dbQSNP

2017/02/16

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

SNP discovery and determination of their allele frequency in various sample groups using pooled DNA-quantitative fluorescent SSCP analysis

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Allele Frequency Data
  3. Sequence Data
  4. Original Dataset
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "dbQSNP" data.
File README_e.html (English)
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2.2 Allele Frequency Data

Data name Allele Frequency Data
Description of data contents

SNP allele frequencies in Japanese and European populations, determined by quantitative fluorescent PCR-SSCP analysis of pooled DNA.
File dbqsnp_frequency.zip (159 KB)

Data items are the following:
Data itemDescription
dbQSNP_id dbQSNP ID.
strand Orientation of the STS compared with contig sequence of GenBank (NT sequence, NCBI Build 36) . Note that SNPs are always described as sequences in forward strand of the STS.
contig_id ID of genomic contigs that showed highest homology to the STS (NT sequence, NCBI Build 36)
rs# dbSNP accession for the refSNP (dbSNP Build 128)
allele_1 sequence of allele 1
allele_2 sequence of allele 2
AF_allele_1 allele frequency of allele 1
AF_allele_2 allele frequency of allele 2
pool_id ID of pooled DNA (see below, DNA samples were extracted from peripheral blood lymphocytes)
"CAU200", prepared from Caucasian Panel of 200, obtained from CORIELL (HD200, https://www.coriell.org) was used as the Caucasian pool in a large part of this study. "CP" (combined CEPH parents, prepared by us from 45 CEPH core family collection) and "COP" (HD100 from CORIELL) were also used.

"JSA426", prepared from DNA derived from apparently healthy individuals enrolled at Kyushu area was used as the Japanese pool in a large part of study. Other pools derived from healthy individuals enrolled at various area of Japan were also used. Those were; JPK, JPK2, JPK3, JCM253, NCEP, NCL_P, NCP269, NCE_SP and JNCL_SP.

The allele frequency data of pools derived from breast cancer patients (BREP, BRLP, JBRE_SP, JBRL_SP) and pools derived from systemic lupus erythematosus patients (SLEP264, SLEP183), obtained in association studies of each diseases, are also included
#individual The number of individuals in the pool
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2.3 Sequence Data

Data name Sequence Data
Description of data contents

SNPs and their flanking sequences were determined by Sanger sequencing of PCR products amplified from randomly picked Japanese individuals (in most cases, eight individuals).
File dbqsnp_fasta.zip (1.0 MB)

Data items are the following:
Data itemDescription
dbQSNP_id dbQSNP ID.
allele_Pos Variation allele position (1st base of variation) on the fasta sequence. It is always the 5' length plus 1.
total_Len Total number of bases of the fasta sequence, a sum of length of 5', 3' and variation (A length of variation can be more than 1 in the case of ins/del polymorphisms).
Internal_STS_ID Internal STS ID
alleles Lists alleles of the SNP separated by '/'.
sequence Sequence
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2.4 Original Dataset

Data name Original Dataset
Description of data contents

Files which were formerly available from the original site ( http://qsnp.gen.kyushu-u.ac.jp/download/ , closed) - Readme.txt, dbQSNP.15.fasta.txt ("Sequence Data" original data), Frequency.15.txt ("Allele Frequency Data" original data) and the subdirectory pml/ is included - the subdirectory old/ is not included - pml/ includes data in PML (Polymorphism Markup Language) which is based on XML to facilitate portability.
File dbQSNPdownload.tar.gz (1.2 MB)
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3. License

Last updated : 2017/02/16

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.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "dbQSNP © Kenshi Hayashi (Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

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

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. 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: ttahira[at]kinjo-u[dot]ac[dot]jp

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2017/02/16 dbQSNP English archive site is opened.
2002/10/23 dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/) is opened.
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5. Literature

Tahira T, Baba S, Higasa K, Kukita Y, Suzuki Y, Sugano S, Hayashi K
dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation
Human Mutation 2005 Aug. 26(2) 69-77
PMID: 15977179

Sasaki T, Tahira T, Suzuki A, Higasa K, Kukita Y, Baba S, Hayashi K.
Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA.
Am J Hum Genet. 2001 Jan;68(1):214-8.
PMID: 11083945

Baba S, Kukita Y, Higasa K, Tahira T, Hayashi K.
Single-stranded conformational polymorphism analysis using automated capillary array electrophoresis apparatuses.
Biotechniques. 2003 Apr;34(4):746-50.
PMID: 12703299

Higasa K, Kukita Y, Baba S, Hayashi K.
Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA)
Biotechniques. 2002 Dec;33(6):1342-8.
PMID: 12503322

Miyagawa H, Yamai M, Sakaguchi D, Kiyohara C, Tsukamoto H, Kimoto Y, Nakamura T, Lee JH, Tsai CY, Chiang BL, Shimoda T, Harada M, Tahira T, Hayashi K, Horiuchi T.
Association of polymorphisms in complement component C3 gene with susceptibility to systemic lupus erythematosus.
Rheumatology (Oxford). 2008 Feb;47(2):158-64
PMID: 18174230

Tahira T, Kukita Y, Higasa K, Okazaki Y, Yoshinaga A, Hayashi K
Estimation of SNP allele frequencies by SSCP analysis of pooled DNA
Methods in Molecular Biology 578:193-207 (2009)
PMID: 19768595

Jespersgaard C, Larsen LA, Baba S, Kukita Y, Tahira T, Christiansen M, Vuust J, Hayashi K, Andersen PS
Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics
Electrophoresis 27: 3816-3822 (2006)
PMID: 16941449

Kukita Y, Hayashi K
Multicolor post-PCR labeling of DNA fragments with fluorescent dideoxynucleotides.
BioTechniques 33: 502-506 (2002)
PMID: 12238759

Kukita Y, Manago S, Baba S, Hayashi K
Hemi-stranded SSCP analysis of single-nucleotide polymorphisms in short sequence-tagged sites.
BioTechniques 33:1118-1121 (2002)
PMID: 12449392

Hayashi K, Wenz HM, Inazuka M, Tahira T, Sasaki T, Atha DH
SSCP analysis of point mutations by multicolor capillary electrophoresis.
Methods in Molecular Biology 163: 109-126 (2001)
PMID: 11242937

Hayashi K
Recent enhancements in SSCP.
Genetic Analysis: Biomolecular Engineering 14: 193-196 (1999)
PMID: 10084114

Kukita Y, Tahira T, Sommer SS, Hayashi K
SSCP analysis of long DNA fragments in low pH gel
Human Mutation 10: 400-407 (1997)
PMID: 9375857

Inazuka M, Tahira T, Hayashi K
One-tube post-PCR fluorescent labeling of DNA fragments
Genome Research 6: 551-557 (1996)
PMID: 8828044

Hayashi K
PCR-SSCP: A method for detection of mutations
Genetic Analsysis: Techniques and Applications 9: 73-79 (1992)
PMID: 1476794

Hayashi, K
PCR-SSCP: A simple and sensitive method for detection of mutations in the genomic DNA
PCR Methods and Applications 1: 34-38 (1991)
PMID: 1842918

Orita M, Suzuki Y, Sekiya T, Hayashi K
Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction
Genomics 5: 874-879 (1989)
PMID: 2687159

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6. Contact address

When you have any question about "dbQSNP", contact the following:

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

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