SNPCheck 3, NGRL’s popular primer-checking tool, now includes an option for users to check primers or probes against the current 1000 Genomes Project dataset in addition to the dbSNP database.

The addition of 1000 Genomes data provides access to important population frequency information that can help to inform primer and probe design, and marks the start of an enhancement programme for SNPCheck, during which further datasets from large, population-based genome sequencing projects will be made available for SNPChecking. The next planned addition will be a dataset from the NHLBI Exome Sequencing Project’s exome variant server.

SNPCheck 3 is a web-based tool for human genetics that allows scientists to check oligonucleotide primers or probes for common single nucleotide polymorphisms (SNPs). This safety check helps to detect any SNPs that may reduce the annealing efficiency of the primers or probes and lead to false results. SNPCheck 3 is used world-wide by diagnostic and research laboratories requiring high levels of quality assurance, in the field of human genetics, as an essential safety step in primer and probe design.


SNPCheck and diagnostic safety
Allelic dropout, where one allele fails to amplify efficiently during PCR and is therefore underrepresented in the post-PCR sample, is a significant risk for diagnostic genetic laboratories. This effect has been known to lead to both false positive and false negative results in the context of genetic testing. Allelic dropout is often the result of a single nucleotide polymorphism (SNP) in the section of DNA that has been chosen as a primer binding site. SNPCheck was designed by NGRL Manchester to enable genetic scientists to easily check their primers for common SNPs as a method to reduce the risk of allelic dropout and thereby comply with the high level of quality assurance required of diagnostic services.


About SNPCheck 3
SNPCheck allows primers designed for use in the polymerase chain reaction (PCR) to be checked for single nucleotide polymorphisms (SNPs) in predicted primer binding regions. The tool works by first searching for the primer sequences in the human reference genome using BLAST - the Basic Local Alignment Search Tool. Having identified the most likely binding sites, a search is performed for SNPs in those sites. The tool searches against data from the latest build of dbSNP, and now also from the current 1000 Genomes Project dataset. The results are presented in the form of a tabular summary and diagrams for each pair of primers entered. Single primer pairs can be checked freely, or laboratories can take an annual subscription to access batch-checking functions (up to 500 primer pairs in a single check) and also primer storage facilities and the ability to save SNPCheck results.