Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing.
Pharmacogenomics J
; 19(2): 136-146, 2019 04.
Article
em En
| MEDLINE
| ID: mdl-29352165
ABSTRACT
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Variação Genética
/
Antígenos de Histocompatibilidade Classe I
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Genoma Humano
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Sequenciamento de Nucleotídeos em Larga Escala
Limite:
Humans
País como assunto:
Asia
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article