TY - JOUR
T1 - Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing
AU - Mimori, Takahiro
AU - Yasuda, Jun
AU - Kuroki, Yoko
AU - Shibata, Tomoko F.
AU - Katsuoka, Fumiki
AU - Saito, Sakae
AU - Nariai, Naoki
AU - Ono, Akira
AU - Nakai-Inagaki, Naomi
AU - Misawa, Kazuharu
AU - Tateno, Keiko
AU - Kawai, Yosuke
AU - Fuse, Nobuo
AU - Hozawa, Atsushi
AU - Kuriyama, Shinichi
AU - Sugawara, Junichi
AU - Minegishi, Naoko
AU - Suzuki, Kichiya
AU - Kinoshita, Kengo
AU - Nagasaki, Masao
AU - Yamamoto, Masayuki
N1 - Funding Information:
Acknowledgements We thank Prof. Katsushi Tokunaga for helpful discussion. This work was partly supported by grants from the Reconstruction Agency, the Ministry of Education, Culture, Sports, Science and Technology (MEXT), the Center of Innovation Program from Japan Science, from Technology Agency (JST), and the Japan Agency for Medical Research and Development (AMED) under Grant Number JP17km0105001, JP17km0105002, JP17km0405001 and JP17km0405205. All computational resources were provided by the ToMMo supercomputer system (http://sc.megabank.tohoku.ac.jp/en). We would like to thank the members of ToMMo and Iwate Medical Megabank Organization (IMM) for seminal contribution to the establishment of the genome cohort and biobank, and for help with the genome analyzes. We are indebted all the volunteers who participated in this project. The full list of participants is available at http://www. megabank.tohoku.ac.jp/english/a150601/ for ToMMo and http://iwate-megabank.org/en/about/departments/ for IMM.
Publisher Copyright:
© 2018, The Author(s).
PY - 2019/4/1
Y1 - 2019/4/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41397-017-0010-4
DO - 10.1038/s41397-017-0010-4
M3 - Article
C2 - 29352165
AN - SCOPUS:85040747295
SN - 1470-269X
VL - 19
SP - 136
EP - 146
JO - Pharmacogenomics Journal
JF - Pharmacogenomics Journal
IS - 2
ER -
