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D-HaploDB


NAR Molecular Biology Database Collection entry number 966
Higasa K., Miyatake K., Kukita Y., Tahira T. and Hayashi K.
Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan

Database Description

D-HaploDB (the Definitive Haplotype Database) is a web-accessible resource of genome-wide definitive haplotypes determined from a collection of Japanese complete hydatidiform moles (CHM), each of which carries a genome derived from a single sperm. Currently, the database contains genotypes for 281,439 common SNPs from 74 CHMs which were determined by a high-throughput array-based oligonucleotide hybridization technique. The database also presents maps of haplotype blocks and linkage disequilibrium (LD) bins together with tagSNPs that might prove useful for association studies of disease genes. D-HaploDB is accessible from http://orca.gen.kyushu-u.ac.jp/.

Recent Developments

A total of 176,152 LD bins were identified by the algorithm of ldSelect program (Carlson et al. AJHG 74: 106-120, 2004) and integrated into D-HaploDB. All of the data set, which includes raw genotypes and analytic results such as block, LD bin, common haplotype, and tagSNPs, is available as a series of text files at http://orca.gen.kyushu-u.ac.jp/download.html.

Acknowledgements

This work was supported by a Grant-in-Aid for Genome Science from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

References

1. Kukita Y, Miyatake K, Stokowski R, Hinds D, Higasa K, Wake N, Hirakawa T, Kato H, Matsuda T, Pant K, Cox D, Tahira T, Hayashi K (2005) Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles. Genome Res. 15: 1511-1518.


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