Presentation

IRIC's Genomics Core Facility offers a range of services, combining expert guidance and state-of-the-art technologies. It serves IRIC and Université de Montréal investigators in the course of their research initiatives and is also accessible to outside scientists from both academia and industry through collaborative and contract research agreements.

Our Genomics Facility is located in the Marcelle-Coutu Pavilion where it shares a 1,500 ft² space with our high throughput screening facility.

Overview of Services

The facility uses a variety of techniques to meet the specific needs of our investigators. Our team also endeavours to develop and improve certain methods currently used in the field of genomics. Services currently offered are:

DNA Sequencing
Our Genomics Facility works with different DNA templates, namely PCR products, plasmids and BACs (bacterial artificial chromosomes). It also offers DNA sequence analysis services including:

• Sequence comparison and identification (including GeneBank searches using BLAST analysis)
• Sequence alignment to build contigs
• Polymorphism and mutation detection

Genotyping
Our Facility routinely uses the following markers:

• Simple PCR markers (with fluorescence)
• Polymorphic microsatellites markers (STR)
• Single nucleotide polymorphic markers (SNP)

High throughput quantitation of gene expression
The facility uses a real-time PCR high throughput detection system to quantify gene expression. Using various technologies – TaqMan Gene Expression Assays, SYBR green –, it is possible to measure the RNA levels of several genes simultaneously. With the Applied Biosystems' new TaqMan Low-Density Array technology, it is also possible to quantify the expression profile of several hundred genes from a single RNA sample.

Our genomics experts also provide advice on the most appropriate experimental approach for a specific initiative and methods to be used, as well as on marker selection and development and sample preparation.

Instrumentation

Applied Biosystems 3730 DNA Analyzer
Our Genomics Facility operates an Applied Biosystems 3730 DNA analyzer for high thoughput DNA sequencing and genotyping. This instrument is equipped with 48 capillaries (upgradeable to 96) and uses 96- or 384-well plates. It has the capacity to perform 1,100 sequences of 700 base pairs or more, or 550 sequences of 850 bases pairs or more, in 24 hours. It can also carry out more than 40,000 genotyping reactions per day. It is possible to program its reading mode (genotyping or sequencing) from plate to plate. Finally, the 3730 DNA analyzer can detect five different fluorophores simultaneously.

Applied Biosystems 7900HT Fast Real-Time PCR system
We use the Applied Biosystems 7900HT Fast Real-Time PCR system to perform two types of analysis: high throughput quantitation of gene expression and post-PCR (end-point) analysis for allelic discrimination (SNP genotyping). This instrument is able to analyze simultaneously 96 or 384 samples and can exploit the new "TaqMan Low Density Array card" technology. The instrument supports two types of chemistry: SYBR Green and fluorogenic 5' nuclease assay with TaqMan probes.

The excitation source of our fast real-time PRC system is an argon laser and the detection system utilizes a spectrograph and a CCD camera to enable continuous wavelength detection from 500 to 600 nm as well as the simultaneous detection of different fluorophores. The system is able to process at least 5,000 real-time quantitative PCR sample wells in 24 hours and a minimum of 10,000 genotyping samples per hour. In real-time PCR mode, it is able to discriminate between two samples of 5,000 and 10,000 copies of DNA, with a confidence level of 99.7%.