc.subject.meshHLA-B Antigensen_US
dc.subject.meshHLA-DR Antigensen_US
dc.subject.meshHLA-DRB1 Chainsen_US
dc.subject.meshHaplotypesen_US
dc.subject.meshHumansen_US
dc.subject.meshLinkage Disequilibriumen_US
dc.subject.meshPhylogenyen_US
dc.subject.meshPolymorphism, Geneticen_US
dc.titleAllele Polymorphism and Haplotype Diversity of HLA-A, -B and -DRB1 Loci in Sequence-Based Typing for Chinese Uyghur Ethnic Groupen_US
dc.typeArticleen_US
dc.identifier.pmcidPMC2973946en_US
dc.contributor.corporatenameVascular Biology Center-
dc.contributor.corporatenameInstitute of Molecular Medicine and Genetics-

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