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)
Identifieur interne : 000636 ( Main/Exploration ); précédent : 000635; suivant : 000637Analysis 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)
Auteurs : J. M. Nunes [Suisse] ; M. E. Riccio [Suisse] ; S. Buhler [Suisse] ; D. Di [Suisse] ; M. Currat [Suisse] ; F. Ries [Suisse] ; A. J. Almada [Brésil] ; S. Benhamamouch [Algérie] ; O. Benitez [France] ; A. Canossi [Italie] ; K. Fadhlaoui-Zid [Tunisie] ; G. Fischer [Autriche] ; B. Kervaire [Suisse] ; P. Loiseau [France] ; D. C. M. De Oliveira [Brésil] ; C. Papasteriades [Grèce] ; D. Piancatelli [Italie] ; M. Rahal [Suisse] ; L. Richard [Australie] ; M. Romero [Brésil] ; J. Rousseau [Afrique du Sud] ; M. Spiroski [Macédoine (pays)] ; G. Sulcebe [Albanie] ; D. Middleton [Royaume-Uni] ; J. Tiercy [Suisse] ; A. Sanchez-Mazas [Suisse]Source :
- Tissue Antigens [ 0001-2815 ] ; 2010-07.
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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.
Url:
DOI: 10.1111/j.1399-0039.2010.01469.x
Affiliations:
- Afrique du Sud, Albanie, Algérie, Australie, Autriche, Brésil, France, Grèce, Italie, Macédoine (pays), Royaume-Uni, Suisse, Tunisie
- Attique (région), Canton de Genève, Gouvernorat de Tunis, Vienne (Autriche), Wilaya d'Oran, État de Rio de Janeiro, Île-de-France
- Athènes, Genève, Oran, Paris, Rio de Janeiro, Tunis, Vienne (Autriche)
- Université de Genève
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Le document en format XML
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Ries</name><affiliation wicri:level="4"><country xml:lang="fr">Suisse</country><wicri:regionArea>Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), University of Geneva, Geneva</wicri:regionArea><orgName type="university">Université de Genève</orgName><placeName><settlement type="city">Genève</settlement><region nuts="3" type="region">Canton de Genève</region></placeName></affiliation></author><author><name sortKey="Almada, A J" sort="Almada, A J" uniqKey="Almada A" first="A. J." last="Almada">A. J. Almada</name><affiliation wicri:level="3"><country xml:lang="fr">Brésil</country><wicri:regionArea>INCA—National Institute of Cancer, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author><author><name sortKey="Benhamamouch, S" sort="Benhamamouch, S" uniqKey="Benhamamouch S" first="S." last="Benhamamouch">S. Benhamamouch</name><affiliation wicri:level="3"><country xml:lang="fr">Algérie</country><wicri:regionArea>Département de Biotechnologie, Faculté des Sciences, University of Oran, Oran</wicri:regionArea><placeName><settlement type="city">Oran</settlement><region nuts="2">Wilaya d'Oran</region></placeName></affiliation></author><author><name sortKey="Benitez, O" sort="Benitez, O" uniqKey="Benitez O" first="O." last="Benitez">O. Benitez</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d’Histocompatibilité et d’immunologie, Hôpital Saint Louis, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Canossi, A" sort="Canossi, A" uniqKey="Canossi A" first="A." last="Canossi">A. Canossi</name><affiliation wicri:level="1"><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto CNR Trapianti D’organo e l’Immunocitologia, L’Aquila</wicri:regionArea><wicri:noRegion>L’Aquila</wicri:noRegion></affiliation></author><author><name sortKey="Fadhlaoui Id, K" sort="Fadhlaoui Id, K" uniqKey="Fadhlaoui Id K" first="K." last="Fadhlaoui-Zid">K. Fadhlaoui-Zid</name><affiliation wicri:level="3"><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratoire de Génétique, Immunologie et Pathologies humaines, Faculté des Sciences de Tunis, Tunis</wicri:regionArea><placeName><settlement type="city">Tunis</settlement><region nuts="2">Gouvernorat de Tunis</region></placeName></affiliation></author><author><name sortKey="Fischer, G" sort="Fischer, G" uniqKey="Fischer G" first="G." last="Fischer">G. Fischer</name><affiliation wicri:level="3"><country xml:lang="fr">Autriche</country><wicri:regionArea>Department for Blood Group Serology, Medical University Vienna, Vienna</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation></author><author><name sortKey="Kervaire, B" sort="Kervaire, B" uniqKey="Kervaire B" first="B." last="Kervaire">B. Kervaire</name><affiliation wicri:level="1"><country xml:lang="fr">Suisse</country><wicri:regionArea>Transplantation Immunology Unit, National Reference Laboratory for Histocompatibility, University Hospital Geneva, Geneva</wicri:regionArea><wicri:noRegion>Geneva</wicri:noRegion></affiliation></author><author><name sortKey="Loiseau, P" sort="Loiseau, P" uniqKey="Loiseau P" first="P." last="Loiseau">P. Loiseau</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d’Histocompatibilité et d’immunologie, Hôpital Saint Louis, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="De Oliveira, D C M" sort="De Oliveira, D C M" uniqKey="De Oliveira D" first="D. C. M." last="De Oliveira">D. C. M. De Oliveira</name><affiliation wicri:level="3"><country xml:lang="fr">Brésil</country><wicri:regionArea>INCA—National Institute of Cancer, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author><author><name sortKey="Papasteriades, C" sort="Papasteriades, C" uniqKey="Papasteriades C" first="C." last="Papasteriades">C. Papasteriades</name><affiliation wicri:level="3"><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Immunology and Histocompatibility, ‘Evangelismos’ Hospital, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Piancatelli, D" sort="Piancatelli, D" uniqKey="Piancatelli D" first="D." last="Piancatelli">D. Piancatelli</name><affiliation wicri:level="1"><country xml:lang="fr">Italie</country><wicri:regionArea>CNR Institute for Organ Transplantation and Immunocytology, L’Aquila</wicri:regionArea><wicri:noRegion>L’Aquila</wicri:noRegion></affiliation></author><author><name sortKey="Rahal, M" sort="Rahal, M" uniqKey="Rahal M" first="M." last="Rahal">M. Rahal</name><affiliation wicri:level="1"><country xml:lang="fr">Suisse</country><wicri:regionArea>Transplantation Immunology Unit, National Reference Laboratory for Histocompatibility, University Hospital Geneva, Geneva</wicri:regionArea><wicri:noRegion>Geneva</wicri:noRegion></affiliation></author><author><name sortKey="Richard, L" sort="Richard, L" uniqKey="Richard L" first="L." last="Richard">L. Richard</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Hema‐Quebec, Montreal, Quebec</wicri:regionArea><wicri:noRegion>Quebec</wicri:noRegion></affiliation></author><author><name sortKey="Romero, M" sort="Romero, M" uniqKey="Romero M" first="M." last="Romero">M. Romero</name><affiliation wicri:level="3"><country xml:lang="fr">Brésil</country><wicri:regionArea>INCA—National Institute of Cancer, Rio de Janeiro</wicri:regionArea><placeName><settlement type="city">Rio de Janeiro</settlement><region type="state">État de Rio de Janeiro</region></placeName></affiliation></author><author><name sortKey="Rousseau, J" sort="Rousseau, J" uniqKey="Rousseau J" first="J." last="Rousseau">J. Rousseau</name><affiliation wicri:level="1"><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Genome Facility, Division of Human Genetics, IIDMM UCT Medical School, Cape Town</wicri:regionArea><wicri:noRegion>Cape Town</wicri:noRegion></affiliation></author><author><name sortKey="Spiroski, M" sort="Spiroski, M" uniqKey="Spiroski M" first="M." last="Spiroski">M. Spiroski</name><affiliation wicri:level="1"><country xml:lang="fr">Macédoine (pays)</country><wicri:regionArea>IIBHG, Faculty of Medicine, Skopje</wicri:regionArea><wicri:noRegion>Skopje</wicri:noRegion></affiliation></author><author><name sortKey="Sulcebe, G" sort="Sulcebe, G" uniqKey="Sulcebe G" first="G." last="Sulcebe">G. Sulcebe</name><affiliation wicri:level="1"><country xml:lang="fr">Albanie</country><wicri:regionArea>Laboratory of Immunology and Tissue Typing, University Hospital Center ‘Mother Teresa’, Tirana</wicri:regionArea><wicri:noRegion>Tirana</wicri:noRegion></affiliation></author><author><name sortKey="Middleton, D" sort="Middleton, D" uniqKey="Middleton D" first="D." last="Middleton">D. Middleton</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Transplant Immunology, Royal Liverpool University Hospital, Liverpool</wicri:regionArea><wicri:noRegion>Liverpool</wicri:noRegion></affiliation></author><author><name sortKey="Tiercy, J" sort="Tiercy, J" uniqKey="Tiercy J" first="J." last="Tiercy">J. Tiercy</name><affiliation wicri:level="1"><country xml:lang="fr">Suisse</country><wicri:regionArea>Transplantation Immunology Unit, National Reference Laboratory for Histocompatibility, University Hospital Geneva, Geneva</wicri:regionArea><wicri:noRegion>Geneva</wicri:noRegion></affiliation></author><author><name sortKey="Sanchez Azas, A" sort="Sanchez Azas, A" uniqKey="Sanchez Azas A" first="A." last="Sanchez-Mazas">A. Sanchez-Mazas</name><affiliation wicri:level="4"><country xml:lang="fr">Suisse</country><wicri:regionArea>Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), University of Geneva, Geneva</wicri:regionArea><orgName type="university">Université de Genève</orgName><placeName><settlement type="city">Genève</settlement><region nuts="3" type="region">Canton de Genève</region></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Suisse</country></affiliation></author></analytic><monogr></monogr><series><title level="j">Tissue Antigens</title><idno type="ISSN">0001-2815</idno><idno type="eISSN">1399-0039</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2010-07">2010-07</date><biblScope unit="volume">76</biblScope><biblScope unit="issue">1</biblScope><biblScope unit="page" from="18">18</biblScope><biblScope unit="page" to="30">30</biblScope></imprint><idno type="ISSN">0001-2815</idno></series><idno type="istex">C253A464077D1D9B52EC38C0C7F66A147AC42F8B</idno><idno type="DOI">10.1111/j.1399-0039.2010.01469.x</idno><idno type="ArticleID">TAN1469</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0001-2815</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>15th International Histocompatibility and Immunogenetics Workshop</term><term>analysis of human leukocyte antigen population data</term><term>anthropology</term><term>bio‐statistics</term><term>human leukocyte antigen</term><term>population genetics</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>Afrique du Sud</li><li>Albanie</li><li>Algérie</li><li>Australie</li><li>Autriche</li><li>Brésil</li><li>France</li><li>Grèce</li><li>Italie</li><li>Macédoine (pays)</li><li>Royaume-Uni</li><li>Suisse</li><li>Tunisie</li></country><region><li>Attique (région)</li><li>Canton de Genève</li><li>Gouvernorat de Tunis</li><li>Vienne (Autriche)</li><li>Wilaya d'Oran</li><li>État de Rio de Janeiro</li><li>Île-de-France</li></region><settlement><li>Athènes</li><li>Genève</li><li>Oran</li><li>Paris</li><li>Rio de Janeiro</li><li>Tunis</li><li>Vienne (Autriche)</li></settlement><orgName><li>Université de Genève</li></orgName></list><tree><country name="Suisse"><region name="Canton de Genève"><name sortKey="Nunes, J M" sort="Nunes, J M" uniqKey="Nunes J" first="J. M." last="Nunes">J. M. Nunes</name></region><name sortKey="Buhler, S" sort="Buhler, S" uniqKey="Buhler S" first="S." last="Buhler">S. Buhler</name><name sortKey="Currat, M" sort="Currat, M" uniqKey="Currat M" first="M." last="Currat">M. Currat</name><name sortKey="Di, D" sort="Di, D" uniqKey="Di D" first="D." last="Di">D. Di</name><name sortKey="Kervaire, B" sort="Kervaire, B" uniqKey="Kervaire B" first="B." last="Kervaire">B. Kervaire</name><name sortKey="Rahal, M" sort="Rahal, M" uniqKey="Rahal M" first="M." last="Rahal">M. Rahal</name><name sortKey="Riccio, M E" sort="Riccio, M E" uniqKey="Riccio M" first="M. E." last="Riccio">M. E. Riccio</name><name sortKey="Ries, F" sort="Ries, F" uniqKey="Ries F" first="F." last="Ries">F. Ries</name><name sortKey="Sanchez Azas, A" sort="Sanchez Azas, A" uniqKey="Sanchez Azas A" first="A." last="Sanchez-Mazas">A. Sanchez-Mazas</name><name sortKey="Sanchez Azas, A" sort="Sanchez Azas, A" uniqKey="Sanchez Azas A" first="A." last="Sanchez-Mazas">A. Sanchez-Mazas</name><name sortKey="Tiercy, J" sort="Tiercy, J" uniqKey="Tiercy J" first="J." last="Tiercy">J. Tiercy</name></country><country name="Brésil"><region name="État de Rio de Janeiro"><name sortKey="Almada, A J" sort="Almada, A J" uniqKey="Almada A" first="A. J." last="Almada">A. J. Almada</name></region><name sortKey="De Oliveira, D C M" sort="De Oliveira, D C M" uniqKey="De Oliveira D" first="D. C. M." last="De Oliveira">D. C. M. De Oliveira</name><name sortKey="Romero, M" sort="Romero, M" uniqKey="Romero M" first="M." last="Romero">M. Romero</name></country><country name="Algérie"><region name="Wilaya d'Oran"><name sortKey="Benhamamouch, S" sort="Benhamamouch, S" uniqKey="Benhamamouch S" first="S." last="Benhamamouch">S. Benhamamouch</name></region></country><country name="France"><region name="Île-de-France"><name sortKey="Benitez, O" sort="Benitez, O" uniqKey="Benitez O" first="O." last="Benitez">O. Benitez</name></region><name sortKey="Loiseau, P" sort="Loiseau, P" uniqKey="Loiseau P" first="P." last="Loiseau">P. Loiseau</name></country><country name="Italie"><noRegion><name sortKey="Canossi, A" sort="Canossi, A" uniqKey="Canossi A" first="A." last="Canossi">A. Canossi</name></noRegion><name sortKey="Piancatelli, D" sort="Piancatelli, D" uniqKey="Piancatelli D" first="D." last="Piancatelli">D. Piancatelli</name></country><country name="Tunisie"><region name="Gouvernorat de Tunis"><name sortKey="Fadhlaoui Id, K" sort="Fadhlaoui Id, K" uniqKey="Fadhlaoui Id K" first="K." last="Fadhlaoui-Zid">K. Fadhlaoui-Zid</name></region></country><country name="Autriche"><region name="Vienne (Autriche)"><name sortKey="Fischer, G" sort="Fischer, G" uniqKey="Fischer G" first="G." last="Fischer">G. Fischer</name></region></country><country name="Grèce"><region name="Attique (région)"><name sortKey="Papasteriades, C" sort="Papasteriades, C" uniqKey="Papasteriades C" first="C." last="Papasteriades">C. Papasteriades</name></region></country><country name="Australie"><noRegion><name sortKey="Richard, L" sort="Richard, L" uniqKey="Richard L" first="L." last="Richard">L. Richard</name></noRegion></country><country name="Afrique du Sud"><noRegion><name sortKey="Rousseau, J" sort="Rousseau, J" uniqKey="Rousseau J" first="J." last="Rousseau">J. Rousseau</name></noRegion></country><country name="Macédoine (pays)"><noRegion><name sortKey="Spiroski, M" sort="Spiroski, M" uniqKey="Spiroski M" first="M." last="Spiroski">M. Spiroski</name></noRegion></country><country name="Albanie"><noRegion><name sortKey="Sulcebe, G" sort="Sulcebe, G" uniqKey="Sulcebe G" first="G." last="Sulcebe">G. Sulcebe</name></noRegion></country><country name="Royaume-Uni"><noRegion><name sortKey="Middleton, D" sort="Middleton, D" uniqKey="Middleton D" first="D." last="Middleton">D. Middleton</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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