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dbQSNP


NAR Molecular Biology Database Collection entry number 595
Tahira, T., Higasa, K., Kukita, Y., Baba, S., Akiyama, J., Miura, K., Hayashi, K.
Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan

Database 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.

Acknowledgements

This work was supported by a Grant-in-Aid for Genome Science from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

References

Baba S, Kukita Y, Higasa K, Tahira T, Hayashi K (2003) Single-stranded conformational polymorphism analysis using automated capillary array electrophoresis apparatus. BioTechniques 34: in press.

Inazuka M, Wenz HM, Sakabe M, Tahira T, Hayashi K (1997) A stream-lined mutation detection system: Multi-color post-PCR fluorescence-labeling and SSCP analysis by capillary electrophoresis. Genome Research 7: 1094-1103.

Hayashi K, Wenz H-M, Inazuka M, Tahira T, Sasaki T, Atha DH (2001) SSCP analysis of point mutations by multi-color capillary electrophoresis. in Methods in Molecular Biology, vol 163: Capillary Electrophoresis of Nucleic Acids: Practical Applications of Capillary Electrophoresis, vol. 2, pp.109-125. K. Mitchelson and J. Cheng eds., Humana Press Inc., NJ, U.S.A.

Higasa K, Kukita Y, Baba S, Hayashi K (2002) A software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA). BioTechniques 33: 1342-1348.

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

Kukita Y, Higasa K, Baba S, Nakamura M, Manago S, Suzuki A, Tahira T, Hayashi K (2002) A high throughput single-strand conformation polymorphism analysis method using capillary-array electrophoresis system. Electrophoresis 23: 2259-2266.

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

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



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