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)
Autor: | J. Rousseau, Soraya Benhamamouch, Derek Middleton, M. Rahal, Maria Eugenia Riccio, Lucie Richard, Alicia Sanchez-Mazas, Angelica Canossi, Karima Fadhlaoui-Zid, Mirko Spiroski, D. Piancatelli, Fabien Ries, Pascale Loiseau, Mathias Currat, Da Di, Jose Manuel Nunes, A. J. Almada, G. Sulcebe, D. C. M. de Oliveira, Stéphane Buhler, Barbara Nelly Kervaire, Gottfried Fischer, Matilde Romero, O. Benitez, C. Papasteriades, Jean-Marie Tiercy |
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Rok vydání: | 2010 |
Předmět: |
Immunology
Population Population genetics Human leukocyte antigen Biology Biochemistry Génétique humaine 03 medical and health sciences 0302 clinical medicine Genetic drift Resampling Genetics Immunology and Allergy education Allele frequency ddc:599.9 030304 developmental biology 0303 health sciences education.field_of_study General Medicine Histocompatibility HLA Transplantation Biostatistique Evolutionary biology 030215 immunology |
Zdroj: | Tissue antigens Tissue Antigens, Vol. 76, No 1 (2010) pp. 18-30 |
ISSN: | 0001-2815 |
DOI: | 10.1111/j.1399-0039.2010.01469.x |
Popis: | 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. |
Databáze: | OpenAIRE |
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