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)

Article Article scientifique Article 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) eng 2010 author Nunes Jose Manuel 122321 author Riccio Maria Eugenia 647913 author Buhler Stéphane 0000-0001-6675-5287 502714 author Di Da 663072 author Currat Mathias 0000-0001-5211-8922 89701 author Ries Fabien 526588 author Almada A. J. author Benhamamouch S. author Benitez O. author Canossi A. author Fadhlaoui-Zid Karima author Fischer Gottfried author Kervaire Barbara author Loiseau Pascale author de Oliveira D. C. M. author Papasteriades C. author Piancatelli D. author Rahal M. author Richard L. author Romero M. author Rousseau J. author Spiroski M. author Sulcebe G. author Middleton D. author Tiercy Jean-Marie 26423 author Sanchez-Mazas Alicia 22545 18-30 10.1111/j.1399-0039.2010.01469.x 20331842 0001-2815 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. Génétique humaine HLA Biostatistique Dewey 599.9 Dewey 616 Dewey 590 44 Département de génétique et évolution 162 140 Département d'anthropologie et écologie 164 56 Département de médecine 221 false 299 Compatibilité tissulaire et transplantation clinique 562 1056 Unité d'anthropologie Tissue antigens 76 1 9b0330f8-3487-4130-933d-638974641b69 Article (Published version) Restricted Nunes ASM 2010.pdf 626310 application/pdf restrictedAccess Faculté des sciences / Section de biologie / Département de génétique et évolution Faculté des sciences / Section de biologie / Département d'anthropologie et écologie Faculté de médecine / Section de médecine clinique / Département de médecine

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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)	Tissue antigens			2010	1,288	7

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