<i>Alu</i>elements within the human major histocompatibility class I region in the Comoros Islands: genetic variation and population relationships

Abeid, Said Nassor; Motrane, Majida; Farhane, Hamid; Harich, Nourdin

doi:10.1080/03014460.2019.1620854

Cited by 4 publications

(2 citation statements)

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“…The advantages of these POALIN lineage markers within the MHC class I and class II regions are their applicability – they are well defined, cheap to prepare and administer in the laboratory, and they produce results that are reasonably easy to interpret. In future work, the more widely studied MHC class I 5-loci POALINs ( Yao et al, 2010 ; Abeid et al, 2019 ; Kulski et al, 2019 ), other autosomal Alu loci ( Antunez-de-Mayolo et al, 2002 ), and STR loci ( Garcia-Obregon et al, 2011 ) could be included in the haplotype analyses to broaden the genetic distances and diversity between and within the various populations.…”

Section: Discussionmentioning

confidence: 99%

Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China

et al. 2021

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The analysis of polymorphic variations in the human major histocompatibility complex (MHC) class II genomic region on the short-arm of chromosome 6 is a scientific enquiry to better understand the diversity in population structure and the effects of evolutionary processes such as recombination, mutation, genetic drift, demographic history, and natural selection. In order to investigate associations between the polymorphisms of HLA-DRB1 gene and recent Alu insertions (POALINs) in the HLA class II region, we genotyped HLA-DRB1 and five Alu loci (AluDPB2, AluDQA2, AluDQA1, AluDRB1, AluORF10), and determined their allele frequencies and haplotypic associations in 12 minority ethnic populations in China. There were 42 different HLA-DRB1 alleles for ethnic Chinese ranging from 12 alleles in the Jinuo to 28 in the Yugur with only DRB1∗08:03, DRB1∗09:01, DRB1∗12:02, DRB1∗14:01, DRB1∗15:01, and DRB1∗15:02 present in all ethnic groups. The POALINs varied in frequency between 0.279 and 0.514 for AluDPB2, 0 and 0.127 for AluDQA2, 0.777 and 0.995 for AluDQA1, 0.1 and 0.455 for AluDRB1 and 0.084 and 0.368 for AluORF10. By comparing the data of the five-loci POALIN in 13 Chinese ethnic populations (including Han-Yunnan published data) against Japanese and Caucasian published data, marked differences were observed between the populations at the allelic or haplotypic levels. Five POALIN loci were in significant linkage disequilibrium with HLA-DRB1 in different populations and AluDQA1 had the highest percentage association with most of the HLA-DRB1 alleles, whereas the nearby AluDRB1 indel was strongly haplotypic for only DRB1∗01, DRB1∗10, DRB1∗15 and DRB1∗16. There were 30 five-locus POALIN haplotypes inferred in all populations with H5 (no Alu insertions except for AluDQA1) and H21 (only AluDPB2 and AluDQA1 insertions) as the two predominant haplotypes. Neighbor joining trees and principal component analyses of the Alu and HLA-DRB1 polymorphisms showed that genetic diversity of these genomic markers is associated strongly with the population characteristics of language family, migration and sociality. This comparative study of HLA-DRB1 alleles and multilocus, lineage POALIN frequencies of Chinese ethnic populations confirmed that POALINs whether investigated alone or together with the HLA class II alleles are informative genetic and evolutionary markers for the identification of allele and haplotype lineages and genetic variations within the same and/or different populations.

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Section: Discussionmentioning

confidence: 99%

Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China

et al. 2021

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“…As part of an investigation into putative associations and functions of TEs in generating human ( Kulski et al, 1997 ; Kulski et al, 1999 ; Kulski et al, 2000 ) and non-human primate ( Kulski et al, 2004 ) MHC haplotypes, two reports by Kulski , Suzuki and Shiina used a set of 95 extended MHC haplotype sequences from a publicly available database ( Norman et al, 2017 ) to study meiotic recombination resulting in haplotype segmental shuffling or crossovers in the MHC class I and II regions. Both studies demonstrated that 1) SNP-density crossovers are associated with putative ancestral recombination sites widely spread across the odortype receptor and MHC class I and class II regions; 2) MHC homozygous cell line genomic sequences are useful for analyzing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions without the need for probabilistic statistical imputation; and 3) TEs are useful genetic markers of recent recombination events and for elucidating population phylogenetics and genetic interrelationships ( Kulski et al, 2011 ; 2019 ; Wang et al, 2017 ; Abeid et al, 2019 ). There was substantial haplotype shuffling between different polymorphic blocks suggesting the presence of numerous putative ancestral recombination sites between specific class II genes.…”

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confidence: 99%

Editorial: Population genomic architecture: Conserved polymorphic sequences (CPSs), not linkage disequilibrium

et al. 2023

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Human population genetics of Comoros islanders: Alu polymorphisms and the peopling of the three major islands

et al. 2021

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Aluelements within the human major histocompatibility class I region in the Comoros Islands: genetic variation and population relationships

Cited by 4 publications

References 38 publications

Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China

Haplotypic Associations and Differentiation of MHC Class II Polymorphic Alu Insertions at Five Loci With HLA-DRB1 Alleles in 12 Minority Ethnic Populations in China

Editorial: Population genomic architecture: Conserved polymorphic sequences (CPSs), not linkage disequilibrium

Human population genetics of Comoros islanders: Alu polymorphisms and the peopling of the three major islands

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