<scp>HLA</scp> population genetics: a Lebanese population

Cano, Pedro; Testi, Manuela; Andreani, Marco; Khoriaty, Evelyne; Monsef, Jad Bou; Galluccio, Tiziana; Troiano, Maria; Fernández-Viña, Marcelo; Inati, Adlette

doi:10.1111/j.1399-0039.2012.01936.x

Cited by 9 publications

(6 citation statements)

References 22 publications

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“…HLA-A*24:02:01:01~C*04:01:01:06~B*35:02:01~DRB3*02:02:01:02~DRB1*11:04:01~DQA1 *05:05:01:01~DQB1*03:01:01:02~DPA1*01:03:01:04~DPB1*04:01:01:01 (HF = 0.030), which is highly conserved and very common in Middle Eastern populations [34] [35]; and HLA-A*01:01:01:01~C*07:01:01:01~B*18:01:01:02~DRB3*02:02:01:02~DRB1*11:04:01~DQ A1*05:05:01:01~DQB1*03:01:01:03~DPA1*01:03:01:05~DPB1*04:02:01:01 (HF = 0.020). Therefore, intron variation (in the latter example according to HLA-DPA1 and -DQB1 loci) appears to be haplotype-specific.…”

Section: Discussionmentioning

confidence: 99%

High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

et al. 2019

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Next-generation sequencing (NGS) at the HLA-A,-B,-C,-DPA1,-DPB1,-DQA1,-DQB1,-DRB1 and-DRB¾/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and-haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17 th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.

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Section: Discussionmentioning

confidence: 99%

High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

et al. 2019

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“…In a recent study of Lebanese families [29], we observed high levels of diversity but no alleles that are unique to this population. Most of the alleles observed in this group are found in either Europeans or Far East Asians; the distribution of HLA alleles in Lebanese is significantly different from those observed in Europeans, Africans and Far East Asians.…”

Section: ------------------Tg -----------A -------------Drb1*08:04:04mentioning

confidence: 99%

“…Alleles at DQA1 and DQB1 that associate tightly with alleles of the DRB1*08 group are shown. These haplotype fragments were classified according to their frequencies in different populations [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] in these populations were from this locus, and it has been postulated that HLA-B has diversified more rapidly in the South American tribes. Interestingly, in many tribes the novel alleles are present at the highest gene frequencies, suggesting that the novel alleles generated in America were positively selected in these populations probably because they provided selective advantages.…”

Section: Hla Studies In Native American Populationsmentioning

confidence: 99%

Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

Viña

Hollenbach²,

Lyke

et al. 2012

Phil. Trans. R. Soc. B

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The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses.

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“…13 Well-documented HLA alleles are available from CWD v.2.0.0 catalog. Population comparisons were made using allele frequencies from the Europeans, Africans, Asians, Amerindians (Table 1; data from http://www.allelefrequencies.net/ and from articles, [13][14][15][16][17][18][19][20], and Brazilians (without ethnic distinction; data from REDOME-Brazilian volunteer bone marrow donors registry; http://imunogenetica.org/resultados/perfil-genomico- do-redome-rereme/; 21 ) and results are shown as population grouping. To create these clusters, a singular value decomposition method of the data base was used, in which the elements were the frequencies of HLA alleles in each population represented by a vector in space.…”

mentioning

confidence: 99%

“…On the other . Data of Brazilian regions are from REDOME and for the other countries data were obtained from articles [13][14][15][16][17][18][19][20] hand, to construct the cluster among the population of this study and several others in the world, HLA-DRB1 and -DQB1 allele frequencies were used because the greater genetic variability through high resolution allows for more reliable results. The population grouping shows the proximity with other Brazilians and with European populations such as Portugal and France.…”

mentioning

confidence: 99%

HLA‐A, ‐B, ‐DRB1, ‐DQA1, and ‐DQB1 profile in a population from southern Brazil

Reis

Ambrosio‐Albuquerque

Fabreti‐Oliveira

et al. 2018

HLA

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The aim of this study was to determine the allele and haplotype frequencies of HLA-A, -B, -DRB1, and -DQB1 in a self-declared White population from the north and northwestern state of Paraná, southern Brazil, and compare the data with populations worldwide. The genotyping was performed with a group of 641 individuals, based on PCR-SSO and -SSP methods, and allele and haplotype frequencies were estimated. Comparisons with European, African, Asian, and Amerindian populations were performed. The most frequent allelic groups, alleles and haplotypes were: HLA-A*02, HLA-B*35, HLA-DRB1*07:01, HLA-DQB1*03:01, and HLA-A*01/B*08/DRB1*03:01. The results reinforced a predominance of a European composition in the self-declared White population from the north and northwestern Paraná.

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HLA population genetics: a Lebanese population

Cited by 9 publications

References 22 publications

High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing

Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

HLA‐A, ‐B, ‐DRB1, ‐DQA1, and ‐DQB1 profile in a population from southern Brazil

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