Development and evaluation of a rapid and cost-efficient NGS-based MHC class I genotyping method for macaques by using a prevalent short-read sequencer.
Immunogenetics
; 73(2): 175-186, 2021 04.
Article
em En
| MEDLINE
| ID: mdl-33447871
ABSTRACT
Rhesus macaque is one of the most widely used primate model animals for immunological research of infectious diseases including human immunodeficiency virus (HIV) infection. It is well known that major histocompatibility complex (MHC) class I genotypes affect the susceptibility and disease progression to simian immunodeficiency virus (SIV) in rhesus macaques, which is resembling to HIV in humans. It is required to convincingly determine the MHC genotypes in the immunological investigations, that is why several next-generation sequencing (NGS)-based methods have been established. In general, NGS-based genotyping methods using short amplicons are not often applied to MHC because of increasing number of alleles and inevitable ambiguity in allele detection, although there is an advantage of short read sequencing systems that are commonly used today. In this study, we developed a new high-throughput NGS-based genotyping method for MHC class I alleles in rhesus macaques and cynomolgus macaques. By using our method, 95% and 100% of alleles identified by PCR cloning-based method were detected in rhesus macaques and cynomolgus macaques, respectively, which were highly correlated with their expression levels. It was noted that the simulation of new-allele detection step using artificial alleles differing by a few nucleotide sequences from a known allele could be identified with high accuracy and that we could detect a real novel allele from a rhesus macaque sample. These findings supported that our method could be adapted for primate animal models such as macaques to reduce the cost and labor of previous NGS-based MHC genotyping.
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Texto completo:
1
Bases de dados:
MEDLINE
Assunto principal:
Antígenos de Histocompatibilidade Classe I
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Sequenciamento de Nucleotídeos em Larga Escala
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Técnicas de Genotipagem
Tipo de estudo:
Health_economic_evaluation
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Prognostic_studies
Limite:
Animals
Idioma:
En
Revista:
Immunogenetics
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Japão