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Goeury T, Creary LE, Fernandez-Vina MA, Tiercy JM, Nunes JM, Sanchez-Mazas A. Mandenka from Senegal: Next Generation Sequencing typings reveal very high frequencies of particular HLA class II alleles and haplotypes. HLA 2019; 91:148-150. [PMID: 29280562 DOI: 10.1111/tan.13197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/19/2017] [Indexed: 01/10/2023]
Affiliation(s)
- T Goeury
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - L E Creary
- Stanford University, School of Medicine, Palo Alto, California
| | | | - J-M Tiercy
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Geneva University Hospital, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - J M Nunes
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - A Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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2
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Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
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Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
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3
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Garcia-Ispierto I, De Rensis F, Pérez-Salas JA, Nunes JM, Pradés B, Serrano-Pérez B, López-Gatius F. The GnRH analogue dephereline given in a fixed-time AI protocol improves ovulation and embryo survival in dairy cows. Res Vet Sci 2018; 122:170-174. [PMID: 30513410 DOI: 10.1016/j.rvsc.2018.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
This study compares the fertility effects of inducing ovulation using the GnRH analogue, dephereline, versus natural GnRH at the end of a 5-day progesterone(P4)-based protocol for fixed-time artificial insemination (FTAI) in in heat-stressed and non-heat stressed lactating dairy cows. Cows were given GnRH (GnRH group, n = 369) or dephereline (DEPH group, n = 379) and were inseminated 14-20 h later. Dephereline treatment increased corpus luteum (CL) size on Day 7 post-AI compared with GnRH (P < .0001) while a one-mm increase in CL size was found to give rise to a 1.1-fold increase in the pregnancy rate at FTAI (P = .001). Based on odds ratios, the interaction between treatment and heat stress had a significant effect on the ovulation failure rate (P < .01). This meant that relative to non-heat-stressed GnRH-treated cows, ovulation failure was 2.9 times more likely in heat-stressed GnRH-treated cows (P = .001), 0.3 times less likely in non-heat-stressed DEPH-treated cows (P = .04) and was similar in heat-stressed DEPH-treated cows. Further, non-heat-stressed DEPH-treated cows were more likely to conceive by a factor of 1.6 than the remaining cows (P = .03). Finally, GnRH-treated multiparous cows were 9.9 times more likely to suffer pregnancy loss than the remaining cows (P = .03). Our results indicate that, compared to treatment with GnRH, dephereline reduced the risk of ovulation failure and consequently increased the pregnancy rate under heat stress conditions. In multiparous cows, dephereline treatment also reduced the negative age effect on pregnancy maintenance.
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Affiliation(s)
- I Garcia-Ispierto
- Department of Animal Science, University of Lleida, Spain; Agrotecnio Center, University of Lleida, Lleida, Spain
| | - F De Rensis
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | | | | | | | - B Serrano-Pérez
- Department of Animal Science, University of Lleida, Spain; Agrotecnio Center, University of Lleida, Lleida, Spain
| | - F López-Gatius
- Agrotecnio Center, University of Lleida, Lleida, Spain; Transfer in Bovine Reproduction SLu, Barbastro, Spain.
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4
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Sanchez-Mazas A, Nunes JM, Middleton D, Sauter J, Buhler S, McCabe A, Hofmann J, Baier DM, Schmidt AH, Nicoloso G, Andreani M, Grubic Z, Tiercy JM, Fleischhauer K. Common and well-documented HLA alleles over all of Europe and within European sub-regions: A catalogue from the European Federation for Immunogenetics. HLA 2018; 89:104-113. [PMID: 28102034 DOI: 10.1111/tan.12956] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND A catalogue of common and well-documented (CWD) human leukocyte antigen (HLA), previously established by the American Society for Histocompatibility and Immunogenetics (ASHI), is widely used as indicator for typing ambiguities to be resolved in tissue transplantation or for checking the universality of any HLA allele in the world. However, European population samples, which are characterized by a substantial level of genetic variation, are underrepresented in the ASHI catalogue. Therefore, the Population Genetics Working Group of the European Federation for Immunogenetics (EFI) has facilitated data collection for an European CWD catalogue. MATERIALS AND METHODS To this end, 2nd-field HLA-A, -B, -C,- DRB1,- DQA1,- DQB1 and -DPB1 data of 77 to 121 European population samples (21 571-3 966 984 individuals) from 3 large databases, HLA-net/Gene[VA], allelefrequencies.net and DKMS, were analysed. RESULTS The total number of CWD alleles is similar in the EFI (N = 1048) and ASHI (N = 1031) catalogues, but the former counts less common (N = 236 vs 377) and more well-documented (N = 812 vs 654) alleles than the latter, possibly reflecting differences in sample numbers and sizes. Interestingly, approximately half of the CWD alleles reported by EFI were not reported by ASHI and vice-versa, underlining the distinct features of the two catalogues. Also, although 78 common alleles are widely distributed across Europe, some alleles are only common within specific sub-regions, showing regional variability. CONCLUSION Although the definition of CWD alleles itself is affected by different parameters, calling for current updates of the list, the EFI CWD catalogue provides new insights into European population genetics and will be a very useful tool for tissue-typing laboratories in and beyond Europe.
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Affiliation(s)
- A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), Geneva, Switzerland.,Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Center (CMU), Geneva, Switzerland.,Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands
| | - D Middleton
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Transplant Immunology Laboratory, Royal Liverpool and Broadgreen University Hospital, Liverpool, UK
| | - J Sauter
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - S Buhler
- Laboratory of Anthropology, Genetics and Peopling history (AGP), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - A McCabe
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - J Hofmann
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - D M Baier
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - A H Schmidt
- DKMS, German Bone Marrow Center, Tübingen, Germany
| | - G Nicoloso
- Swiss Transfusion Swiss Red Cross (SRC)/Swiss Blood Stem Cells, Bern, Switzerland
| | - M Andreani
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Z Grubic
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Tissue Typing Center, University Hospital Center Zagreb, Zagreb, Croatia
| | - J-M Tiercy
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - K Fleischhauer
- Population Genetics Working Group of the European Federation for Immunogenetics (EFI), EFI Central Office, Leiden, The Netherlands.,Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
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5
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Černý V, Kulichová I, Poloni ES, Nunes JM, Pereira L, Mayor A, Sanchez-Mazas A. Genetic history of the African Sahelian populations. HLA 2018; 91:153-166. [DOI: 10.1111/tan.13189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/03/2017] [Indexed: 12/13/2022]
Affiliation(s)
- V. Černý
- Department of Anthropology, Faculty of Natural Sciences; Comenius University, Ilkovicova 6; 842 15 Bratislava Slovakia
| | - I. Kulichová
- Department of Anthropology and Human Genetics, Faculty of Science; Charles University in Prague; Prague Czech Republic
| | - E. S. Poloni
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3); Geneva Switzerland
| | - J. M. Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3); Geneva Switzerland
| | - L. Pereira
- Instituto de Investigação e Inovação em Saúde; Universidade do Porto (i3S); Porto Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto Portugal
| | - A. Mayor
- Laboratory of African Archaeology and Peopling History (APA), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
| | - A. Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP), Department of Genetics and Evolution, Anthropology Unit; University of Geneva; Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3); Geneva Switzerland
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6
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Boquett JA, Nunes JM, Buhler S, de Oliveira MZ, Jobim LF, Jobim M, Fagundes NJR, Schüler-Faccini L, Sanchez-Mazas A. The HLA-A, -B and -DRB1 polymorphism in a large dataset of South Brazil bone marrow donors from Rio Grande do Sul. HLA 2016; 89:29-38. [PMID: 27910249 DOI: 10.1111/tan.12933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/12/2016] [Accepted: 10/26/2016] [Indexed: 12/18/2022]
Abstract
Human leukocyte antigen (HLA) genes are very informative in population genetics studies and their variability has been widely used to reconstruct the history of geographic and/or demographic expansions of human populations. The characterization of HLA diversity at the population level is also fundamental in clinical studies, particularly for bone marrow transplantation programs. In this study, we investigated the HLA molecular variation in Rio Grande do Sul, South Brazil, in order to identify possible regional differences across this state. More than 97,000 bone marrow donors were typed at the HLA- A, -B and -DRB1 loci and analyzed by considering two kinds of subdivisions based on both self-identified ethnicity and place of residence: (a) the official geographic subdivision defined by the Brazilian Institute of Geography and Statistics and (b) known information about the colonization history of the state. HLA allele and haplotype frequencies were estimated and compared among the defined subgroups. The results indicate a lack of correlation between genetic variation and geography and thus no clear HLA genetic structure based on geographic criteria. On the other hand, major differences were observed regarding ethnicity. In addition, local populations from Rio Grande do Sul were found to be genetically similar to their corresponding parental European populations from Germany, Italy and Portugal, as documented by historical data. Overall, this study provides a thorough characterization of the HLA genetic variation in Rio Grande do Sul and a better understanding of its demographic history, being most useful for the development of more efficient strategies in bone marrow donors' recruitment.
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Affiliation(s)
- J A Boquett
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - S Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - M Z de Oliveira
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Advanced Visualization Laboratory (VIZLab), Universidade do Vale dos Sinos, São Leopoldo, Brazil
| | - L F Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - M Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - N J R Fagundes
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - L Schüler-Faccini
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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7
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Testi M, Battarra M, Lucarelli G, Isgro A, Morrone A, Akinyanju O, Wakama T, Nunes JM, Andreani M, Sanchez-Mazas A. HLA-A-B-C-DRB1-DQB1 phased haplotypes in 124 Nigerian families indicate extreme HLA diversity and low linkage disequilibrium in Central-West Africa. ACTA ACUST UNITED AC 2015; 86:285-92. [DOI: 10.1111/tan.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 06/18/2015] [Accepted: 07/20/2015] [Indexed: 12/01/2022]
Affiliation(s)
- M. Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - M. Battarra
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - G. Lucarelli
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - A. Isgro
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - A. Morrone
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | | | | | - J. M. Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit; University of Geneva; Geneva Switzerland
| | - M. Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Policlinic of the University of Tor Vergata; Rome Italy
| | - A. Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit; University of Geneva; Geneva Switzerland
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8
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Inotai D, Szilvasi A, Benko S, Boros-Major A, Illes Z, Bors A, Kiss KP, Rajczy K, Gelle-Hossó A, Buhler S, Nunes JM, Sanchez-Mazas A, Tordai A. HLA genetic diversity in Hungarians and Hungarian Gypsies: complementary differentiation patterns and demographic signals revealed by HLA-A, -B and -DRB1 in Central Europe. ACTA ACUST UNITED AC 2015; 86:115-21. [PMID: 26149581 DOI: 10.1111/tan.12600] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 06/02/2015] [Indexed: 11/30/2022]
Abstract
Systematic analyses of human leukocyte antigen (HLA) profiles in different populations may increase the efficiency of bone marrow donor selection and help reconstructing human peopling history. We typed HLA-A, -B, and -DRB1 allele groups in two bone marrow donor cohorts of 2402 Hungarians and 186 Hungarian Gypsies and compared them with several Central-European, Spanish Gypsy, and Indian populations. Our results indicate that different European Gypsy populations share a common origin but diverged genetically as a consequence of founder effect and rapid genetic drift, whereas other European populations are related genetically in relation to geography. This study also suggests that while HLA-A accurately depicts the effects of genetic drift, HLA-B, and -DRB1 conserve more signatures of ancient population relationships, as a result of balancing selection.
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Affiliation(s)
- D Inotai
- Laboratory of Transplantation Immunogenetics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - A Szilvasi
- Laboratory of Transplantation Immunogenetics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - S Benko
- Laboratory of Transplantation Immunogenetics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - A Boros-Major
- Laboratory of Transplantation Immunogenetics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - Z Illes
- Laboratory of Transplantation Immunogenetics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - A Bors
- Molecular Diagnostics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - K P Kiss
- Molecular Diagnostics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - K Rajczy
- Bone Marrow Donor Registry, Hungarian Blood Transfusion Service, Budapest, Hungary
| | - A Gelle-Hossó
- Bone Marrow Donor Registry, Hungarian Blood Transfusion Service, Budapest, Hungary
| | - S Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - A Tordai
- Laboratory of Transplantation Immunogenetics, Hungarian National Blood Transfusion Service, Budapest, Hungary.,Molecular Diagnostics, Hungarian National Blood Transfusion Service, Budapest, Hungary
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9
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Buhler S, Nunes JM, Sanchez-Mazas A, Richard L. HLA-A, B and DRB1 genetic heterogeneity in Quebec. Int J Immunogenet 2015; 42:69-77. [PMID: 25639978 DOI: 10.1111/iji.12177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/19/2014] [Accepted: 01/09/2015] [Indexed: 12/24/2022]
Abstract
Recent studies have shown that under specific conditions such as high sample sizes and Hardy-Weinberg equilibrium, bone marrow donor registry data can be used to describe HLA molecular variation across a specific geographic area, thus providing excellent data sets to infer human migrations history. The province of Quebec is known to have experienced a complex history of settlement, characterized by multiple migrations and demographic changes. We thus analysed the data of more than 13 000 unrelated individuals acting as volunteer bone marrow donors who were molecularly typed for HLA-A, B and DRB1 polymorphisms in the Héma-Quebec registry. HLA allelic and haplotypic frequencies were estimated and compared among regions. The results indicate that, despite an overall low genetic diversity in Quebec, genetic variation is correlated with geography, compatible with isolation-by-distance across the province. However, some localities also harbour contrasting genetic profiles, that is a highly diversified genetic pool in the two main urban centres (Montréal and Laval) and a more pronounced genetic divergence of two specific regions characterized by a peculiar peopling history (Saguenay-Lac-St-Jean and Gaspésie-Îles-De-La-Madeleine). In agreement with other independent molecular markers, the observations based on HLA data thus account for the main demographic mechanisms that shaped the genetic structure of the present day Quebecer population. In addition, the detailed analysis of the Héma-Quebec registry provides key genetic information on which an efficient bone marrow transplantation recruitment strategy can be settled.
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Affiliation(s)
- S Buhler
- Laboratory of Anthropology, Genetics and Peopling history (AGP lab), Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
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10
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Nunes JM, Buhler S, Roessli D, Sanchez-Mazas A. TheHLA-net GENE[RATE]pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas. ACTA ACUST UNITED AC 2014; 83:307-23. [DOI: 10.1111/tan.12356] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- J. M. Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution; Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva; Geneva Switzerland
| | - S. Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution; Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva; Geneva Switzerland
| | - D. Roessli
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution; Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva; Geneva Switzerland
| | - A. Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution; Anthropology Unit and Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva; Geneva Switzerland
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Nunes JM, Buhler S, Sanchez-Mazas A. NO to obsolete definitions: YES to blanks. ACTA ACUST UNITED AC 2014; 83:119-20. [PMID: 24397387 DOI: 10.1111/tan.12276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 11/28/2013] [Indexed: 11/29/2022]
Affiliation(s)
- J M Nunes
- Laboratory of Anthropology, Genetics and Peopling history (AGP lab), Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sanchez-Mazas A, Vidan-Jeras B, Nunes JM, Fischer G, Little AM, Bekmane U, Buhler S, Buus S, Claas FHJ, Dormoy A, Dubois V, Eglite E, Eliaou JF, Gonzalez-Galarza F, Grubic Z, Ivanova M, Lie B, Ligeiro D, Lokki ML, da Silva BM, Martorell J, Mendonça D, Middleton D, Voniatis DP, Papasteriades C, Poli F, Riccio ME, Vlachou MS, Sulcebe G, Tonks S, Nevessignsky MT, Vangenot C, van Walraven AM, Tiercy JM. Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations. Int J Immunogenet 2012; 39:459-72; quiz 473-6. [PMID: 22533604 PMCID: PMC3533781 DOI: 10.1111/j.1744-313x.2012.01113.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
HLA-NET (a European COST Action) aims at networking researchers working in bone marrow transplantation, epidemiology and population genetics to improve the molecular characterization of the HLA genetic diversity of human populations, with an expected strong impact on both public health and fundamental research. Such improvements involve finding consensual strategies to characterize human populations and samples and report HLA molecular typings and ambiguities; proposing user-friendly access to databases and computer tools and defining minimal requirements related to ethical aspects. The overall outcome is the provision of population genetic characterizations and comparisons in a standard way by all interested laboratories. This article reports the recommendations of four working groups (WG1-4) of the HLA-NET network at the mid-term of its activities. WG1 (Population definitions and sampling strategies for population genetics’ analyses) recommends avoiding outdated racial classifications and population names (e.g. ‘Caucasian’) and using instead geographic and/or cultural (e.g. linguistic) criteria to describe human populations (e.g. ‘pan-European’). A standard ‘HLA-NET POPULATION DATA QUESTIONNAIRE’ has been finalized and is available for the whole HLA community. WG2 (HLA typing standards for population genetics analyses) recommends retaining maximal information when reporting HLA typing results. Rather than using the National Marrow Donor Program coding system, all ambiguities should be provided by listing all allele pairs required to explain each genotype, according to the formats proposed in ‘HLA-NET GUIDELINES FOR REPORTING HLA TYPINGS’. The group also suggests taking into account a preliminary list of alleles defined by polymorphisms outside the peptide-binding sites that may affect population genetic statistics because of significant frequencies. WG3 (Bioinformatic strategies for HLA population data storage and analysis) recommends the use of programs capable of dealing with ambiguous data, such as the ‘gene[rate]’ computer tools to estimate frequencies, test for Hardy–Weinberg equilibrium and selective neutrality on data containing any number and kind of ambiguities. WG4 (Ethical issues) proposes to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. All HLA-NET guidelines and tools are available through its website http://hla-net.eu.
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Nunes JM, Riccio ME, Buhler S, Di D, Currat M, Ries F, Almada AJ, Benhamamouch S, Benitez O, Canossi A, Fadhlaoui-Zid K, Fischer G, Kervaire B, Loiseau P, de Oliveira DCM, Papasteriades C, Piancatelli D, Rahal M, Richard L, Romero M, Rousseau J, Spiroski M, Sulcebe G, Middleton D, Tiercy JM, Sanchez-Mazas A. Analysis of the HLA population data (AHPD) submitted to the 15th International Histocompatibility/Immunogenetics Workshop by using the Gene[rate] computer tools accommodating ambiguous data (AHPD project report). ACTA ACUST UNITED AC 2010; 76:18-30. [PMID: 20331842 DOI: 10.1111/j.1399-0039.2010.01469.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
During the 15th International Histocompatibility and Immunogenetics Workshop (IHIWS), 14 human leukocyte antigen (HLA) laboratories participated in the Analysis of HLA Population Data (AHPD) project where 18 new population samples were analyzed statistically and compared with data available from previous workshops. To that aim, an original methodology was developed and used (i) to estimate frequencies by taking into account ambiguous genotypic data, (ii) to test for Hardy-Weinberg equilibrium (HWE) by using a nested likelihood ratio test involving a parameter accounting for HWE deviations, (iii) to test for selective neutrality by using a resampling algorithm, and (iv) to provide explicit graphical representations including allele frequencies and basic statistics for each series of data. A total of 66 data series (1-7 loci per population) were analyzed with this standard approach. Frequency estimates were compliant with HWE in all but one population of mixed stem cell donors. Neutrality testing confirmed the observation of heterozygote excess at all HLA loci, although a significant deviation was established in only a few cases. Population comparisons showed that HLA genetic patterns were mostly shaped by geographic and/or linguistic differentiations in Africa and Europe, but not in America where both genetic drift in isolated populations and gene flow in admixed populations led to a more complex genetic structure. Overall, a fruitful collaboration between HLA typing laboratories and population geneticists allowed finding useful solutions to the problem of estimating gene frequencies and testing basic population diversity statistics on highly complex HLA data (high numbers of alleles and ambiguities), with promising applications in either anthropological, epidemiological, or transplantation studies.
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Affiliation(s)
- J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), University of Geneva, Geneva, Switzerland
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Affiliation(s)
- R A Cabrera
- Serviços de Patologia Morfológica e Pediatria, Instituto Português de Oncologia de Francisco Gentil. CROL, SA, Lisbon, Portugal.
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Abstract
The authors discuss procurement and provision of pharmaceutical products from the perspective of supply management in the public health sector, focusing on two main aspects: quality and cost. The article analyzes issues to be considered by buyers when evaluating drug quality, especially formulation stability, bioequivalence, and the role of generics. Also discussed are factors involving costs and cost management in relation to technological innovations and consumer demands. New alternatives and suggestions are examined and presented for procurement of high-quality, cost-effective drug products.
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Affiliation(s)
- V L Luiza
- Serviço de Farmácia, Hospital Evandro Chagas, Fundação Oswaldo Cruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro, RJ 21045-900, Brasil.
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Porto MT, Ferreira F, Borralho J, Sobrinho L, Pais E, Branco H, Nunes JM, Martins B. Thyroid disease and histocompatibility antigens. Hum Immunol 1996. [DOI: 10.1016/0198-8859(96)84855-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Serras AC, Ricardo JA, Liberato MA, Nunes JM, Barata AM, Arruda AC. [A case of digestive hemorrhage caused by Whipple's disease]. ACTA MEDICA PORT 1984; 5:323-5. [PMID: 6084946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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da Silva Horta J, Nunes JM. Historadiographies and autoradiographies form pieces of organs of people injected systemically with thorotrast. RISO Rep 1973:259-66. [PMID: 4549664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
Terrinha, António M. (National Laboratory for Veterinary Research, Lisbon, Portugal), José D. Vigário, José L. Nunes Petisca, J. Moura Nunes, and Armando L. Bastos. Autoradiographic study on sheeppox virus infection. J. Bacteriol. 90:1703-1709. 1965.-An autoradiographic study of sheep embryo cell cultures infected with sheeppox virus showed that viral deoxyribonucleic acid (DNA) synthesis starts at 10 to 11 hr after infection. The number of cells which supported viral DNA synthesis increased until 22 to 23 hr. The extent of cytoplasmic continuity between cells might permit the cell-to-cell transfer of mature virus or perhaps viral DNA. There is evidence of an inhibitory action on cellular DNA synthesis in cells which supported viral DNA synthesis, but, in all cellular populations infected, a small proportion of cells was encountered which supported viral DNA synthesis in compartment S. No evidence for cellular division of sheeppox virus-infected cells has been found. Enzymatic digestion by deoxyribonuclease combined with autoradiography provided an indirect demonstration of the time at which the first viral structural proteins were found to be synthesized, that is, 18 hr after infection. A progressive increase in synthesis of viral structural proteins was demonstrated. Virus maturation occurred within the cells in the cytoplasm, predominantly in the same sites as viral DNA synthesis.
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