<scp>NO</scp> to obsolete definitions: <scp>YES</scp> to blanks

Nunes, José Manuel; Bühler, Stéphane; Sanchez‐Mazas, Alicia

doi:10.1111/tan.12276

Cited by 9 publications

(16 citation statements)

References 6 publications

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“…These ethnoracial categories were adopted because they constitute the classification officially adopted in Brazil. Despite the conceptual problems associated with the use of this ethnoracial classification, these classes are associated with biogeographic ancestry …”

Section: Methodsmentioning

confidence: 99%

Human leukocyte antigen distribution and genomic ancestry in Brazilian patients with sickle cell disease

Silva-Malta

Rodrigues

Zuccherato

et al. 2017

HLA

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Hematopoietic stem-cell transplantation (HSCT) is currently the only established curative treatment for sickle cell disease (SCD), but is limited by donor availability. Ethnicity is thought to have an impact on the complications experienced by patients that undergo HSCT and on the likelihood of identifying an human leukocyte antigen (HLA) matched donor. In the present study, we investigated the genomic ancestry and the distribution of HLA allele groups in Brazilian patients with SCD, compared these HLA profiles to worldwide populations and evaluate the availability of HLA-matched donors. A broad intercontinental admixture of patients with SCD was observed, with African ancestry ranging from 6.7% to 93.4%. In a dendrogram based on HLA frequencies, Brazilian patients with SCD were included in a branch containing only populations with a significant African component. Among the 126 patients evaluated, 10 (8%) found a HLA-matched unrelated donor in a database of 18 134 donors. Self-reported white, brown and black matched donors were identified, and no significant difference in the percentage of compatible donors was observed between these ethnic groups. Our results show that Brazilian patients with SCD are very admixed, indicating that this group is a promising target for admixture mapping of genes involved in complications after HSCT. Additional studies may help to clarify the impact of the genetic diversity and admixture of these patients on the donor availability.

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Section: Methodsmentioning

confidence: 99%

Human leukocyte antigen distribution and genomic ancestry in Brazilian patients with sickle cell disease

Silva-Malta

Rodrigues

Zuccherato

et al. 2017

HLA

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“…Independently from the SPLIT-TEST approach, a blank allele was systematically added in putative homozygotes as a mandatory precaution for potentially missed alleles during typing (some alleles cross-react between generic specificities (Holdsworth et al, 2009), and new HLA alleles are discovered on a daily basis (Robinson et al, 2011)). This practice follows the most rigorous approach to deal with recessive-like data in population genetics (Nunes et al, 2014b). Because molecular methods were used, the rate of false homozygotes is expected to be rather low, but, to be on the safe side, adding putative blank remains the most rigorous strategy.…”

Section: Treatment Of Typing Ambiguitiesmentioning

confidence: 99%

HLA‐A, B and DRB1 genetic heterogeneity in Quebec

Bühler

Nunes

Sanchez‐Mazas

et al. 2015

Int J Immunogenetics

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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.

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“…Population stratification may indeed lead to spurious associations, as already stressed for variable DNA sites [7] , although this remains to be formally demonstrated. Very often, 'Caucasian' samples are used as controls; but as European populations are genetically diverse, the term 'Caucasian' -used to describe indifferently any population from Europe and its surrounding regions -should be abandoned as it does not correspond to any scientific reality, and the use of data defined in this way should be banned [35,76] . This would certainly improve the robustness of the associations found, as the majority of them are currently observed in specific studies and not confirmed by others.…”

Section: Implications Of European Regional Genetic Diversity For Humamentioning

confidence: 99%

A New HLA Map of Europe: Regional Genetic Variation and Its Implication for Peopling History, Disease-Association Studies and Tissue Transplantation

Sanchez‐Mazas

Bühler

Nunes³

2013

Hum Hered

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Objectives: HLA genes are highly polymorphic in human populations as a result of diversifying selection related to their immune function. However, HLA geographic variation worldwide suggests that demographic factors also shaped their evolution. We here analyzed in detail HLA genetic variation in Europe in order to identify signatures of migration history and/or natural selection. Methods: Relationships between HLA diversity and geography were analyzed at 7 loci through several approaches including linear regression on gene diversity and haplotype frequencies. Regional variation was also assessed on HLA multi-locus phenotypes through structure analysis. Deviation from neutrality was tested by resampling. Results: Geographic distance was a strong predictor of HLA variation at 5 loci (A, B, C, DRB1 and DPB1) in Europe, and latitude significantly shaped HLA gene diversity and haplotype frequencies. Whereas the main level of genetic diversity was found within populations, both HLA gene frequencies and phenotypic profiles revealed regional variation, Southeast Europe, Great Britain and Finland being the most distinctive. Effects of natural selection were suggested at the DQ loci. Conclusions: HLA regional variation was observed in Europe and can be related to population history, locus HLA-A providing by far the strongest signals. This new HLA map of Europe represents an invaluable reference for disease-association studies and tissue transplantation.

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NO to obsolete definitions: YES to blanks

Cited by 9 publications

References 6 publications

Human leukocyte antigen distribution and genomic ancestry in Brazilian patients with sickle cell disease

Human leukocyte antigen distribution and genomic ancestry in Brazilian patients with sickle cell disease

HLA‐A, B and DRB1 genetic heterogeneity in Quebec

A New HLA Map of Europe: Regional Genetic Variation and Its Implication for Peopling History, Disease-Association Studies and Tissue Transplantation

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