Genotyping

High throughput genotyping

In collaboration with Dr. Sean Ennis at University College Dublin as part of the Autism Genome Project, the group currently operates the Illumina BeadArray System, a whole genome genotyping platform that supports integrated single nucleotide polymorphism (SNP) and copy number variation (CNV) analysis. Using the Human1M-duo Infinium HD Beadchip, samples can be assayed genome-wide for over one million DNA markers.

Low throughput genotyping

There are a range of low throughput genotyping techniques available in our laboratory. These techniques can be applied to different types of genetic variants, e.g. SNPs, insertion/deletion polymorphisms (indels), microsatellite markers and variable number tandem repeats (VNTRs).

SNPs can be assayed using either the Taqman® genotyping method (see figure 1) on a 7900HT Real-Time PCR System (Applied Biosystems) or the SNaPshot® genotyping method on a 3130xl Genetic Analyzer (Applied Biosystems). We can increase the throughput of both methods by using robotics and operating in a 384-well format. Indels, microsatellite markers and VNTRs can be genotyped by size separation of fluorescently labelled PCR product on the 3130xl DNA Analyzer.