A multi-ethnic reference panel to impute HLA classical and non-classical class I alleles in admixed samples: Testing imputation accuracy in an admixed sample from Brazil

Registro completo de metadados
MetadadosDescriçãoIdioma
Autor(es): dc.contributorEcole Centrale Nantes-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorHospital Sírio-Libanes-
Autor(es): dc.contributorUniversidade de São Paulo (USP)-
Autor(es): dc.creatorSilva, Nayane S. B.-
Autor(es): dc.creatorBourguiba-Hachemi, Sonia-
Autor(es): dc.creatorCiriaco, Viviane A. O.-
Autor(es): dc.creatorKnorst, Stefan H. Y.-
Autor(es): dc.creatorCarmo, Ramon T.-
Autor(es): dc.creatorMasotti, Cibele-
Autor(es): dc.creatorMeyer, Diogo-
Autor(es): dc.creatorNaslavsky, Michel S.-
Autor(es): dc.creatorDuarte, Yeda A. O.-
Autor(es): dc.creatorZatz, Mayana-
Autor(es): dc.creatorGourraud, Pierre-Antoine-
Autor(es): dc.creatorLimou, Sophie-
Autor(es): dc.creatorCastelli, Erick C.-
Autor(es): dc.creatorVince, Nicolas-
Data de aceite: dc.date.accessioned2025-08-21T18:23:12Z-
Data de disponibilização: dc.date.available2025-08-21T18:23:12Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2024-06-01-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1111/tan.15543-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/298461-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/298461-
Descrição: dc.descriptionThe MHC class I region contains crucial genes for the innate and adaptive immune response, playing a key role in susceptibility to many autoimmune and infectious diseases. Genome-wide association studies have identified numerous disease-associated SNPs within this region. However, these associations do not fully capture the immune-biological relevance of specific HLA alleles. HLA imputation techniques may leverage available SNP arrays by predicting allele genotypes based on the linkage disequilibrium between SNPs and specific HLA alleles. Successful imputation requires diverse and large reference panels, especially for admixed populations. This study employed a bioinformatics approach to call SNPs and HLA alleles in multi-ethnic samples from the 1000 genomes (1KG) dataset and admixed individuals from Brazil (SABE), utilising 30X whole-genome sequencing data. Using HIBAG, we created three reference panels: 1KG (n = 2504), SABE (n = 1171), and the full model (n = 3675) encompassing all samples. In extensive cross-validation of these reference panels, the multi-ethnic 1KG reference exhibited overall superior performance than the reference with only Brazilian samples. However, the best results were achieved with the full model. Additionally, we expanded the scope of imputation by developing reference panels for non-classical, MICA, MICB and HLA-H genes, previously unavailable for multi-ethnic populations. Validation in an independent Brazilian dataset showcased the superiority of our reference panels over the Michigan Imputation Server, particularly in predicting HLA-B alleles among Brazilians. Our investigations underscored the need to enhance or adapt reference panels to encompass the target population's genetic diversity, emphasising the significance of multiethnic references for accurate imputation across different populations.-
Descrição: dc.descriptionCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionCenter for Research in Transplantation and Translational Immunology Nantes Université INSERM Ecole Centrale Nantes-
Descrição: dc.descriptionMolecular Genetics and Bioinformatics Laboratory School of Medicine São Paulo State University, State of São Paulo-
Descrição: dc.descriptionGenetics Program Institute of Biosciences of Botucatu São Paulo State University, State of São Paulo-
Descrição: dc.descriptionDepartment of Molecular Oncology Hospital Sírio-Libanes-
Descrição: dc.descriptionDepartment of Genetics and Evolutionary Biology Biosciences Institute University of São Paulo, State of São Paulo-
Descrição: dc.descriptionHuman Genome and Stem Cell Research Center University of São Paulo, State of São Paulo-
Descrição: dc.descriptionMedical-Surgical Nursing Department School of Nursing University of São Paulo, State of São Paulo-
Descrição: dc.descriptionMolecular Genetics and Bioinformatics Laboratory School of Medicine São Paulo State University, State of São Paulo-
Descrição: dc.descriptionGenetics Program Institute of Biosciences of Botucatu São Paulo State University, State of São Paulo-
Descrição: dc.descriptionFAPESP: 2021/02815-8-
Descrição: dc.descriptionFAPESP: 2021/14851-9-
Idioma: dc.languageen-
Relação: dc.relationHLA-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectAdmixed Population-
Palavras-chave: dc.subjectHLA class I-
Palavras-chave: dc.subjectHLA imputation-
Palavras-chave: dc.subjectReference Panel-
Título: dc.titleA multi-ethnic reference panel to impute HLA classical and non-classical class I alleles in admixed samples: Testing imputation accuracy in an admixed sample from Brazil-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

Não existem arquivos associados a este item.