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  1. dbQSNP (View Publication)
    Full Name of the Resource : Quantification of SNP allele frequencies database
    Resource Category : Databases -> Human Genes and Diseases -> General Polymorphism Databases

    Brief Description : We have established a streamlined and cost-efficient SNP discovery/ quantification method that is based on SSCP analysis using capillary electrophoresis (Orita et al., 1989; Inazuka et al., 1997; Sasaki et al., 2001; Hayashi et al., 2001; Tahira et al., 2002; Kukita et al., 2002; Baba et al., 2003). In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights of pooled DNA. The raw data of SSCP analysis obtained from various capillary-array apparatuses are interpreted by a newly developed fragment analysis software, "QUISCA" (Higasa et al., 2002). To manage SSCP and sequencing analyses for discovering SNPs and determining their allele frequency at a large scale, we developed a relational database, "dbQSNP Conductor", that runs on postgreSQL, and supports designing experiments, analyzing results of SSCP/sequencing from various capillary-array DNA sequencers, and verifying these results to minimize error (Baba et al., in preparation). This site, "dbQSNP Public", is a repository of STS/SNP information obtained by "dbQSNP conductor". SSCP and sequence trace data are just a few clicks away, and thus, integrity of the data can be confirmed. In dbQSNP, a project is defined as a set of STSs that are amplifiable with primer pairs in a pair of 96-well plates. Each project belongs to a series of experiments (Series) aimed at characterizing SNPs in genomic regions of particular interest. The Series can be to characterize regulatory SNPs (reg), regulatory SNPs in micro-STS configuration (regm), SNPs in tumor suppressor genes (tsg), etc. Usually, a project has a name, which is series name followed by number, such as reg14, regm6, or tsg4. The Series "reg" and "regm" are a collaborative work with Dr. Sumio Sugano and his group, Human Genome Center, Institute of Medical Science, University of Tokyo.

    Institute/s :
    Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
    Country : Japan


    Authors/Contributors : Hayashi, K.
    Contact Email : khayashi@gen.kyushu-u.ac.jp
    Year : 2002

    Keywords : Alleles; Computational Biology / methods; DNA, Complementary / metabolism; *Gene Expression Regulation; Gene Frequency; Genetic Variation; Humans; Internet; *Polymorphism, Single Nucleotide; *Polymorphism, Single-Stranded Conformational; *Promoter Regions, Genetic; Sequence Analysis, DNA