Immunogenetics of HLA-B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgrounds

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dc.contributor.authorSilva, Nayane dos Santos Brito [UNESP]
dc.contributor.authorSouza, Andreia da Silva [UNESP]
dc.contributor.authorAndrade, Heloisa de Souza
dc.contributor.authorPereira, Raphaela Neto [UNESP]
dc.contributor.authorCastro, Camila Ferreira Bannwart [UNESP]
dc.contributor.authorVince, Nicolas
dc.contributor.authorLimou, Sophie
dc.contributor.authorNaslavsky, Michel Satya
dc.contributor.authorZatz, Mayana
dc.contributor.authorDuarte, Yeda Aparecida de Oliveira
dc.contributor.authorMendes-Junior, Celso Teixeira
dc.contributor.authorCastelli, Erick da Cruz [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionNantes Université
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionCentro Universitário Sudoeste Paulista
dc.contributor.institutionHospital Israelita Albert Einstein
dc.date.accessioned2023-07-29T14:01:21Z
dc.date.available2023-07-29T14:01:21Z
dc.date.issued2023-06-01
dc.description.abstractHLA-B is among the most variable gene in the human genome. This gene encodes a key molecule for antigen presentation to CD8+ T lymphocytes and NK cell modulation. Despite the myriad of studies evaluating its coding region (with an emphasis on exons 2 and 3), few studies evaluated introns and regulatory sequences in real population samples. Thus, HLA-B variability is probably underestimated. We applied a bioinformatics pipeline tailored for HLA genes on 5347 samples from 80 different populations, which includes more than 1000 admixed Brazilians, to evaluate the HLA-B variability (SNPs, indels, MNPs, alleles, and haplotypes) in exons, introns, and regulatory regions. We observed 610 variable sites throughout HLA-B; the most frequent variants are shared worldwide. However, the haplotype distribution is geographically structured. We detected 920 full-length haplotypes (exons, introns, and untranslated regions) encoding 239 different protein sequences. HLA-B gene diversity is higher in admixed populations and Europeans while lower in African ancestry individuals. Each HLA-B allele group is associated with specific promoter sequences. This HLA-B variation resource may improve HLA imputation accuracy and disease-association studies and provide evolutionary insights regarding HLA-B genetic diversity in human populations.en
dc.description.affiliationMolecular Genetics and Bioinformatics Laboratory School of Medicine São Paulo State University - Unesp, São Paulo
dc.description.affiliationINSERM Ecole Centrale Nantes Center for Research in Transplantation and Translational Immunology Nantes Université, UMR 1064
dc.description.affiliationDepartment of Genetics and Evolutionary Biology Biosciences Institute University of São Paulo (USP), São Paulo
dc.description.affiliationUniFSP Centro Universitário Sudoeste Paulista, São Paulo
dc.description.affiliationHuman Genome and Stem Cell Research Center University of São Paulo, São Paulo
dc.description.affiliationHospital Israelita Albert Einstein, São Paulo
dc.description.affiliationMedical-Surgical Nursing Department School of Nursing University of São Paulo, São Paulo
dc.description.affiliationDepartamento de Química Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo, São Paulo
dc.description.affiliationUnespMolecular Genetics and Bioinformatics Laboratory School of Medicine São Paulo State University - Unesp, São Paulo
dc.description.sponsorshipCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
dc.format.extent634-646
dc.identifierhttp://dx.doi.org/10.1111/tan.15043
dc.identifier.citationHLA, v. 101, n. 6, p. 634-646, 2023.
dc.identifier.doi10.1111/tan.15043
dc.identifier.issn2059-2310
dc.identifier.issn2059-2302
dc.identifier.scopus2-s2.0-85151938692
dc.identifier.urihttp://hdl.handle.net/11449/249062
dc.language.isoeng
dc.relation.ispartofHLA
dc.sourceScopus
dc.subjectevolutionary aspects
dc.subjecthaplotypes
dc.subjectHLA-B
dc.subjectNGS
dc.subjectpolymorphism
dc.subjectvariability
dc.subjectworldwide populations
dc.titleImmunogenetics of HLA-B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgroundsen
dc.typeArtigo
unesp.author.orcid0000-0001-5511-8426[1]
unesp.author.orcid0000-0002-6853-1559[2]
unesp.author.orcid0000-0001-5090-7127[3]
unesp.author.orcid0000-0002-8010-4496[5]
unesp.author.orcid0000-0002-3767-6210[6]
unesp.author.orcid0000-0002-7702-8234[7]
unesp.author.orcid0000-0002-9068-1713[8]
unesp.author.orcid0000-0003-3970-8025[9]
unesp.author.orcid0000-0003-3933-2179[10]
unesp.author.orcid0000-0002-7337-1203[11]
unesp.author.orcid0000-0003-2142-7196[12]

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