Centre for Integrative Genetics (CIGENE)

SNPs are a common type of genomic sequence variation found to occur on average once every 1000bp. Coding SNPs (cSNPs) are of particular importance due to their potential to alter the coding sequence of genes and possibly also gene functionality. However, non-coding SNPs located throughout the genome can be used to provide information crucial for linkage and association studies.

Despite the significant amounts of sequence data in public databases, validated and informative SNPs are often unavailable for specific user projects. CIGENE has extensive experience and can provide assistance with SNP discovery in specific candidate gene regions or in specific organisms (see here for prices).

The CIGENE SNP detection pipeline is designed to give users a complete solution from sequence information to validated SNPs.

Assay development and primer design
SNP discovery begins with re-sequencing. RepeatMasker software is used to analyze genomic regions containing potentially useful SNPs, primers are designed to amplify these regions in forward and reverse directions, and number of samples to be re-sequenced is chosen.

PCR and Sequencing reactions
A Beckman Biomek FX pipetting robot is used to assemble PCR reactions in 96 and 384-well formats. These are subsequently purified using a post-PCR pipetting robot. Amplicons are sequenced with fluorescent dye-terminator chemistry in our ABI 3730 sequencer.

SNP detection
Traces are compiled into contigs (when applicable) and uploaded to our SNP detection software pipeline utilizing Phred/Phrap/Consed and Polybayes algorithms. Strong Phred base call confidence scores identify high probability heterozygotes. Variations are mapped back to the original sequence and the variation together with the flanking sequence is used to design assays for SNP genotyping.

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