Sequencing and SNP Genotyping

The Pharmacogenomics Centre offers a full range of clinical genotyping services on a variety of platforms. We work with our clients to identify the technology that best suits their needs and offer genotyping on standard commercially available panels, or on custom panels, developed according to client specifications.

For more information about any of the technologies described below, please contact Marie-Pierre Dubé at marie-pierre.dube@pgx.ca.

Small- to Medium-Scale SNP Technologies

AutoGenomics INFINITI™ Analyzer

Infiniti

This system is ideal for low-throughput genotyping needs (24-96 samples per day) of up to 25 SNPs/panel. This automated system includes hybridization matrices (BioFilmChip(TM) microarray), PCR primers, thermal cycler, an imager (confocal microscope) with software for multiplexed detection and genotyping. Clients can select standard panels (e.g. warfarin, 2D6, 3A4, 3A5, tamoxifen) or request custom panels that incorporate SNPs of interest. For more information, visit www.autogenomics.com.

GenomeLab SNPstream Genotyping Technology (formerly Orchid SNPstream UHT)

SNPstream technology (BeckmanCoulter) is ideal for medium sized projects where scoring between 10 and 300 SNPs on hundreds to a few thousands of DNA samples is needed. The genotyping personnel are available to facilitate in the selection of SNPs based on your region and density requirements.

The genotyping reaction consists of a 12-plex or a 48-plex PCR followed by a single-base extension reaction using dye-labeled dideoxynucleotides (ddNTPs). The products are then separated by hybridization on an array of tags printed on a glass surface. Although designed for SNP genotyping, it can also accommodate certain insertions/deletions, but not microsatellite markers.

The GenomeLab SNPstream technology has an average assay conversion rate of about 80-85%. The call rate is about 90-95% and the error rate is less than 0.5%. See Bell et al., 2002, BioTechniques 32: S70-S77. More details can also be found at http://www.beckmancoulter.com.

Sequenom MassARRAY Compact Analyzer

The MassARRAY Compact Analyzer is an automated benchtop MALDI-TOF mass spectrometer specifically designed for genetic applications. iPLEX Gold technology uses single-base primer extension biochemistry and assays can be multiplexed up to 40 SNPs in one individual reaction allowing for throughput levels of up 150,000 genotypes per day per instrument. Applications of iPLEX genotyping include follow up whole genome association studies, mutation detection, and disease association studies. Our technical staff can develop and validate panels according to client specifications. In addition, the Centre offers in-house developed Sequenom-based blood antigen or nutrigenomic panels.

The assay conversion rate is between 80-90% depending on the projects. The call rate is about 90-95% and the error rate is less than 0.5%. More details can be found in Ehrich et al., 2005 Nucl Acids Res 33:e38 or at: http://www.sequenom.com.

Large-Scale SNP Technologies

Illumina iScan Reader

iScan Reader

The Centre offers high-quality, high-throughput genotyping on Illumina’s technology platforms. The new iScan system, which supports all BeadChip-based genetic analysis products, can report up to 225 million genotypes per day using Infinium HD BeadChips. Genotyping can be carried out on any Infinium BeadArray product (e.g. Human IM-Duo, Human 610-Quad, Human CNV370-Quad, Human 510S-Duo, iSelect custom BeadChips). iSelect custom panels can accommodate from 6,000 to 60,000 user selected SNPs. We can also perform GoldenGate assays on standard or custom SNP marker sets. For more information, visit www.illumina.com.

Illumina BeadXpress Reader

The BeadXpress Reader, using VeraCode technology, offers 1-384 assays per sample and the ability to process up to 96 samples in parallel for flexible, customizable, and cost-effective analysis. The Illumina GoldenGate genotyping assay is designed for large scale SNP genotyping. The platform has a capacity of over 1,000,000 genotypes a day and enables parallel typing from 384 to 1536 SNPs.

The GoldenGate genotyping reaction consists of an initial allele-specific extension reaction followed by PCR amplification. Amplified products are hybridized to an array matrix of bead-based probe sequences where each bead is coated with universal probes (up to 1536 different bead types) and represented multiple times for increased accuracy (average of 25 times).

Illumina Genome Analyzer II (Solexa)

The Genome Analyzer II(available late 2008), using Solexa sequencing technology, is a high-throughput sequencing system that generates >3 TB of data per run at 1/1000th the cost of conventional sequencing. It has a wide range of genome sequencing applications.

Discover and confirm SNPs
Identify chromosomal rearrangements, including Copy Number Variations (CNVs)
Map break points
Detect rare variants

For more information, please contact marie-pierre.dube@pgx.ca