D-HaploDB

2016/12/13

Web Site: (Closed)http://orca.gen.kyushu-u.ac.jp/
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/dhaplodb/

This database presents true haplotypes and LD structures of Japanese genome, determined using DNA samples obtained from complete hydatidiform moles.

README Content

Database Component
Data Description
License
Update History
Literature
Contact address

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2. Data Description

2.1 README

Data name	README
Description of data contents	HTML file to describe "D-HaploDB" data.
File	README_e.html (English)

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2.2 SNP List (Phase II)

Data name	SNP List (Phase II)
Description of data contents	A list of SNPs in D2 (Phase II). SNP genotypes in D1 (Phase I, Perlegen 281K SNPs) and those determined using Affymetrix 500K Array for overlapping 74 CHM samples were merged and QC'ed. LD bins were then determined.
File	dhaplo_d2_snp_list.zip (16.6MB)

Data items are the following:

Data item	Description
RefSNP ID	RefSNP ID (rs number) given by dbSNP. (Linked to dbSNP in Quick Search)
Affy/Perlegen ID	SNP ID given by Affymetrix or Perlegen
Chromosome	Chromosome number that each SNP resides
Position	Chromosomal nucleotide position (NCBI Build 35) of each SNP
Alleles	Alleles
MAF	Minor allele frequency
Genotypes	Genotypes for the 74 CHM samples
LD bin	Name of LD bin (Linked to LD bin list in Quick Search)
tagSNP	The flag that indicates whether the SNP is a tagSNP or not. 1: tagSNP 0: non-tagSNP -: SNP not included in LD bin calculation (MAF<0.05) td="">
Best tagSNP	The flag that indicates whether the SNP is the best tagSNP or not. 1: Best tagSNP 0: non-best tagSNP -: SNP not included in LD bin calculation (MAF<0.05) td="">

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2.3 SNP List (Phase III)

Data name	SNP List (Phase III)
Description of data contents	A list of SNPs in D3 (Phase III). The data is essentially the same as those described in Kukita et al. (2010) paper, but contains additional samples (CHM010 and CHM035) because their data were judged to be acceptable with regard to genotypes, though they were excluded at QC steps in the previous report. LD bins were then determined.
File	dhaplo_d3_snp_list.zip (23.9MB)

Data items are the following:

Data item	Description
RefSNP ID	RefSNP ID (rs number) given by dbSNP. (Linked to dbSNP in Quick Search)
Affy/Perlegen ID	SNP ID given by Affymetrix
Chromosome	Chromosome number that each SNP resides
Position	Chromosomal nucleotide position (NCBI Build 36) of each SNP
Alleles	Alleles
MAF	Minor allele frequency
Genotypes	Genotypes for the 87 CHM samples
LD bin	Name of LD bin (Linked to LD bin list in Quick Search)
tagSNP	The flag that indicates whether the SNP is a tagSNP or not. 1: tagSNP 0: non-tagSNP -: SNP not included in LD bin calculation (MAF<0.05) td="">
Best tagSNP	The flag that indicates whether the SNP is the best tagSNP or not. 1: Best tagSNP 0: non-best tagSNP -: SNP not included in LD bin calculation (MAF<0.05) td="">

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2.4 LD bin list (Phase II)

Data name	LD bin list (Phase II)
Description of data contents	LD bin list of D2 (Phase II). LD bin is a group of SNPs that mutually shows high LD (r² > 0.8). See below for detail.
File	dhaplo_d2_ld_bin_list.zip (3.0MB)

Data items are the following:

Data item	Description
LD bin	Name of LD bin
Chromosome	Chromosome number each LD bin resides (Chr1 - Chr22, ChrX)
Position Start	Start position of LD bin (nucleotide position in each chromosome, according to NCBI Build 35)
Position End	End position of LD bin (nucleotide position in each chromosome, according to NCBI Build 35)
SNPs Count	Number of SNPs in LD bin
tagSNPs Count	Number of tagSNPs in LD bin
Best tagSNP	tagSNP that showed the highest mean r², given by RefSNP ID (rs number)

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2.5 LD bin list (Phase III)

Data name	LD bin list (Phase III)
Description of data contents	LD bin list of D3 (Phase III). LD bin is a group of SNPs that mutually shows high LD (r² > 0.8). See below for detail.
File	dhaplo_d3_ld_bin_list.zip (3.1MB)

Data items are the following:

Data item	Description
LD bin	Name of LD bin
Chromosome	Chromosome number each LD bin resides (Chr1 - Chr22, ChrX)
Position Start	Start position of LD bin (nucleotide position in each chromosome, according to NCBI Build 36)
Position End	End position of LD bin (nucleotide position in each chromosome, according to NCBI Build 36)
SNPs Count	Number of SNPs in LD bin
tagSNPs Count	Number of tagSNPs in LD bin
Best tagSNP	tagSNP that showed the highest mean r², given by RefSNP ID (rs number) (Link to dbSNP available in quick search)

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2.6 Genotype Data (Phase II)

Data name	Genotype Data (Phase II)
Description of data contents	A list of SNP genotypes in D2(Phase II). SNP genotypes in D1 (Phase I, Perlegen 281K SNPs) and those determined using Affymetrix 500K Array for overlapping 74 CHM samples were merged and QC'ed.
File	mole_info_DhaploD2.txt.gz (13.7MB)

Data items are the following:

Data Item	Description
rs	RefSNP accession ID (rs number)
chr	Chromosome number that the SNP resides (1 - 22, X)
pos	Nucleotide position on chromosome that the SNP resides
allele1	allele 1
allele2	allele 2
gtype	genotypes of 74 samples of CHMs

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2.7 Genotype Data (Phase III)

Data name	Genotype Data (Phase III)
Description of data contents	Genotype data (876K SNPs, 87 samples). Essentially the same as described in Kukita et al. paper (2010), except that two additional samples (CHM010 and CHM035) were included. No CNV information is included in the download data.
File	mole_info_DhaploD3.txt.gz (23.8MB)

Data items are the following:

Data Item	Description
chr	Chromosome number (1-22,X)
sample	Sample (CHM) name
rs	RefSNP accession ID (rs number)
pos	Nucleotide position on chromosome
allele1	allele 1
allele2	allele 2
gtype	genotypes of 87 CHM samples
ss	Unique ID, given by Affymetrix

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2.8 LD_bin Data (Phase II)

Data name	LD_bin Data (Phase II)
Description of data contents	Results of LD bin calculations for D2 (Phase II) data sets. Files are in GFF format, and contains two kinds of lines, that are distinguishable by column# 3. - LD_BIN line: SNPs in LD bin. tagSNPs and best tagSNPs () are marked. - LD_BIN_BOUNDARIES: Limit of LD bin SNP that shows the highest mean r² among the SNPs in the bin
File	bin_2R80M5.gff.gz (12.1MB)

Data items are the following:

Column Number	Definition in GFF format	Description
#1	seqname	Chromosome that the SNP resides (e.g. Chr1)
#2	source	name of dataset (e.g. CHM_2R80M5Z)
#3	feature	description of data. SNP information or LD bin boundary(e.g. LD_BIN, LD_BIN_BOUNDARIES)
#4	start	Chromosomal position of SNP or start position of bin (NCBI Build 35)
#5	end	Chromosomal position of SNP or end position of bin
#6	score	LD_BIN line: 2 for Best tagSNP, and 1 for tagSNP, and 0 for other SNP. LD_BIN_BOUNDARIES line: always "."
#7	strand	always "+"
#8	frame	always ","
#9	attributes	This column contains the following items. - ld_bin: LD bin name - RSID: RefSNP ID (rs number) - tagging: flag that indicates tagSNP - besttag: flag that indicates Best tagSNP - SNPID: unique ID given by Affymetrix (e.g. ld_bin 2R80M5Z_10_1 ; RSID rs16930466 ; tagging 1 ; besttag 0 ; SNPID SNP_A-2110939)

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2.9 LD_bin Data (Phase III)

Data name	LD_bin Data (Phase III)
Description of data contents	Results of LD bin calculations for D3 (Phase III) data sets. Files are in GFF format, and contains two kinds of lines, that are distinguishable by column# 3. - LD_BIN line: SNPs in LD bin. tagSNPs and best tagSNPs () are marked. - LD_BIN_BOUNDARIES: Limit of LD bin SNP that shows the highest mean r² among the SNPs in the bin
File	bin_3R80M5Zb36.gff.gz (12.8MB)

Data items are the following:

Column Number	Definition in GFF format	Description
#1	seqname	Chromosome that the SNP resides (e.g. Chr1)
#2	source	name of dataset (e.g. CHM_3R80M5Z)
#3	feature	description of data. SNP information or LD bin boundary (e.g. LD_BIN, LD_BIN_BOUNDARIES)
#4	start	Chromosomal position of SNP or start position of bin (NCBI Build 36)
#5	end	Chromosomal position of SNP or end position of bin
#6	score	LD_BIN line: 2 for Best tagSNP, and 1 for tagSNP, and 0 for other SNP. LD_BIN_BOUNDARIES line: always "."
#7	strand	always "+"
#8	frame	always "."
#9	attributes	This column contains the following items - ld_bin: LD bin name - RSID: RefSNP ID (rs number) - tagging: flag that indicates tagSNP - besttag: flag that indicates Best tagSNP - SNPID: unique ID given by Affymetrix (e.g. ld_bin 3R80M5Z_10_2 ; RSID rs16930466 ; tagging 1 ; besttag 0 ; SNPID SNP_A-2110939)

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3. License

Last updated : 2011/08/25

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "D-HaploDB © Kenshi Hayashi (Kyushu Univ.) licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.

With regard to this database, you are licensed to:

freely access part or whole of this database, and acquire data;
freely redistribute part or whole of the data from this database; and
freely create and distribute database and other derivative works based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
You must distribute any derivative work based on part or whole of the data from this database under the license.
You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Tomoko Tahira
Kinjo Gakuin University
E-mail: E-mail: ttahira[at]kinjo-u[dot]ac[dot]jp

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4. Update History

Date	Update contents
2016/12/13	Description of the original site is updated.
2011/09/22	D-HaploDB English archive site is opened.
2005/07/20	D-HaploDB (http://orca.gen.kyushu-u.ac.jp/) is released.

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5. Literature

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.
Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles.
Genome Res. 2005 Nov;15(11):1511-8.
PMID: 16251461

Higasa K, Miyatake K, Kukita Y, Tahira T, Hayashi K.
D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples.
Nucleic Acids Res. 2007 Jan;35(Database issue):D685-9.
PMID: 17166862

Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K.
Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions.
PLoS Genetics, 2009 May;5(5):e1000468.
PMID: 19424418

Kukita Y, Yahara K, Tahira T, Higasa K, Sonoda M, Yamamoto K, Kato K, Wake N, Hayashi K.
A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy-number variation events.
Am. J. Hum. Genet. 2010 Jun;86(6):918-28.
PMID: 20537301

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6. Contact address

When you have any question about "D-HaploDB", contact the following:

Tomoko Tahira
Kinjo Gakuin University
E-mail: E-mail: ttahira[at]kinjo-u[dot]ac[dot]jp

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