Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression

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Autor(es): dc.contributorUniversidade de São Paulo (USP)-
Autor(es): dc.contributorHarvard Medical School-
Autor(es): dc.contributorBroad Institute of MIT and Harvard-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorUniversity of Vermont-
Autor(es): dc.contributorNational Cancer Institute-
Autor(es): dc.contributorUniversity of KwaZulu-Natal-
Autor(es): dc.contributorTexas Biomedical Research Institute-
Autor(es): dc.contributorThe University of North Carolina at Charlotte-
Autor(es): dc.contributorUniversidade Federal do Paraná (UFPR)-
Autor(es): dc.contributorMIT and Harvard-
Autor(es): dc.creatorAguiar, Vitor R. C.-
Autor(es): dc.creatorCastelli, Erick C.-
Autor(es): dc.creatorSingle, Richard M.-
Autor(es): dc.creatorBashirova, Arman-
Autor(es): dc.creatorRamsuran, Veron-
Autor(es): dc.creatorKulkarni, Smita-
Autor(es): dc.creatorAugusto, Danillo G.-
Autor(es): dc.creatorMartin, Maureen P.-
Autor(es): dc.creatorGutierrez-Arcelus, Maria-
Autor(es): dc.creatorCarrington, Mary-
Autor(es): dc.creatorMeyer, Diogo-
Data de aceite: dc.date.accessioned2025-08-21T19:08:53Z-
Data de disponibilização: dc.date.available2025-08-21T19:08:53Z-
Data de envio: dc.date.issued2023-07-29-
Data de envio: dc.date.issued2023-07-29-
Data de envio: dc.date.issued2023-06-01-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1007/s00251-023-01296-7-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/246732-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/246732-
Descrição: dc.descriptionHuman leukocyte antigen (HLA) class I and II loci are essential elements of innate and acquired immunity. Their functions include antigen presentation to T cells leading to cellular and humoral immune responses, and modulation of NK cells. Their exceptional influence on disease outcome has now been made clear by genome-wide association studies. The exons encoding the peptide-binding groove have been the main focus for determining HLA effects on disease susceptibility/pathogenesis. However, HLA expression levels have also been implicated in disease outcome, adding another dimension to the extreme diversity of HLA that impacts variability in immune responses across individuals. To estimate HLA expression, immunogenetic studies traditionally rely on quantitative PCR (qPCR). Adoption of alternative high-throughput technologies such as RNA-seq has been hampered by technical issues due to the extreme polymorphism at HLA genes. Recently, however, multiple bioinformatic methods have been developed to accurately estimate HLA expression from RNA-seq data. This opens an exciting opportunity to quantify HLA expression in large datasets but also brings questions on whether RNA-seq results are comparable to those by qPCR. In this study, we analyze three classes of expression data for HLA class I genes for a matched set of individuals: (a) RNA-seq, (b) qPCR, and (c) cell surface HLA-C expression. We observed a moderate correlation between expression estimates from qPCR and RNA-seq for HLA-A, -B, and -C (0.2 ≤ rho ≤ 0.53). We discuss technical and biological factors which need to be accounted for when comparing quantifications for different molecular phenotypes or using different techniques.-
Descrição: dc.descriptionSouth African Medical Research Council-
Descrição: dc.descriptionFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)-
Descrição: dc.descriptionConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)-
Descrição: dc.descriptionDivision of Intramural Research, National Institute of Allergy and Infectious Diseases-
Descrição: dc.descriptionNational Institute of General Medical Sciences-
Descrição: dc.descriptionFrederick National Laboratory for Cancer Research-
Descrição: dc.descriptionDepartment of Genetics and Evolutionary Biology Institute of Biosciences University of São Paulo, SP-
Descrição: dc.descriptionDivision of Immunology Boston Children’s Hospital Harvard Medical School-
Descrição: dc.descriptionBroad Institute of MIT and Harvard-
Descrição: dc.descriptionMolecular Genetics and Bioinformatics Laboratory Experimental Research Unit School of Medicine São Paulo State University, SP-
Descrição: dc.descriptionDepartment of Mathematics and Statistics University of Vermont-
Descrição: dc.descriptionBasic Science Program Frederick National Laboratory for Cancer Research National Cancer Institute-
Descrição: dc.descriptionLaboratory of Integrative Cancer Immunology Center for Cancer Research National Cancer Institute-
Descrição: dc.descriptionCentre for the AIDS Programme of Research in South Africa (CAPRISA) University of KwaZulu-Natal-
Descrição: dc.descriptionSchool of Laboratory Medicine and Medical Sciences University of KwaZulu-Natal-
Descrição: dc.descriptionHost-Pathogen Interactions Program Texas Biomedical Research Institute-
Descrição: dc.descriptionDepartment of Biological Sciences The University of North Carolina at Charlotte-
Descrição: dc.descriptionPrograma de Pós-Graduação em Genética Universidade Federal do Paraná, PR-
Descrição: dc.descriptionRagon Institute of MGH MIT and Harvard-
Descrição: dc.descriptionMolecular Genetics and Bioinformatics Laboratory Experimental Research Unit School of Medicine São Paulo State University, SP-
Descrição: dc.descriptionFAPESP: 2012/18010-0-
Descrição: dc.descriptionFAPESP: 2013/22007-7-
Descrição: dc.descriptionFAPESP: 2014/12123-2-
Descrição: dc.descriptionFAPESP: 2016/24734-1-
Descrição: dc.descriptionCNPq: 470043/2014-8-
Descrição: dc.descriptionDivision of Intramural Research, National Institute of Allergy and Infectious Diseases: AI157850-
Descrição: dc.descriptionNational Institute of General Medical Sciences: GM075091-
Descrição: dc.descriptionFrederick National Laboratory for Cancer Research: HHSN261200800001E-
Formato: dc.format249-262-
Idioma: dc.languageen-
Relação: dc.relationImmunogenetics-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectExpression-
Palavras-chave: dc.subjectHLA-
Palavras-chave: dc.subjectPCR-
Palavras-chave: dc.subjectRNA-seq-
Título: dc.titleComparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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