Optimal population-specific HLA imputation with dimension reduction

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Autor(es): dc.contributorCenter for Research in Transplantation and Translational Immunology-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorUniversidade de São Paulo (USP)-
Autor(es): dc.contributorHospital Israelita Albert Einstein-
Autor(es): dc.contributorCHU de Nantes-
Autor(es): dc.creatorDouillard, Venceslas-
Autor(es): dc.creatordos Santos Brito Silva, Nayane-
Autor(es): dc.creatorBourguiba-Hachemi, Sonia-
Autor(es): dc.creatorNaslavsky, Michel S.-
Autor(es): dc.creatorScliar, Marilia O.-
Autor(es): dc.creatorDuarte, Yeda A. O.-
Autor(es): dc.creatorZatz, Mayana-
Autor(es): dc.creatorPassos-Bueno, Maria Rita-
Autor(es): dc.creatorLimou, Sophie-
Autor(es): dc.creatorGourraud, Pierre-Antoine-
Autor(es): dc.creatorLaunay, Élise-
Autor(es): dc.creatorCastelli, Erick C.-
Autor(es): dc.creatorVince, Nicolas-
Data de aceite: dc.date.accessioned2025-08-21T19:56:37Z-
Data de disponibilização: dc.date.available2025-08-21T19:56:37Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2023-12-31-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1111/tan.15282-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/305438-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/305438-
Descrição: dc.descriptionHuman genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.-
Descrição: dc.descriptionConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionInstitut National de la Santé et de la Recherche Médicale-
Descrição: dc.descriptionH2020 Marie Skłodowska-Curie Actions-
Descrição: dc.descriptionConseil Régional des Pays de la Loire-
Descrição: dc.descriptionUniversité de Nantes-
Descrição: dc.descriptionNantes Université INSERM Ecole Centrale Nantes Center for Research in Transplantation and Translational Immunology-
Descrição: dc.descriptionSão Paulo State University Molecular Genetics and Bioinformatics Laboratory School of Medicine-
Descrição: dc.descriptionHuman Genome and Stem Cell Research Center University of São Paulo-
Descrição: dc.descriptionDepartment of Genetics and Evolutionary Biology Biosciences Institute University of São Paulo-
Descrição: dc.descriptionHospital Israelita Albert Einstein-
Descrição: dc.descriptionMedical-Surgical Nursing Department School of Nursing University of São Paulo-
Descrição: dc.descriptionEpidemiology Department Public Health School University of São Paulo-
Descrição: dc.descriptionDepartment of Pediatrics and Pediatric Emergency Hôpital Femme Enfant Adolescent CHU de Nantes-
Descrição: dc.descriptionSão Paulo State University Molecular Genetics and Bioinformatics Laboratory School of Medicine-
Idioma: dc.languageen-
Relação: dc.relationHLA-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectAdmixed populations-
Palavras-chave: dc.subjectDimension reduction-
Palavras-chave: dc.subjectHLA imputation-
Palavras-chave: dc.subjectImmunogenomics-
Título: dc.titleOptimal population-specific HLA imputation with dimension reduction-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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