Genotyping with medium and high through-put technologies

In its capacity as a SNP Genotyping service for Norways academic community, CIGENE has served more than 25 different external users on a wide variety of projects involving samples from bacteria, plants, humans, birds and elephants.

Our SNP service has an architecture designed to handle low, medium and high though-put genotyping. Depending upon the number of SNPs and samples that need to be genotyped, and the species under investigation, one of our three alternative technologies will be suitable for the majority of users.

• MassARRAY (Sequenom) pipeline. For investigations involving relatively low SNP numbers (<50) and few samples (10’s to 100’s) the MassARRAY system from Sequenom is highly suitable. This was the first genotyping technology to be established at CIGENE and is the most frequently used platform due to its reliability and flexibility.

• SNPlex (Applied Biosystems) pipeline. When larger numbers of samples (>1000) are to be analysed for few SNPs (<50), the SNPlex system from Applied Biosystems is employed. This was adopted at CIGENE in late 2005, and despite higher set-up costs this is a more cost effective strategy than the MassARRAY on a per-SNP basis.

• Affymetrix platform. For genotyping very large numbers of SNPs the GeneChip Scanner from Affymetrix is used. This technology uses standard microarrays to genotype as many at 500,000 SNPs in a single human sample. A wide selection of standard arrays is available for SNP genotyping, and we are pleased to be the only non-commercial providers offering the 25K bovine genotyping array.

The preferred choice between these technologies will vary, depending on the size of the project (number of samples and number of SNPs), its costs and also the user's preference. Please contact us to discuss you best option, information on our prices is available here.

For our current users, we would be most grateful if you would take the time to fill out our Feedback Form. Your comments will help us in our efforts to continually improve the services we offer.