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Fan B, Huang X, Zhang X, Huang L, Yang Z, Ma S, Chu J, Huang K, Weng Y, Zhang L, Lin K, Sun H. Comprehensive research on the distribution of HLA-DRB1 in Chinese populations. HLA 2023; 101:239-248. [PMID: 36479840 DOI: 10.1111/tan.14923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/27/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
By presenting antigen peptides, HLA-DRB1 plays an important role in the immune system. However, the allele frequency of HLA-DRB1 exon 2 across China has not been comprehensively studied, especially in minority populations. We sampled 3757 individuals from 59 population. The HLA-DRB1 region from 212 to 463 bp (NM_002124.4 exon 2) in each population was sequenced by Sanger sequencing and genotyped via SBTengine® software, and the allele frequency was calculated by GenAlEx 6.5. Eighty-two DRB1 alleles were identified. The expected heterozygosity of DRB1 was lower in the south than in the north, which was inconsistent with the Y chromosome and mitochondrial DNA results. The Mantel test and nonparametric correlation analysis showed that the correlations of the genetic distance with geographical distance and of DRB1 allele frequencies with latitude weakened after the southern and northern groups were considered separately. Principal coordinate analysis showed that populations speaking the same languages were not codistributed. Compared with other genetic markers, the distribution of DRB1 seems less affected by geographic distance and ethnic origin. Local factors such as gene flow with neighbouring populations, geographic isolation or natural selection are important forces shaping the DRB1 gene pool of local populations.
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Affiliation(s)
- Baitong Fan
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Xiaoqin Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Xiaochao Zhang
- Pharmaceutical College & Key Laboratory of Pharmacology for Natural Products of Yunnan Province, Kunming Medical University, Kunming, China
| | - Lifan Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Shaohui Ma
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jiayou Chu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Kai Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yuting Weng
- The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lin Zhang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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2
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Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R. An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 2023; 14:866407. [PMID: 37035735 PMCID: PMC10076764 DOI: 10.3389/fgene.2023.866407] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
HLA frequencies show widespread variation across human populations. Demographic factors as well as selection are thought to have shaped HLA variation across continents. In this study, a worldwide comparison of HLA class I and class II diversity was carried out. Multidimensional scaling techniques were applied to 50 HLA-A and HLA-B (class I) as well as 13 HLA-DRB1 (class II) first-field frequencies in 200 populations from all continents. Our results confirm a strong effect of geography on the distribution of HLA class I allele groups, with principal coordinates analysis closely resembling geographical location of populations, especially those of Africa-Eurasia. Conversely, class II frequencies stratify populations along a continuum of differentiation less clearly correlated to actual geographic location. Double clustering analysis revealed finer intra-continental sub-clusters (e.g., Northern and Western Europe vs. South East Europe, North Africa and Southwest Asia; South and East Africa vs. West Africa), and HLA allele group patterns characteristic of these clusters. Ancient (Austronesian expansion) and more recent (Romani people in Europe) migrations, as well as extreme differentiation (Taiwan indigenous peoples, Native Americans), and interregional gene flow (Sámi, Egyptians) are also reflected by the results. Barrier analysis comparing DST and geographic location identified genetic discontinuities caused by natural barriers or human behavior explaining inter and intra-continental HLA borders for class I and class II. Overall, a progressive reduction in HLA diversity from African to Oceanian and Native American populations is noted. This analysis of HLA frequencies in a unique set of worldwide populations confirms previous findings on the remarkable similarity of class I frequencies to geography, but also shows a more complex development for class II, with implications for both human evolutionary studies and biomedical research.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
- *Correspondence: Esteban Arrieta-Bolaños,
| | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
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3
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Cun Y, Shi L, Kulski JK, Liu S, Yang J, Tao Y, Zhang X, Shi L, Yao Y. Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China. Front Genet 2021; 12:636236. [PMID: 34305999 PMCID: PMC8292818 DOI: 10.3389/fgene.2021.636236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/08/2021] [Indexed: 01/11/2023] Open
Abstract
The analysis of polymorphic variations in the human major histocompatibility complex (MHC) class II genomic region on the short-arm of chromosome 6 is a scientific enquiry to better understand the diversity in population structure and the effects of evolutionary processes such as recombination, mutation, genetic drift, demographic history, and natural selection. In order to investigate associations between the polymorphisms of HLA-DRB1 gene and recent Alu insertions (POALINs) in the HLA class II region, we genotyped HLA-DRB1 and five Alu loci (AluDPB2, AluDQA2, AluDQA1, AluDRB1, AluORF10), and determined their allele frequencies and haplotypic associations in 12 minority ethnic populations in China. There were 42 different HLA-DRB1 alleles for ethnic Chinese ranging from 12 alleles in the Jinuo to 28 in the Yugur with only DRB1∗08:03, DRB1∗09:01, DRB1∗12:02, DRB1∗14:01, DRB1∗15:01, and DRB1∗15:02 present in all ethnic groups. The POALINs varied in frequency between 0.279 and 0.514 for AluDPB2, 0 and 0.127 for AluDQA2, 0.777 and 0.995 for AluDQA1, 0.1 and 0.455 for AluDRB1 and 0.084 and 0.368 for AluORF10. By comparing the data of the five-loci POALIN in 13 Chinese ethnic populations (including Han-Yunnan published data) against Japanese and Caucasian published data, marked differences were observed between the populations at the allelic or haplotypic levels. Five POALIN loci were in significant linkage disequilibrium with HLA-DRB1 in different populations and AluDQA1 had the highest percentage association with most of the HLA-DRB1 alleles, whereas the nearby AluDRB1 indel was strongly haplotypic for only DRB1∗01, DRB1∗10, DRB1∗15 and DRB1∗16. There were 30 five-locus POALIN haplotypes inferred in all populations with H5 (no Alu insertions except for AluDQA1) and H21 (only AluDPB2 and AluDQA1 insertions) as the two predominant haplotypes. Neighbor joining trees and principal component analyses of the Alu and HLA-DRB1 polymorphisms showed that genetic diversity of these genomic markers is associated strongly with the population characteristics of language family, migration and sociality. This comparative study of HLA-DRB1 alleles and multilocus, lineage POALIN frequencies of Chinese ethnic populations confirmed that POALINs whether investigated alone or together with the HLA class II alleles are informative genetic and evolutionary markers for the identification of allele and haplotype lineages and genetic variations within the same and/or different populations.
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Affiliation(s)
- Yina Cun
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Lei Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jerzy K Kulski
- Faculty of Health and Medical Sciences, University of Western Australia Medical School, Crawley, WA, Australia
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jia Yang
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yufen Tao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Xinwen Zhang
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Li Shi
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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4
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Ahmed AF, Sukasem C, Sabbah MA, Musa NF, Mohamed Noor DA, Daud NAA. Genetic Determinants in HLA and Cytochrome P450 Genes in the Risk of Aromatic Antiepileptic-Induced Severe Cutaneous Adverse Reactions. J Pers Med 2021; 11:383. [PMID: 34067134 PMCID: PMC8150699 DOI: 10.3390/jpm11050383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Adverse drug reaction (ADR) is a pressing health problem, and one of the main reasons for treatment failure with antiepileptic drugs. This has become apparent in the event of severe cutaneous adverse reactions (SCARs), which can be life-threatening. In this review, four hypotheses were identified to describe how the immune system is triggered in the development of SCARs, which predominantly involve the human leukocyte antigen (HLA) proteins. Several genetic variations in HLA genes have been shown to be strongly associated with the susceptibility to developing SCARs when prescribed carbamazepine or phenytoin. These genetic variations were also shown to be prevalent in certain populations. Apart from the HLA genes, other genes proposed to affect the risk of SCARs are genes encoding for CYP450 drug-metabolising enzymes, which are involved in the pharmacokinetics of offending drugs. Genetic variants in CYP2C9 and CYPC19 enzymes were also suggested to modulate the risk of SCARs in some populations. This review summarizes the literature on the manifestation and aetiology of antiepileptic-induced SCARs, updates on pharmacogenetic markers associated with this reaction and the implementation of pre-emptive testing as a preventive strategy for SCARs.
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Affiliation(s)
- Ali Fadhel Ahmed
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
| | - Chonlaphat Sukasem
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok 10400, Thailand
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) Research Group, Chulalongkorn University, Bangkok 10330, Thailand
- Advanced Research and Development Laboratory, Bumrungrad International Hospital, Bangkok 10110, Thailand
| | - Majeed Arsheed Sabbah
- Forensic DNA for Research and Training Centre, Alnahrain University, Baghdad 64074, Iraq;
| | - Nur Fadhlina Musa
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
| | - Dzul Azri Mohamed Noor
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
| | - Nur Aizati Athirah Daud
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia or (A.F.A.); (D.A.M.N.)
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kota Bharu 16150, Malaysia;
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5
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Association of HLA-DRB1*04:05 allele with drug-induced interstitial lung disease in Japanese population. THE PHARMACOGENOMICS JOURNAL 2020; 20:823-830. [PMID: 32467566 DOI: 10.1038/s41397-020-0172-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 12/23/2022]
Abstract
Drug-induced interstitial lung disease (DILD) is a life-threatening adverse reaction. The Japanese population is more susceptible to DILD as compared with other populations, suggesting its pathogenesis could vary depending on ethnic genetic background. We conducted case-control studies to elucidate the association between DILD and HLA alleles in the Japanese. The 177 clinically diagnosed DILD patients and 3002 healthy controls for exploration and 55 DILD patients and 201 healthy controls for validation were genotyped for four HLA genes. HLA-DRB1*04:05 was significantly associated with DILD (corrected p = 0.014); this was also validated in the other set of patients/controls. Chemical drugs other than protein therapeutics showed this association (p = 1.7 × 10-4) . The Japanese population showed a higher HLA-DRB1*04:05 frequency than most other populations. In conclusion, HLA-DRB1*04:05 could be associated with DILD susceptibility in Japanese individuals, and its high general frequency may explain the high reported incidence of DILD in Japanese.
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6
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Sanchez-Mazas A, Nunes JM. Does NGS typing highlight our understanding of HLA population diversity? Hum Immunol 2019; 80:62-66. [DOI: 10.1016/j.humimm.2018.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/08/2023]
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7
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Re-dating Zhoukoudian Upper Cave, northern China and its regional significance. J Hum Evol 2018; 121:170-177. [DOI: 10.1016/j.jhevol.2018.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/29/2023]
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8
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9
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Bae CJ, Douka K, Petraglia MD. Human Colonization of Asia in the Late Pleistocene. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694420] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Sanchez-Mazas A, Černý V, Di D, Buhler S, Podgorná E, Chevallier E, Brunet L, Weber S, Kervaire B, Testi M, Andreani M, Tiercy JM, Villard J, Nunes JM. The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection. Mol Ecol 2017; 26:6238-6252. [PMID: 28950417 DOI: 10.1111/mec.14366] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/11/2017] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA) genes play a key role in the immune response to infectious diseases, some of which are highly prevalent in specific environments, like malaria in sub-Saharan Africa. Former case-control studies showed that one particular HLA-B allele, B*53, was associated with malaria protection in Gambia, but this hypothesis was not tested so far within a population genetics framework. In this study, our objective was to assess whether pathogen-driven selection associated with malaria contributed to shape the HLA-B genetic landscape of Africa. To that aim, we first typed the HLA-A and -B loci in 484 individuals from 11 populations living in different environments across the Sahel, and we analysed these data together with those available for 29 other populations using several approaches including linear modelling on various genetic, geographic and environmental parameters. In addition to relevant signatures of populations' demography and migrations history in the genetic differentiation patterns of both HLA-A and -B loci, we found that the frequencies of three HLA alleles, B*53, B*78 and A*74, were significantly associated with Plasmodium falciparum malaria prevalence, suggesting their increase through pathogen-driven selection in malaria-endemic environments. The two HLA-B alleles were further identified, by high-throughput sequencing, as B*53:01:01 (in putative linkage disequilibrium with one HLA-C allele, C*04:01:01:01) and B*78:01 in all but one individuals tested, making them appropriate candidates to malaria protection. These results highlight the role of environmental factors in the evolution of the HLA polymorphism and open key perspectives for functional studies focusing on HLA peptide-binding properties.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Viktor Černý
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Da Di
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Stéphane Buhler
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Eliška Podgorná
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Elodie Chevallier
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Lydie Brunet
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Stephan Weber
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Barbara Kervaire
- Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Jean-Marie Tiercy
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Jean Villard
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - José Manuel Nunes
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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11
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Kongmaroeng C, Romphruk A, Puapairoj C, Leelayuwat C, Kulski JK, Inoko H, Dunn DS, Romphruk AV. HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand. ACTA ACUST UNITED AC 2016; 86:199-204. [PMID: 26265055 DOI: 10.1111/tan.12637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/02/2015] [Accepted: 07/14/2015] [Indexed: 11/28/2022]
Abstract
This is the first report on human leukocyte antigen (HLA) allele and haplotype frequencies at three class I loci and two class II loci in unrelated healthy individuals from two ethnic groups, 170 Burmese and 200 Karen, originally from Burma (Myanmar), but sampled while residing in Thailand. Overall, the HLA allele and haplotype frequencies detected by polymerase chain reaction sequence-specific primer (PCR-SSP) at five loci (A, B, C, DRB1 and DRQB1) at low resolution showed distinct differences between the Burmese and Karen. In Burmese, five HLA-B*15 haplotypes with different HLA-A and HLA-DR/DQ combinations were detected with three of these not previously reported in other Asian populations. The data are important in the fields of anthropology, transplantation and disease-association studies.
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Affiliation(s)
- C Kongmaroeng
- Department of Blood Bank, Faculty of Medical Technology, Huachiew Chalermprakiet University, Samut Prakarn, Thailand
| | - A Romphruk
- Department of Clinical Immunology and Transfusion Sciences, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - C Puapairoj
- Blood Transfusion Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - C Leelayuwat
- Department of Clinical Immunology and Transfusion Sciences, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - J K Kulski
- Centre for Forensic Science, The University of Western Australia, Nedlands, Australia
| | - H Inoko
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Tokyo, Japan
| | - D S Dunn
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - A V Romphruk
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Blood Transfusion Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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12
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Nunes JM. Using uniformat and gene[rate] to Analyze Data with Ambiguities in Population Genetics. Evol Bioinform Online 2016; 11:19-26. [PMID: 26917942 PMCID: PMC4762493 DOI: 10.4137/ebo.s32415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/13/2023] Open
Abstract
Some genetic systems frequently present ambiguous data that cannot be straightforwardly analyzed with common methods of population genetics. Two possibilities arise to analyze such data: one is the arbitrary simplification of the data and the other is the development of methods adapted to such ambiguous data. In this article, we present an attempt at such a development, the uniformat grammar and The gene[rate] tools, highlighting the specific aspects and the adaptations required to analyze ambiguous nominal data in population genetics.
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Affiliation(s)
- José Manuel Nunes
- Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
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13
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Poh SS, Chua MLK, Wee JTS. Carcinogenesis of nasopharyngeal carcinoma: an alternate hypothetical mechanism. CHINESE JOURNAL OF CANCER 2016; 35:9. [PMID: 26738743 PMCID: PMC4704291 DOI: 10.1186/s40880-015-0068-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/28/2015] [Indexed: 02/06/2023]
Abstract
Current proposed mechanisms implicate both early and latent Epstein-Barr virus (EBV) infection in the carcinogenic cascade, whereas epidemiological studies have always associated nasopharyngeal carcinoma (NPC) with early childhood EBV infection and with chronic ear, nose, and sinus conditions. Moreover, most patients with NPC present with IgA antibody titers to EBV capsid antigen (VCA-IgA), which can precede actual tumor presentation by several years. If early childhood EBV infection indeed constitutes a key event in NPC carcinogenesis, one would have to explain the inability to detect the virus in normal nasopharyngeal epithelium of patients at a high risk for EBV infection. It is perhaps possible that EBV resides within the salivary glands, instead of the epithelium, during latency. This claim is indirectly supported by observations that the East Asian phenotype shares the characteristics of an increased susceptibility to NPC and immature salivary gland morphogenesis, the latter of which is influenced by the association of salivary gland morphogenesis with an evolutionary variant of the human ectodysplasin receptor gene (EDAR), EDARV370A. Whether the immature salivary gland represents a more favorable nidus for EBV is uncertain, but in patients with infectious mononucleosis, EBV has been isolated in this anatomical organ. The presence of EBV-induced lymphoepitheliomas in the salivary glands and lungs further addresses the possibility of submucosal spread of the virus. Adding to the fact that the fossa of Rosen Müller contains a transformative zone active only in the first decade of life, one might be tempted to speculate the possibility of an alternative carcinogenic cascade for NPC that is perhaps not dissimilar to the model of human papillomavirus and cervical cancer.
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Affiliation(s)
- Sharon Shuxian Poh
- Division of Radiation Oncology, National Cancer Centre, 11 Hospital Drive, Singapore, 169610, Singapore.
| | - Melvin Lee Kiang Chua
- Division of Radiation Oncology, National Cancer Centre, 11 Hospital Drive, Singapore, 169610, Singapore.
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Joseph T S Wee
- Division of Radiation Oncology, National Cancer Centre, 11 Hospital Drive, Singapore, 169610, Singapore.
- Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
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14
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Tassi F, Ghirotto S, Mezzavilla M, Vilaça ST, De Santi L, Barbujani G. Early modern human dispersal from Africa: genomic evidence for multiple waves of migration. INVESTIGATIVE GENETICS 2015; 6:13. [PMID: 26550467 PMCID: PMC4636834 DOI: 10.1186/s13323-015-0030-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/27/2015] [Indexed: 12/22/2022]
Abstract
Background Anthropological and genetic data agree in indicating the African continent as the main place of origin for anatomically modern humans. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab Peninsula into southern Asia and Oceania, and later through a northern route crossing the Levant. Results Here, we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of either hybridization with archaic human forms in Australo-Melanesia or back migration from Europe into Africa. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0030-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Massimo Mezzavilla
- Institute for Maternal and Child Health-IRCCS "BurloGarofolo", University of Trieste, Trieste, Italy
| | - Sibelle Torres Vilaça
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy.,Present Address: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Lisa De Santi
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
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Di D, Sanchez-Mazas A, Currat M. Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia. BMC Evol Biol 2015; 15:240. [PMID: 26530905 PMCID: PMC4632674 DOI: 10.1186/s12862-015-0512-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recent genetic studies have suggested that the colonization of East Asia by modern humans was more complex than a single origin from the South, and that a genetic contribution via a Northern route was probably quite substantial. Results Here we use a spatially-explicit computer simulation approach to investigate the human migration hypotheses of this region based on one-route or two-route models. We test the likelihood of each scenario by using Human Leukocyte Antigen (HLA) − A, −B, and − DRB1 genetic data of East Asian populations, with both selective and demographic parameters considered. The posterior distribution of each parameter is estimated by an Approximate Bayesian Computation (ABC) approach. Conclusions Our results strongly support a model with two main routes of colonization of East Asia on both sides of the Himalayas, with distinct demographic histories in Northern and Southern populations, characterized by more isolation in the South. In East Asia, gene flow between populations originating from the two routes probably existed until a remote prehistoric period, explaining the continuous pattern of genetic variation currently observed along the latitude. A significant although dissimilar level of balancing selection acting on the three HLA loci is detected, but its effect on the local genetic patterns appears to be minor compared to those of past demographic events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0512-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Da Di
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, Geneva, CH-1211, Geneva 4, Switzerland.
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland.
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16
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Sun H, Yang Z, Lin K, Liu S, Huang K, Wang X, Chu J, Huang X. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China. PLoS One 2015; 10:e0134334. [PMID: 26230582 PMCID: PMC4521750 DOI: 10.1371/journal.pone.0134334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/08/2015] [Indexed: 01/18/2023] Open
Abstract
Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.
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Affiliation(s)
- Hao Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Zhaoqing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Keqin Lin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Kai Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiuyun Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Jiayou Chu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiaoqin Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- * E-mail:
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17
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Di D, Sanchez-Mazas A. HLA variation reveals genetic continuity rather than population group structure in East Asia. Immunogenetics 2014; 66:153-60. [PMID: 24449274 DOI: 10.1007/s00251-014-0757-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 01/07/2014] [Indexed: 01/15/2023]
Abstract
Genetic differences between Northeast Asian (NEA) and Southeast Asian (SEA) populations have been observed in numerous studies. At the among-population level, despite a clear north-south differentiation observed for many genetic markers, debates were led between abrupt differences and a continuous pattern. At the within-population level, whether NEA or SEA populations have higher genetic diversity is also highly controversial. In this study, we analyzed a large set of HLA data from East Asia in order to map the genetic variation among and within populations in this continent and to clarify the distribution pattern of HLA lineages and alleles. We observed a genetic differentiation between NEA and SEA populations following a continuous pattern from north to south, and we show a significant and continuous decrease of HLA diversity by the same direction. This continuity is shaped by clinal distributions of many HLA lineages and alleles with increasing or decreasing frequencies along the latitude. These results bring new evidence in favor of the "overlapping model" proposed previously for East Asian peopling history, whereby modern humans migrated eastward from western Eurasia via two independent routes along each side of the Himalayas and, later, overlapped in East Asia across open land areas. Our study strongly suggests that intensive gene flow between NEA and SEA populations occurred and shaped the latitude-related continuous pattern of genetic variation and the peculiar HLA lineage and allele distributions observed in this continent. Probably for a very long period, the exact duration of these events remains to be estimated.
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Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling History (AGP lab), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 12 rue Gustave-Revilliod, CH-1211, Geneva, Switzerland,
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18
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Correlation between the linguistic affinity and genetic diversity of Chinese ethnic groups. J Hum Genet 2013; 58:686-93. [DOI: 10.1038/jhg.2013.79] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/01/2013] [Accepted: 07/03/2013] [Indexed: 01/07/2023]
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19
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Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. PLoS One 2013; 8:e60793. [PMID: 23577161 PMCID: PMC3618337 DOI: 10.1371/journal.pone.0060793] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 03/03/2013] [Indexed: 01/11/2023] Open
Abstract
The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.
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20
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Riccio ME, Buhler S, Nunes JM, Vangenot C, Cuénod M, Currat M, Di D, Andreani M, Boldyreva M, Chambers G, Chernova M, Chiaroni J, Darke C, Di Cristofaro J, Dubois V, Dunn P, Edinur HA, Elamin N, Eliaou JF, Grubic Z, Jaatinen T, Kanga U, Kervaire B, Kolesar L, Kunachiwa W, Lokki ML, Mehra N, Nicoloso G, Paakkanen R, Voniatis DP, Papasteriades C, Poli F, Richard L, Romón Alonso I, Slavčev A, Sulcebe G, Suslova T, Testi M, Tiercy JM, Varnavidou A, Vidan-Jeras B, Wennerström A, Sanchez-Mazas A. 16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report). Int J Immunogenet 2012; 40:21-30. [PMID: 23280239 DOI: 10.1111/iji.12033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 01/05/2023]
Abstract
We present here the results of the Analysis of HLA Population Data (AHPD) project of the 16th International HLA and Immunogenetics Workshop (16IHIW) held in Liverpool in May-June 2012. Thanks to the collaboration of 25 laboratories from 18 different countries, HLA genotypic data for 59 new population samples (either well-defined populations or donor registry samples) were gathered and 55 were analysed statistically following HLA-NET recommendations. The new data included, among others, large sets of well-defined populations from north-east Europe and West Asia, as well as many donor registry data from European countries. The Gene[rate] computer tools were combined to create a Gene[rate] computer pipeline to automatically (i) estimate allele frequencies by an expectation-maximization algorithm accommodating ambiguities, (ii) estimate heterozygosity, (iii) test for Hardy-Weinberg equilibrium (HWE), (iv) test for selective neutrality, (v) generate frequency graphs and summary statistics for each sample at each locus and (vi) plot multidimensional scaling (MDS) analyses comparing the new samples with previous IHIW data. Intrapopulation analyses show that HWE is rarely rejected, while neutrality tests often indicate a significant excess of heterozygotes compared with neutral expectations. The comparison of the 16IHIW AHPD data with data collected during previous workshops (12th-15th) shows that geography is an excellent predictor of HLA genetic differentiations for HLA-A, -B and -DRB1 loci but not for HLA-DQ, whose patterns are probably more influenced by natural selection. In Europe, HLA genetic variation clearly follows a north to south-east axis despite a low level of differentiation between European, North African and West Asian populations. Pacific populations are genetically close to Austronesian-speaking South-East Asian and Taiwanese populations, in agreement with current theories on the peopling of Oceania. Thanks to this project, HLA genetic variation is more clearly defined worldwide and better interpreted in relation to human peopling history and HLA molecular evolution.
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Affiliation(s)
- M E Riccio
- Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, Geneva, Switzerland
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21
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Sanchez-Mazas A, Lemaître JF, Currat M. Distinct evolutionary strategies of human leucocyte antigen loci in pathogen-rich environments. Philos Trans R Soc Lond B Biol Sci 2012; 367:830-9. [PMID: 22312050 PMCID: PMC3267122 DOI: 10.1098/rstb.2011.0312] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human leucocyte antigen (HLA) loci have a complex evolution where both stochastic (e.g. genetic drift) and deterministic (natural selection) forces are involved. Owing to their extraordinary level of polymorphism, HLA genes are useful markers for reconstructing human settlement history. However, HLA variation often deviates significantly from neutral expectations towards an excess of genetic diversity. Because HLA molecules play a crucial role in immunity, this observation is generally explained by pathogen-driven-balancing selection (PDBS). In this study, we investigate the PDBS model by analysing HLA allelic diversity on a large database of 535 populations in relation to pathogen richness. Our results confirm that geographical distances are excellent predictors of HLA genetic differentiation worldwide. We also find a significant positive correlation between genetic diversity and pathogen richness at two HLA class I loci (HLA-A and -B), as predicted by PDBS, and a significant negative correlation at one HLA class II locus (HLA-DQB1). Although these effects are weak, as shown by a loss of significance when populations submitted to rapid genetic drift are removed from the analysis, the inverse relationship between genetic diversity and pathogen richness at different loci indicates that HLA genes have adopted distinct evolutionary strategies to provide immune protection in pathogen-rich environments.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, University of Geneva, Geneva 4, Switzerland.
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22
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Riccio ME, Nunes JM, Rahal M, Kervaire B, Tiercy JM, Sanchez-Mazas A. The Austroasiatic Munda population from India and Its enigmatic origin: a HLA diversity study. Hum Biol 2011; 83:405-35. [PMID: 21740156 DOI: 10.3378/027.083.0306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Austroasiatic linguistic family disputes its origin between two geographically distant regions of Asia, India, and Southeast Asia, respectively. As genetic studies based on classical and gender-specific genetic markers provided contradictory results to this debate thus far, we investigated the HLA diversity (HLA-A, -B, and -DRB1 loci) of an Austroasiatic Munda population from Northeast India and its relationships with other populations from India and Southeast Asia. Because molecular methods currently used to test HLA markers often provide ambiguous results due to the high complexity of this polymorphism, we applied two different techniques (reverse PCR-SSO typing on microbeads arrays based on Luminex technology, and PCR-SSP typing) to type the samples. After validating the resulting frequency distributions through the original statistical method described in our companion article ( Nunes et al. 2011 ), we compared the HLA genetic profile of the sampled Munda to those of other Asiatic populations, among which Dravidian and Indo-European-speakers from India and populations from East and Southeast Asia speaking languages belonging to different linguistic families. We showed that the Munda from Northeast India exhibit a peculiar genetic profile with a reduced level of HLA diversity compared to surrounding Indian populations. They also exhibit less diversity than Southeast Asian populations except at locus DRB1. Several analyses using genetic distances indicate that the Munda are much more closely related to populations from the Indian subcontinent than to Southeast Asian populations speaking languages of the same Austroasiatic linguistic family. On the other hand, they do not share a closer relationship with Dravidians compared with Indo-Europeans, thus arguing against the idea that the Munda share a common and ancient Indian origin with Dravidians. Our results do not favor either a scenario where the Munda would be representative of an ancestral Austroasiatic population giving rise to an eastward Austroasiatic expansion to Southeast Asia. Rather, their peculiar genetic profile is better explained by a decrease in genetic diversity through genetic drift from an ancestral population having a genetic profile similar to present-day Austroasiatic populations from Southeast Asia (thus suggesting a possible southeastern origin), followed by intensive gene flow with neighboring Indian populations. This conclusion is in agreement with archaeological and linguistic information. The history of the Austroasiatic family represents a fascinating example where complex interactions among culturally distinct human populations occurred in the past.
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Affiliation(s)
- Maria Eugenia Riccio
- Laboratory of Anthropology, Genetics, and Peopling History (AGP), Laboratory of Anthropology, Genetics, and Peopling History (AGP), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Switzerland.
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23
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Sanchez-Mazas A, Fernandez-Viña M, Middleton D, Hollenbach JA, Buhler S, Di D, Rajalingam R, Dugoujon JM, Mack SJ, Thorsby E. Immunogenetics as a tool in anthropological studies. Immunology 2011; 133:143-64. [PMID: 21480890 DOI: 10.1111/j.1365-2567.2011.03438.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The genes coding for the main molecules involved in the human immune system--immunoglobulins, human leucocyte antigen (HLA) molecules and killer-cell immunoglobulin-like receptors (KIR)--exhibit a very high level of polymorphism that reveals remarkable frequency variation in human populations. 'Genetic marker' (GM) allotypes located in the constant domains of IgG antibodies have been studied for over 40 years through serological typing, leading to the identification of a variety of GM haplotypes whose frequencies vary sharply from one geographic region to another. An impressive diversity of HLA alleles, which results in amino acid substitutions located in the antigen-binding region of HLA molecules, also varies greatly among populations. The KIR differ between individuals according to both gene content and allelic variation, and also display considerable population diversity. Whereas the molecular evolution of these polymorphisms has most likely been subject to natural selection, principally driven by host-pathogen interactions, their patterns of genetic variation worldwide show significant signals of human geographic expansion, demographic history and cultural diversification. As current developments in population genetic analysis and computer simulation improve our ability to discriminate among different--either stochastic or deterministic--forces acting on the genetic evolution of human populations, the study of these systems shows great promise for investigating both the peopling history of modern humans in the time since their common origin and human adaptation to past environmental (e.g. pathogenic) changes. Therefore, in addition to mitochondrial DNA, Y-chromosome, microsatellites, single nucleotide polymorphisms and other markers, immunogenetic polymorphisms represent essential and complementary tools for anthropological studies.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Department of Genetics and Evolution, Anthropology unit, Laboratory of Anthropology, Genetics and peopling history, University of Geneva, 12 rue Gustave-Revilliod, Geneva, Switzerland.
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24
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Buhler S, Sanchez-Mazas A. HLA DNA sequence variation among human populations: molecular signatures of demographic and selective events. PLoS One 2011; 6:e14643. [PMID: 21408106 PMCID: PMC3051395 DOI: 10.1371/journal.pone.0014643] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 12/21/2010] [Indexed: 12/14/2022] Open
Abstract
Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC) genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies.Our study shows that the global patterns of HLA nucleotide diversity among populations are significantly correlated to geography, although in some specific cases the molecular information reveals unexpected genetic relationships. At all loci except HLA-DPB1, populations have accumulated a high proportion of very divergent alleles, suggesting an advantage of heterozygotes expressing molecularly distant HLA molecules (asymmetric overdominant selection model). However, both different intensities of selection and unequal levels of gene conversion may explain the heterogeneous mismatch distributions observed among the loci. Also, distinctive patterns of sequence divergence observed at the HLA-DPB1 locus suggest current neutrality but old selective pressures on this gene. We conclude that HLA DNA sequences advantageously complement HLA allele frequencies as a source of data used to explore the genetic history of human populations, and that their analysis allows a more thorough investigation of human MHC molecular evolution.
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Affiliation(s)
- Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Anthropology, University of Geneva, Geneva, Switzerland.
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