dbQSNP: A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods

Tomoko Tahira, Shingo Baba, Koichiro Higasa, Yoji Kukita, Yutaka Suzuki, Sumio Sugano, Kenshi Hayashi

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5′ ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.

Original languageEnglish
Pages (from-to)69-77
Number of pages9
JournalHuman mutation
Volume26
Issue number2
DOIs
Publication statusPublished - Aug 1 2005

Fingerprint

Genetic Promoter Regions
Gene Frequency
Single Nucleotide Polymorphism
Databases
Ethnic Groups
Transcription Initiation Site
Genes
Complementary DNA
Clone Cells
DNA
Population

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

dbQSNP : A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods. / Tahira, Tomoko; Baba, Shingo; Higasa, Koichiro; Kukita, Yoji; Suzuki, Yutaka; Sugano, Sumio; Hayashi, Kenshi.

In: Human mutation, Vol. 26, No. 2, 01.08.2005, p. 69-77.

Research output: Contribution to journalArticle

Tahira, Tomoko ; Baba, Shingo ; Higasa, Koichiro ; Kukita, Yoji ; Suzuki, Yutaka ; Sugano, Sumio ; Hayashi, Kenshi. / dbQSNP : A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods. In: Human mutation. 2005 ; Vol. 26, No. 2. pp. 69-77.
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