Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method.

Gene Frequency Genetic Loci HLA Antigens / genetics Haplotypes High-Throughput Nucleotide Sequencing Humans Polymorphism, Single Nucleotide Predictive Value of Tests RNA-Seq Reproducibility of Results
HLA allele RNA expression level capture RNA-Seq genotyping human leukocyte antigen next-generation sequencing

Journal

Frontiers in immunology
ISSN: 1664-3224
Titre abrégé: Front Immunol
Pays: Switzerland
ID NLM: 101560960

Informations de publication

Date de publication:
2020
Historique:
received: 03 12 2019
accepted: 22 04 2020
entrez: 18 6 2020
pubmed: 18 6 2020
medline: 7 4 2021
Statut: epublish

Résumé

The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (

Identifiants

DOI: 10.3389/fimmu.2020.00941 PMID: 32547543 PMC: PMC7272581
pubmed: 32547543
doi: 10.3389/fimmu.2020.00941
pmc: PMC7272581
doi:

Substances chimiques

HLA Antigens 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

941

Informations de copyright

Copyright © 2020 Yamamoto, Suzuki, Mizutani, Shigenari, Ito, Kametani, Kato, Fernandez-Viña, Murata, Morishima, Morishima, Tanaka, Kulski, Bahram and Shiina.

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Auteurs

Fumiko Yamamoto (F)

Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States.
Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Shingo Suzuki (S)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Akiko Mizutani (A)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.
Faculty of Health and Medical Science, Teikyo Heisei University, Toshima-ku, Tokyo, Japan.

Atsuko Shigenari (A)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Sayaka Ito (S)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Yoshie Kametani (Y)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Shunichi Kato (S)

Division of Hematopoietic Cell Transplantation, Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan.

Marcelo Fernandez-Viña (M)

Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States.
Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Stanford Health Care, Palo Alto, CA, United States.

Makoto Murata (M)

Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.

Satoko Morishima (S)

Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.

Yasuo Morishima (Y)

Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan.

Masafumi Tanaka (M)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Jerzy K Kulski (JK)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.
Faculty of Health and Medical Sciences, The University of Western Australia Medical School, Crawley, WA, Australia.

Seiamak Bahram (S)

Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Fédération Hospitalo-Universitaire OMICARE, Laboratoire International Associé INSERM FJ-HLA-Japan, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Faculté de Médecine, Université de Strasbourg, Service d'Immunologie Biologique, Nouvel Hôpital Civil, Strasbourg, France.

Takashi Shiina (T)

Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Fréquence d'allèle › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Locus génétiques › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Facteurs biologiques › Antigènes › Isoantigènes › Antigènes d'histocompatibilité › Antigènes HLA › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Haplotypes › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Valeur prédictive des tests › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ARN › RNA-Seq › Capturing Differential Allele-Level Expression...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › Capturing Differential Allele-Level Expression...