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In this site, we present genome-wide definitive haplotypes, determined using a collection of 100 Japanese complete hydatidiform moles (CHMs), each carrying a genome derived from a single sperm. The haplotypes incorporate 281 k (D-Haplo Phase I: D1), 581k (D-Haplo Phase II: D2), or 1M (D-Haplo Phase III: D3) SNPs, genotyped with high throughput array-based oligonucleotide hybridization techniques. The Definitive Haplotype Browser can be used to view various information, such as SNP alleles, haplotype blocks, LD-bins and extended shared haplotypes (ESHs) in our study.
News
2009-09-02, Genotype data file of D-Haplo Phase II is now downloadable.
2008-05-27, Genotypes and LD bin data for D-Haplo Phase III release are now browsable.
Getting Started
You can get started browsing by selecting a chromosome, gene, genomic region, or reference SNP for study. You will then be able to customize your view using the functionality of the Generic Genome Browser.
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By Chromosome
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By Genomic Region
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By Gene Name
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By refSNP Identifier
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Track descriptions of the Definitive Haplotype Browser
Data Availability
The genotype data of Definitive Haplotype Database are freely available for academic, nonprofit, and personal use, at Data Download section of this web site.
We request that authors who use data of D-HaploDB refer the following papers:
Y. Kukita, K. Miyatake, R. Stokowski, D. Hinds, K. Higasa, N. Wake, T. Hirakawa, H. Kato, T. Matsuda, K. Pant, D. Cox, T. Tahira, K. Hayashi (2005) Genome-Wide Definitive Haplotypes Determined Using a Collection of Complete Hydatideform Moles. Genome Research 15: 1511-1518.
Higasa K, Miyatake K, Kukita Y, Tahira T, Hayashi K (2007) D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. Nucleic Acids Res. 35: D685-689.
Contact us
Questions or comments regarding this site are welcome at 
Track descriptions of the Definitive Haplotype Browser
Fig. 1. Example of a browser view
Cytoband
Cytoband from the UCSC Genome Browser
Density HapMapSNPs
The number of polymorphic SNPs genotyped in HapMap Japanese population (JPT, release 21) per 100 kb
Density CHMSNPs
The number of SNPs genotyped in complete hydatidiform mole (CHM) samples per 100 kb
Transcripts
Transcripts from NCBI
HapMapSNPs
SNPs genotyped in HapMap JPT (magenta: polymorphic; yellow: monomorphic)
CHMSNPs
SNPs used for genotyping of CHM samples (red: genotyped only in CHMs; blue: genotyped both in CHMs and HapMap JPT)
Blocks
Haplotype blocks deduced from 74 Japanese CHM haplotypes. Construction of haplotype block partitions was done using HapBlock v30 (http://www.cmb.usc.edu/msms/HapBlock/). The following parameters were used: the methods for block definition and tag SNP selection were those used in Patil et al. (Science 294: 1719-1723, 2001). A set of consecutive SNPs forms a block if the number of common haplotypes account for at least 80% of all the observed haplotypes, and the haplotypes represented more than 5% are considered as common haplotypes. The minimum set of SNPs that can uniquely distinguish a subset of common haplotypes that can account for at least 80% of all the observed haplotypes are considered as a set of tag SNPs. In the selection of tag SNPs, the minimum frequency for common haplotypes was set to 5%.
LD bins
The pair-wise r2 tagging was done using ldSelect program (Carlson et al. AJHG 74: 106-120, 2004) with the threshold of r2 = 0.80 and SNPs whose minor allele frequency (MAF) is at least 5 or 10%. In the LD bin track, the best-tags (i.e., the tagSNP that showed the highest average r2 for the remaining members within the bin) are highlighted in red.
Simulated locus
The regions examined by pseudoindividual analysis for phasing accuracy assessment. We constructed 100 sets of pseudoindividuals for each genomic region. This was done by randomly choosing pairs of samples from the selected CHMs without replacement. This was repeated 100 times to produce 100 sets of pseudoindividuals. Phasing for each set was done using PHASE v2.1.1 (Bayesian method with approximate "coalescent with recombination" prior distribution) (http://www.stat.washington.edu/stephens/software.html). Then, inferred haplotypes of 100 sets of pseudoindividuals were used to deduced block partitions (using HapBlock), and compared with those from CHM haplotypes. Block partitionins in simulated regions are shown in a separated window (Fig. 2; green: CHM blocks; blue: pseudo blocks), which is opened by clicking blue boxes at the bottom track of the Definitive Haplotype Browser.
Note: Because only SNPs in each region (50 SNPs) were used for these simulations, each block partition deduced from CHM haplotypes may not be same as each portion of whole-genome partitions.
Fig. 2. A view of the simulated region presented in Fig. 1
ESH_*
The density of ESHs longer than 1 Mb among all pairs of haplotypes of 74 HapMap CEU (Caucasian) chromosomes, 74 HapMap JPT (Japanese) chromosomes, and 74 CHM chromosomes from this study. When unusually large gaps greater than 200 kb were found between adjacent polymorphic SNPs, those gaps was treated as 200 kb regardless of their actual length. This was done to limit the impact of very large sequence gaps such as centromeres. The density was determined as the number of overlapping ESHs at 100 kb intervals. The bars in the overview track are color-coded to indicate ESH density, i.e., white to dark blue for 0 to nC2.
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