Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans

Barquera, Rodrigo; Zúñiga, Joaquı́n; Flores‐Rivera, José; Corona, Teresa; Penman, Bridget S.; Hernández-Zaragoza, Diana Iraíz; Soler, Manuel; Jonapá-Gómez, Letisia; Mallempati, Kalyan C.; Yescas, Petra; Ochoa, Adriana; Barsakis, Konstantinos; Aguilar-Vázquez, José Artemio; García-Lechuga, Maricela; Mindrinos, Michael; Yunis, María; Jiménez-Álvarez, Luis Armando; Mena-Hernández, Lourdes; Ortega, Esteban; Cruz‐Lagunas, Alfredo; Tovar-Méndez, Víctor Hugo; Granados, Julio; Fernández-Viña, Marcelo; Yunis, Edmond J.

doi:10.1038/s41598-020-58897-5

Cited by 15 publications

(20 citation statements)

References 118 publications

(173 reference statements)

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“…In addition, the 7.1AH and the 8.1AH are among the most common European haplotypes with population frequencies of 8.1AH up to at least 18% (Sanchez-Velasco et al, 2003 ; Kiszel et al, 2007 ; Sanchez-Mazas et al, 2013 ; Robinson et al, 2019 ). In addition, seven of the other nine HERVK9 + /SVA-B- haplotypes ( Supplementary Table 5 ) are common in Europeans (Suslova et al, 2012 ; Robinson et al, 2019 ) or Japanese (Ikeda et al, 2015 ), whereas A * 31/C01:02/B * 15:01 is from the cell line of a Warao South American Indian, which may be moderately common in some Amerindians (Watkins et al, 1992 ; Cadavid and Watkins, 1997 ), but not in others (Barquera et al, 2020 ). Taken together, these observations suggest that the human MHC ERVK9 + /SVA-HB − haplotype might be broadly spread at relatively high frequency within many different worldwide populations.…”

Section: Discussionmentioning

confidence: 99%

“…The absence of SNPs over megabases of continuous sequence within the same MHC haplotypes is described as conserved sequence polymorphisms (CSPs) within conserved extended haplotypes (CEHs) (Yunis et al, 2003 ; Alper et al, 2006 ) and/or ancestral haplotypes (AHs) (Degli-Esposti et al, 1992 ; Dawkins et al, 1999 ), such as 8.1CEH/AH (Price et al, 1999 ; Aly et al, 2006 ; Smith et al, 2006 ; Gambino et al, 2018 ), 7.1CEH/AH (Gaudieri et al, 1997 ; Dunn et al, 2005 ), 57.1CEH/AH (Dunn et al, 2005 ), 38.1CEH/AH (Romero et al, 2007 ) and the Sardinian haplotype 18.2CEH/AH (Contu et al, 1989 ; Bilbao et al, 2006 ). The non-LD, SNP-poor, long-range haplotypic sequences are mainly contained within polymorphic frozen blocks (PFBs) (Gaudieri et al, 1997 ; Dawkins et al, 1999 ) or fixed (conserved) haplospecific blocks (Alper et al, 2006 ; Barquera et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction

2021

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The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction

2021

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“…TheHLA-DRB3, -DRB4, -DRB5 allele is associated with HLA-DRB1 allele,now the AFs data of HLA-DRB3, -DRB4, -DRB5 was rare at highresolution level in the Chinese population.HLA-DRB4*01:03:01(25.72%) was the common alleles for HLA-DRB4 locusin our study. However, HLA-DRB4*01:01 (34.93%) and DRB4*01:03:01(34.03%) were the most common in the nativeAmericans [27].For the HLA-DRB3 locus, the DRB3*02:02:01 was common in theZhejiang Han population, but DRB3*01:01 was common in the nativeAmericans. The data of our study was supported that the view of thedistribution of HLA alleles was various in the differentethnicity.…”

Section: Discussionmentioning

confidence: 91%

“…Now NGS technology is increasingly used in HLA genotyping forhigh resolution [18][19][20][21][22][23][24][25][26][27],it has high throughput and can bedecreased the rate of the ambiguous allele combinations. Here weused a commercial NGS method for HLA genotyping.…”

Section: Discussionmentioning

confidence: 99%

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

Wang

Dong

Wang

et al. 2020

Preprint

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Background The allele and haplotype frequencies of HLA loci are various in the populations. Most of the data for HLA alleles and haplotypes were at low resolution or two fields resolution. Here, the data for HLA alleles and haplotypes at three fields resolution was reported in Chinese Han population. Methods All samples were come from the Zhejiang Cord Blood Bank, China after information consent. HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci was genotyped using next generation sequencing (NGS) method. The allele frequencies of HLA loci were analyzed at three fields resolution. The haplotype estimation and linkage disequilibrium analysis was used Arlequin software 3.5.2.2. Result The top three frequent alleles of HLA-A, -B, -C, -DRB1, -DQB1 loci were A*11:01:01 (25.81%), A*24:02:01 (16.70%), A*02:01:01 (10.61%); B*40:01:02 (15.97%), B*46:01:01 (11.48%), B*58:01:01 (7.96%); C*07:02:01 (19.03%), C*01:02:01 (17.65%), C*03:04:01 (10.41%); DRB1*09:01:02 (17.96%), DRB1*12:02:01 (9.57%), DRB1*08:03:02 (9.54%); DQB1*03:01:01(21.05%), DQB1*03:03:02 (19.15%), DQB1*06:01:01 (12.08%); DRB4*01:03:01(25.72%), DRB3*02:02:01(20.27%), DRB5*01:01:01(10.96%) respectively. A total of 1542 distinct A-B-C-DRB1-DQB1-DRB3/4/5 haplotypes were identified. The alleles of HLA loci were showed strong linkage disequilibrium. Conclusion The data of allele and haplotype of HLA-A, -B, -C, -DRB1, -DQB1 and -DRB3/4/5 loci at three fields resolution level was obtained, which will help to analyze the HLA ploymorphism in the populations.

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“…This analysis was based on HLA-B. Besides, we included other Mexican Native American groups to deepen the comparison; the groups added were: Lacandon Mayans ( Barquera et al, 2020f ), Oaxaca Mixe ( Hollenbach et al, 2001 ; Single et al, 2020 ), Oaxaca Zapotecans ( Hollenbach et al, 2001 ), and Seri ( Gorodezky, 2006 ). The genetic distance analysis included Nei’s distance performed with the Arlequin genetics population program.…”

Section: Subjects Materials and Methodsmentioning

confidence: 99%

Heterogeneity of Genetic Admixture Determines SLE Susceptibility in Mexican

et al. 2021

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Systemic Lupus Erythematosus (SLE) is an autoimmune inflammatory disorder for which Major Histocompatibility Complex (MHC) genes are well identified as risk factors. SLE patients present different clinical phenotypes, which are partly explained by admixture patterns variation among Mexicans. Population genetic has insight into the high genetic variability of Mexicans, mainly described through HLA gene studies with anthropological and biomedical importance. A prospective, case-control study was performed. In this study, we recruited 146 SLE patients, and 234 healthy individuals were included as a control group; both groups were admixed Mexicans from Mexico City. The HLA typing methods were based on Next Generation Sequencing and Sequence-Based Typing (SBT). The data analysis was performed with population genetic programs and statistical packages. The admixture estimations based on HLA-B and -DRB1 revealed that SLE patients have a higher Southwestern European ancestry proportion (48 ± 8%) than healthy individuals (30 ± 7%). In contrast, Mexican Native American components are diminished in SLE patients (44 ± 1%) and augmented in Healthy individuals (63 ± 4%). HLA alleles and haplotypes’ frequency analysis found variants previously described in SLE patients from Mexico City. Moreover, a conserved extended haplotype that confers risk to develop SLE was found, the HLA-A∗29:02∼C∗16:01∼B∗44:03∼DRB1∗07:01∼DQB1∗02:02, pC = 0.02, OR = 1.41. Consistent with the admixture estimations, the origin of all risk alleles and haplotypes found in this study are European, while the protection alleles are Mexican Native American. The analysis of genetic distances supported that the SLE patient group is closer to the Southwestern European parental populace and farthest from Mexican Native Americans than healthy individuals. Heterogeneity of genetic admixture determines SLE susceptibility and protection in Mexicans. HLA sequencing is helpful to determine susceptibility alleles and haplotypes restricted to some populations.

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Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans

Abstract: genetic diversity and distance from Africa in the global dataset, but no relationship between HLA genetic diversity and distance from Africa when native American populations were considered alone.

Cited by 15 publications

References 118 publications

SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction

SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction

The Polymorphism of HLA-A,-B,-C,-DRB1,-DQB1,-DRB3/4/5 loci in Zhejiang Han Population,China Using NGS Technology

Heterogeneity of Genetic Admixture Determines SLE Susceptibility in Mexican

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