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cSNPs on chromosome 21
  
By Bijal P. Trivedi

Swiss scientists have developed a new set of algorithms to find specific gene variants called cSNPs. They tested their method on the human chromosome 21 (HC21) and found 377 variations that are distributed among 65 percent of the genes. Variations within genes are expected to be particularly useful in explaining differences in disease susceptibility and drug response among individuals. Hence, identifying cSNPs could provide the basis for a range of diagnostic tests.

Out of 377 cSNPs only 10, or about 2 percent, actually produce an amino acid change that has the potential to alter the structure and function of the protein, the researchers report in Genome Research.

While several large research consortiums have made a concerted effort to mine SNPs from all the chromosomes, Samuel Deutsch, of the University of Geneva Medical School, and colleagues claim there is very little overlap between their cSNPs and those in other public databases. According to their calculations, less than 20 percent of cSNPs were contained in other databases.

The researchers present their findings in a cSNP database at http://csnp.unige.ch/

Overlap with Other Databases
Database Web address SNP overlap
CGAP http://lpg.nci.nih.gov/ 25
Human SNP Database http://www.genome.wi.mit.edu/SNP/human 2
NCBI SNP Database http://www.ncbi.nlm.nih.gov/SNP/ 2
SNP Consortium http://snp.cshl.org/ 24

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Deutsch, S. et al. A cSNP map and database for human chromosome 21. Genome Res 11, 300-307 (February 2001).
 

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