Lucie Richard

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)

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.

16(th) IHIW: analysis of HLA population data, with updated results for 1996 to 2012 workshop data (AHPD project report).

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.

HLA-A, B and DRB1 genetic heterogeneity in Quebec.

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.

Performance of an allele-level multi-locus HLA genotype imputation tool in hematopoietic stem cell donors from Quebec

Donor‐recipient HLA compatibility is an important determinant of transplant outcomes. Allele‐group to allele‐level imputations help assign HLA genotypes when allele‐level genotypes are not available during donor selection.

Inaccuracies in epitope repertoire estimations when using multilocus allele-level HLA genotype imputation tools

Limited availability of allele‐level HLA genotypes prompts their imputation from allele‐group genotypes to estimate epitope mismatches. We evaluated the accuracy of epitope load and repertoire assignment when imputing allele‐level HLA genotypes. Analyses were conducted on 175 hematopoietic stem cell (HSC) donors from the Héma‐Québec registry (HQR) and 57 HSC donor‐recipient pairs from McGill University Health Centre (MUHC), Québec, Canada, genotyped for HLA‐A, ‐B, ‐C, ‐DRB1, and ‐DQB1. Multilocus allele‐level imputation was performed using HaploStats. Disagreement in B‐ and T‐cell epitope assignment and epitope mismatches were ascertained for imputed vs measured allele‐level HLA genotypes in HSC donors and donor‐recipient pairs, respectively. Imputation resulted in no differences in overall eplet mismatches and Predicted Indirectly ReCognizable HLA Epitopes (PIRCHE‐II) for HLA‐A, ‐B, and ‐C in 83.4% and 93.7% of HQR donors and 87.7% and 87.7% of MUHC donors, respectively. HLA‐DRB1‐ and ‐DQB1‐derived eplet mismatches and PIRCHE‐II were correctly assigned in 72.0% and 85.1% of HQR donors and 70.2% and 71.9% of MUHC donors, respectively. No discrepancies in eplet load or PIRCHE‐II were observed in 96.5% and 86.0% of HSC donor‐recipient pairs and in 70.2% and 70.1% of pairs for HLA‐A, ‐B, ‐C, ‐DRB1, and ‐DQB1, respectively. Kappa statistics of 0.9708 and 0.9725, 0.8724 and 0.8177, 0.9827 and 0.9022, 0.5644 and 0.4939, 0.5085 and 0.6361 were estimated when assessing agreement between eplet mismatches and PIRCHE‐II of imputed vs measured HLA‐A, ‐B, ‐C, ‐DRB1, and ‐DQB1 types, respectively. To avoid inaccuracies in epitope compatibility estimation, mainly for HLA class II, multilocus allele‐level genotype measurement is recommended.