Autor(es): Vince, Nicolas ; Douillard, Venceslas ; Geffard, Estelle ; Meyer, Diogo ; Castelli, Erick C. [UNESP] ; Mack, Steven J. ; Limou, Sophie ; Gourraud, Pierre-Antoine
Data: 2020
Identificador Persistente: http://hdl.handle.net/11449/199112
Origem: Oasisbr
Assunto(s): consortium; HLA; imputation; SNP
Made available in DSpace on 2020-12-12T01:31:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-10-01
Genome-wide associations studies have repeatedly identified the major histocompatibility complex genomic region (6p21.3) as key in immune pathologies. Researchers have also aimed to extend the biological interpretation of associations by focusing directly on human leukocyte antigen (HLA) polymorphisms and their combination as haplotypes. To circumvent the effort and high costs of HLA typing, statistical solutions have been developed to infer HLA alleles from single-nucleotide polymorphism (SNP) genotyping data. Though HLA imputation methods have been developed, no unified effort has yet been undertaken to share large and diverse imputation models, or to improve methods. By training the HIBAG software on SNP + HLA data generated by the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) to create reference panels, we highlighted the importance of (a) the number of individuals in reference panels, with a twofold increase in accuracy (from 10 to 100 individuals) and (b) the number of SNPs, with a 1.5-fold increase in accuracy (from 500 to 24,504 SNPs). Results showed improved accuracy with CAAPA compared to the African American models available in HIBAG, highlighting the need for precise population-matching. The SNP-HLA Reference Consortium is an international endeavor to gather data, enhance HLA imputation and broaden access to highly accurate imputation models for the immunogenomics community.
Centre de Recherche en Transplantation et Immunologie ITUN UMR 1064 Université de Nantes CHU Nantes Inserm
University of São Paulo
UNESP—Universidade Estadual Paulista
Department of Pediatrics University of California San Francisco UCSF Benioff Children's Hospital Oakland
Ecole Centrale de Nantes
UNESP—Universidade Estadual Paulista
