SNPCheck v2.1 launched with SNP filter capability
NGRL Manchester has expanded the functionality of its popular primer checking tool with the launch of SNPCheck v2.1. This version introduces a number of new features including the ability to filter variants from results. The changes have been made in order to address the problem of ‘SNP overload’ created by the rapid expansion of dbSNP over the last year.
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. 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.
The quantity of data in dbSNP has grown rapidly over recent years. Moreover, in certain gene regions there is now a high density of data that does not pertain to common polymorphisms. For applications like SNPCheck where the interest is only in common human variation this has begun to be problematic. SNPCheck v2.1 introduces filtering options to enable the separation of variants that are rare, have little supporting evidence or both, from those that are likely to be common polymorphisms.
Filter settings are customisable and filtered SNPs are reported separately rather than being eliminated, providing the user with a full, but more manageable, view of the results.
Further information about SNPCheck v2.1 can be found at https://ngrl.manchester.ac.uk/SNPCheckV2/docs.htm. SNPCheck itself can be found at https://ngrl.manchester.ac.uk/SNPCheckV2/snpcheck.htm.
Save this page as a PDF