The number of SNPs (single nucleotide polymorphisms) discovered by Japan Science and Technology Corp (JST) and Tokyo University's Institute of Medical Science, in an initiative that is part of the government-driven Millennium Project, has risen to 193,037, according to recently published data.

JST and Tokyo University released the latest data from the SNP database in late October, and expect to release related analysis in December, according to officials working on the project. The data is the fruit of two years of research into SNPs, and exceeds the original goals of the project, which was to discover 150,000 SNPs.

The project was initiated to identify disease-related genes and help avoid drug side-effects. JST, a publicly funded organisation, and Tokyo University searched for SNPs throughout the entire human genome using DNA from 24 Japanese people. The project team started publicly releasing data from its SNP database in July 2000. Though the project has concluded its effort in SNP discovery, it will publish additional analysis of the results, officials said.

SNPs are the most common form of DNA sequence variation. Each individual has different SNPs and there are 5 million to 10 million SNPs in the entire human genome.

SNPs are useful polymorphic markers in the investigation of genes susceptible to diseases, or those related to drug responsiveness. By discovering as many SNPs as possible, the project undertaken by JST and Tokyo University aims to help doctors prescribe drugs that efficiently target diseases, without having side-effects on patients.

While the SNP database was being put together, Tokyo University and the Japan Biological Informatics Consortium (JBIC) analysed allele frequencies for some of the SNP data, using a group of 768 Japanese people. With this analysis, 78,570 SNPs out of the 193,037 that have been discovered are now accompanied by allele frequencies.

Alleles are alternative forms of a gene that may produce different phenotypes. Allele frequency refers to the fraction of all the alleles of a gene in a population that are of one type.

The allele frequency analysis conducted by Tokyo University and JBIC was the world's largest in terms of the number of SNPs and people studied, according to a statement issued by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) and Ministry of Economy, Trade and Industry (METI).

Allele analysis requires a high speed SNP typing technology that determines the SNP profiles of a group of individuals for a panel of known SNPs at particular locations. The project team conducted the analysis using Third Wave Technologies' Invader operating system and the Tokyo University laboratory's newly developed 384-well card, an 11cm by 8cm plate for chemical reaction, JBIC said in a statement.

The database of SNPs and allele frequencies was developed with software from Mitsui Knowledge Industry Co.

The SNP database and allele frequency analysis, as well as a related project to develop polymorphism analysis software, was part of the Japanese government's Millennium Project. The Millennium Project, which got under way in April 2000, involves a broad range of research and development projects involving, among other things, ecology, the Internet and aging populations.

The SNP database is intended to help promote drug discovery for 'personalised' medications, especially in light of Japan's aging demographic, according to MEXT and METI.

Information on the SNP database can be found at http://snp.ims.u-tokyo.ac.jp.