Journal Article10.1111/IJI.12033
16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report).
Maria Eugenia Riccio,Stéphane Buhler,Jose Manuel Nunes,Christelle Vangenot,Mélanie Cuenod,Mathias Currat,Da Di,Marco Andreani,M. Boldyreva,Geoffrey K. Chambers,M. S. Chernova,Jacques Chiaroni,C. Darke,J. Di Cristofaro,Valérie Dubois,P. P. J. Dunn,Hisham Atan Edinur,N. Elamin,J.-F. Eliaou,Zorana Grubic,Taina Jaatinen,Uma Kanga,Barbara Nelly Kervaire,L. Kolesar,W. Kunachiwa,M. L. Lokki,Narinder K. Mehra,Grazia Nicoloso,Riitta Paakkanen,D. Papaioannou Voniatis,C. Papasteriades,F. Poli,Lucie Richard,I. Romón Alonso,Antonij Slavcev,G. Sulcebe,T. Suslova,Manuela Testi,Jean-Marie Tiercy,A. Varnavidou,B. Vidan-Jeras,Annika Wennerström,Alicia Sanchez-Mazas +42 more
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TL;DR: The comparison of the 16IHIW AHPD data with data collected during previous workshops 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.
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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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Allele Frequencies Net Database: Improvements for storage of individual genotypes and analysis of existing data.
Eduardo Jose Melos dos Santos,Antony McCabe,Faviel F. Gonzalez-Galarza,Andrew R. Jones,Derek Middleton +4 more
TL;DR: A data submission tool to assist users in the collection of the genotypes of the individuals (raw data), facilitating submission of short population reports to Human Immunology, as well as simplifying the submission of population demographics and frequency data is introduced.
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The HLA-net GENE[RATE] pipeline for effective HLA data analysis and its application to 145 population samples from Europe and neighbouring areas.
TL;DR: An integrated version of theGene[rate] computer tools which have been developed during the last 5 years to analyse human leukocyte antigen (HLA) data in human populations, as well as the results of their application to a large dataset of 145 HLA-typed population samples from Europe and its two neighbouring areas, North Africa and West Asia, now forming part of the Gene[va] database.
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The relevance of HLA sequencing in population genetics studies
Alicia Sanchez-Mazas,Diogo Meyer +1 more
TL;DR: This review explains how HLA sequencing allows a better assessment of the HLA diversity in human populations, and shows how analyzing HLA sequence variation may improve the comprehension of population genetic relationships by facilitating the identification of demographic events that marked human evolution.
High-risk genotypes HLA-DR3-DQ2/DR3-DQ2 and DR3-DQ2/DR4-DQ8 in co-occurrence of type 1 diabetes and celiac disease.
Darja Smigoc Schweiger,Andrijana Mendez,Sabina Kunilo Jamnik,Nina Bratanic,Natasa Bratina,Tadej Battelino,Jernej Brecelj,Blanka Vidan-Jeras +7 more
TL;DR: It is suggested that individuals carrying high-risk genotypes DR3-DQ2/DR3- DQ2 or DR3/DR4/DQ8 would more likely develop both T1D and CD than either disease alone.
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Associations of HLA-A, HLA-B and HLA-C alleles frequency with prevalence of herpes simplex virus infections and diseases across global populations: implication for the development of an universal CD8+ T-cell epitope-based vaccine.
Sarah Samandary,Hédia Kridane-Miledi,Jacqueline S. Sandoval,Zareen S. Choudhury,Francina Langa-Vives,Doran Spencer,Aziz Alami Chentoufi,François Lemonnier,Lbachir BenMohamed +8 more
TL;DR: Overall, high prevalence of herpes infection and disease appears to be associated with high frequency of HLA-A,HLA-B and HLA -C alleles, which will aid in developing a T-cell epitope-based universal herpes vaccine and immunotherapy.
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