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The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Toshiaki Katayama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2014 Nucleic Acids Research  
DDBJ Center provides the JGA database system which securely stores genotype and phenotype data collected from individuals whose consent agreements authorize data release only for specific research use.  ...  The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Takeshi Tsurusawa, Koji Watanabe, Chiharu Kawagoe and all members of the DDBJ Center for their assistance in data collection, annotation, release  ... 
doi:10.1093/nar/gku1120 pmid:25477381 pmcid:PMC4383935 fatcat:tcpa3elm3zglbo5lauuatx3nca

DNA Data Bank of Japan: 30th anniversary

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2017 Nucleic Acids Research  
The DDBJ Center also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database Center to collect genotype and phenotype data of human individuals.  ...  Furthermore, we highlight our responses to the amended Japanese rules for the protection of personal information and the launch of the DDBJ Group Cloud service for sharing pre-publication data among research  ...  Data contents: the Japanese genotype-phenotype archive (JGA) The JGA is a permanent archiving service for human genotype and phenotype data (8) .  ... 
doi:10.1093/nar/gkx926 pmid:29040613 pmcid:PMC5753283 fatcat:3n45p6fz6bcfzgtv6j2prd44vq

DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Osamu Ogasawara
2018 Nucleic Acids Research  
The DDBJ Center collects nucleotide sequence data and associated biological information from researchers and also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database  ...  Center for collecting human data.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge Koji Watanabe, Naofumi Ishikawa, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi, Masanori Arita and all members of the DDBJ Center for their support in data  ... 
doi:10.1093/nar/gky1002 pmid:30357349 pmcid:PMC6323915 fatcat:3bgfc6a3lvf6fjavejrvwixzne

DDBJ progress report: a new submission system for leading to a correct annotation

Takehide Kosuge, Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura
2013 Nucleic Acids Research  
JGA permanently archives and shares all types of individual human genetic and phenotypic data. We also introduce improvements in the DDBJ services and databases made during the past year.  ...  The DNA Data Bank of Japan (DDBJ; http://www. ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Takeshi Tsurusawa, Keiichi Nagai and all members of DDBJ for their assistance in data collection, annotation, release and software development.  ... 
doi:10.1093/nar/gkt1066 pmid:24194602 pmcid:PMC3964987 fatcat:vc62xknuzret3iehrzgxhzqhve

DNA data bank of Japan (DDBJ) progress report

Jun Mashima, Yuichi Kodama, Takehide Kosuge, Takatomo Fujisawa, Toshiaki Katayama, Hideki Nagasaki, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2015 Nucleic Acids Research  
Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan.  ...  The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for their assistance in data collection, annotation, release, and software development  ... 
doi:10.1093/nar/gkv1105 pmid:26578571 pmcid:PMC4702806 fatcat:dsvzn2iivjb7jhqnqhoehswhtu

DNA Data Bank of Japan

Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2016 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ) (http://www. ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987).  ...  We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc. org), in collaboration with the  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for  ... 
doi:10.1093/nar/gkw1001 pmid:27924010 pmcid:PMC5210514 fatcat:sbslos5mnbgnpfurvzabh2svki

DDBJ Database updates and computational infrastructure enhancement

2019 Nucleic Acids Research  
The NIG operates the NIG supercomputer as a computational basis for the construction of DDBJ databases and as a large-scale computational resource for Japanese biologists and medical researchers.  ...  The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Naofumi Ishikawa and all members of Bioinformation and DDBJ Center for their assistance in data collection, annotation, release  ... 
doi:10.1093/nar/gkz982 pmid:31724722 pmcid:PMC7145692 fatcat:uubxnpbeqvabrkkaw5ah4q7hzm

Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish [article]

Mikhail Spivakov, Thomas O. Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi, Felix Loosli, Kiyoshi Naruse, Ewan Birney (+1 others)
2013 arXiv   pre-print
Conclusions These data indicate that the genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based  ...  Oryzias latipes (Medaka) has been established as a vertebrate genetic model for over a century, and has recently been rediscovered outside its native Japan.  ...  the Sanger Instute Sequencing Facility for sequencing of the inbred Trios, Tetsuaki Kimura for assistance with FISH sampling, Wei Chen for advice on TrioCaller, and the NBRP Core Facility Upgrading Program  ... 
arXiv:1304.4515v2 fatcat:qnfmlagh7bfbply6r5radbbhvi

DNAdigest and Repositive: Connecting the World of Genomic Data

Nadezda V. Kovalevskaya, Charlotte Whicher, Timothy D. Richardson, Craig Smith, Jana Grajciarova, Xocas Cardama, José Moreira, Adrian Alexa, Amanda A. McMurray, Fiona G. G. Nielsen
2016 PLoS Biology  
DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients.  ...  Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human  ...  Matthew Young for the critical reading of the manuscript; Carolina Rabei for help with illustrations; Sebastian Place, Francis Menson, and Daniel Gynn for assistance with the development of the Repositive  ... 
doi:10.1371/journal.pbio.1002418 pmid:27011302 pmcid:PMC4807091 fatcat:ax6h6r6jw5db3jn7lnf634folm

Nonsense mutation in PMEL is associated with yellowish plumage colour phenotype in Japanese quail

Satoshi Ishishita, Mayuko Takahashi, Katsushi Yamaguchi, Keiji Kinoshita, Mikiharu Nakano, Mitsuo Nunome, Shumpei Kitahara, Shoji Tatsumoto, Yasuhiro Go, Shuji Shigenobu, Yoichi Matsuda
2018 Scientific Reports  
The L strain of Japanese quail exhibits a plumage phenotype that is light yellowish in colour.  ...  Genotypes at the site of the nonsense mutation were fully concordant with plumage colour phenotypes in 196 F 2 offspring.  ...  This study was carried out under the NIBB Cooperative Research Program for Next-generation DNA Sequencing . Computational resources were provided by the Data Integration and Analysis Facility, NIBB.  ... 
doi:10.1038/s41598-018-34827-4 pmid:30425278 pmcid:PMC6233202 fatcat:rkk6g4ine5dhjh7zpzfvkd2uce

Functional variants in ADH1B and ALDH2 are non-additively associated with all-cause mortality in Japanese population

Saori Sakaue, Masato Akiyama, Makoto Hirata, Koichi Matsuda, Yoshinori Murakami, Michiaki Kubo, Yoichiro Kamatani, Yukinori Okada
2019 European Journal of Human Genetics  
genotype and follow-up survival data.  ...  The heterogenous combinatory effect between rs1229984 and rs671 genotype was also observed (HRs for AA genotype at rs671 were 1.03, 0.80, and 0.90 for GG, GA, and AA genotype at rs1229984, respectively  ...  The genotype data in this study is deposited on the Japanese Genotype-phenotype Archive affiliated to the DDBJ (DNA Data Bank of Japan), via National Bioscience Database Center (NBDC), Japan.  ... 
doi:10.1038/s41431-019-0518-y pmid:31558841 pmcid:PMC7028931 fatcat:astuq4hvibbkxm24x6t4zkikhi

Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don)

Kentaro Mishima, Tomonori Hirao, Miyoko Tsubomura, Miho Tamura, Manabu Kurita, Mine Nose, So Hanaoka, Makoto Takahashi, Atsushi Watanabe
2018 BMC Genomics  
Conclusions: More than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar.  ...  These marker loci explained 100% of the phenotypic variation.  ...  More than half of the collected ESTs and SNPs were new, enlarging the genomic basis for genetic research on Japanese cedar.  ... 
doi:10.1186/s12864-018-4581-5 pmid:29685102 pmcid:PMC5914023 fatcat:glm4oxbumne27h5tznzt5vowzy

Genomic and Phenotypic Characterization of a Wild Medaka Population: Towards the Establishment of an Isogenic Population Genetic Resource in Fish

Mikhail Spivakov, Thomas O. Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi, Felix Loosli, Kiyoshi Naruse, Ewan Birney (+1 others)
2014 G3: Genes, Genomes, Genetics  
First, as the same genotype can be produced multiple times from the panel, genotypic and phenotypic resources can be shared on the same panel between research groups and experiments.  ...  These data indicate that the genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population  ...  the Sanger Institute Sequencing Facility for sequencing of the inbred trios, Tetsuaki Kimura and Yusuke Takehana for assistance with fish sampling, Wei Chen for advice on TrioCaller, and the National BioResource  ... 
doi:10.1534/g3.113.008722 pmid:24408034 pmcid:PMC3962483 fatcat:amd2szajmfa4hbdohijtlxbq7u

Open Access DNA, Rna and Amino Acid Sequences: The Consequences and Solutions for the International Regulation of Access and Benefit Sharing

Charles Lawson, Michelle Rourke
2016 Social Science Research Network  
Tracing the evolution of open access databases, the article posits models for reconciling open access and benefit sharing; the article concludes, however, that none of the proposed solutions -monitoring  ...  and tracing, the contract model, and the copyright and database right model -provides a perfect solution.  ...  Association Studies (GWAS Policy). 137 dbGaP was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype, including sequence data.  ... 
doi:10.2139/ssrn.2848136 fatcat:a3tnue3ec5er3nydp4vm3bxu2m

DNA/RNA heteroduplex oligonucleotide for highly efficient gene silencing

Kazutaka Nishina, Wenying Piao, Kie Yoshida-Tanaka, Yumiko Sujino, Tomoko Nishina, Tsuyoshi Yamamoto, Keiko Nitta, Kotaro Yoshioka, Hiroya Kuwahara, Hidenori Yasuhara, Takeshi Baba, Fumiko Ono (+10 others)
2015 Nature Communications  
These results suggest that DNA/RNA heteroduplex can serve as the basic technology of the oligonucleotide drug, and opens up a new horizon for human gene therapy as a novel class of oligonucleotide drugs  ...  HDO is found to be significantly potent at reducing expression of the target RNA, and also effectively improves the phenotype in disease models.  ...  The Japanese HLA reference panel is publicly available from the Japanese Genotype-phenotype Archive (URL: https://ddbj. nig.ac.jp/jga/viewer/view/study/ JGAS00000000018).  ... 
doi:10.1038/ncomms8969 pmid:26258894 pmcid:PMC4918363 fatcat:bprwijseafeqjnuft6mog3pe5u
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