Major funding for the Centre d’expertise et de services Génome Québec (CES) is provided by the ministère de l'Économie et de l'Innovation (MEI) of Québec. The CES offers high-quality services to the scientific community and has become a resource and a networking site for various research initiatives in human health, forestry, infectious diseases, agriculture and sustainable development. Ambitious projects in recent years are a testimony of the ability of Génome Québec to provide data of exceptional quality in the pursuit of various genomics studies. The CES provides complete DNA and RNA analysis services, from a few samples to several tens of thousands per week. Large-scale genomics services at the CES are articulated around sequencing (including massively parallel sequencing), genotyping, functional genomics and nucleic acid extraction supported by a solid infrastructure, tools (Nanuq) and unique expertise in bioinformatics. The CES works in close collaboration with the Canadian Centre for Computational Genomics (C3G) in order to offer bioinformatics services All services work in parallel to provide reliable, comprehensive services to the Québec, Canadian and international scientific community. Located at the Sainte-Justine University Health Centre in the heart of Montréal, the CES acts as a vast resource of knowledge and technology to the academic and industrial sectors.
The PacBio Sequel Single Molecule Real-Time (SMRT ® ) sequencing technology produces thousands of base pairs from single molecules in real time, allowing observations of structural and cell type variation not accessible with other technologies. These unique capabilities of the PacBio Sequel system are ideally suited for a variety of applications: - from de novo assembly of small genomes (ex. bacterial or fungal) - targeted sequencing of long cDNA molecules - detecting base modifications - RNA sequencing As more scientists adopt the SMRT ® technology, we expect numerous other applications of sequencing to become feasible for the first time.
Different technologies are available for genotyping bi-allelic markers such as SNPs (Single Nucleotide Polymorphisms) and indels (insertion/deletion polymorphisms) depending on the number of markers to test in parallel and the desired applications, .
The Centre d’expertise et de service Génome Québec offers transcriptome analysis by performing cDNA library constructions from total RNA to allow subsequent sequencing using Illumina sequencing platforms (MiSeq, HiSeq 4000, NovaSeq 6000). Library preparation services include the following types of RNA-Seq libraries: - Eukaryotic protein coding transcripts (mRNA stranded libraries) - Prokaryotic long transcripts (bacterial rRNA-depleted libraries) - Eukaryotic long non coding and coding transcripts (rRNA-depleted libraries) - Prokaryotic and eukaryotic long non coding and coding transcripts for metagenomic studies (rRNA-depleted libraries) - All transcripts (total RNA) - Eukaryotic small transcripts (<200 nt) - Eukaryotic miRNA (enriched in species 22-50 nt) - Targeted human protein coding transcripts (minimum of 48 samples) - Human protein coding transcripts from FFPE samples (minimum of 48 samples) All libraries are strand-specific. Ribosomal RNA depletion yields vary according to species.
GeneChip® expression arrays enable the measurement of expression levels of transcripts both quantitatively and qualitatively. Affymetrix array technology involves the in-situ synthesis of hundreds of thousands of distinct oligonucleotide sequences onto a glass array using photolithography and combinatorial chemistry. Each 25-mer oligonucleotide is represented by millions of copies in a specific area. Each transcriptional sequence is spanned by 11-20 pairs of oligonucleotide probes randomly spaced throughout the array. All sequences designed on the array are selected from GenBank, dbEST and RefSeq. Target RNA is reverse transcribed into cDNA and in-vitro transcription is performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA is stained with streptavidin phycoerythrin and arrays are scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the GeneChip® array.
Arrays are currently available for many biologically relevant model organisms.
The verification of RNA integrity and concentration is crucial for all samples coming to the CES for expression analysis. However, it is possible to bring your samples to have their quality checked without requiring other services. *Available technologies* - NanoDrop (Thermoscientific): The NanoDrop ND 1000 is used in the lab to verify the concentration of RNA samples. This spectrophotometer is working with 1 uL of RNA sample and will measure the absorbance at 260, 280 and 230 nm. The detection limit is 2 ng/uL. - Bioanalyzer 2100 (Agilent): The Agilent Bioanalyzer 2100 in concert with the Agilent RNA 6000 nano or pico kit is a microfluidics-based platform used for quality control and integrity checks of RNA samples.
The Centre d’expertise et de service Génome Québec offers a custom SNP Discovery service and a service of de novo sequencing of complete plasmids by primer walking. Full SNP Discovery/Validation services by Next-Generation Sequencing (NGS) include: - Designing and ordering primers to amplify target regions. - Target region amplification using the Fluidigm Access Array System. - Sequencing of PCR products using various NGS Technologies (Illumina HiSeq or MiSeq, PacBio). - Transmission of a SNP report. Full SNP Discovery services include: - Designing and ordering primers to amplify target regions - PCR amplification of target regions from genomic DNA of test samples based on Sanger Sequencing - Detection of variations in test samples or between test samples and a reference sequence - Preparation and transmission of a SNP report including several annotations on the variations. The de novo sequencing service includes: - Sanger sequencing with any entry primer - Designing and ordering all primers needed to sequence entire plasmids or regions
The Centre d’expertise et de service Génome Québec offers a Sanger Sequencing Service using Applied Biosystem's 3730xl DNA Analyzer technology. In addition to the regular service, the Innovation Centre also offers the 24hr BaseXpress Sequencing Service. Sanger sequencing is often used to proofread plasmid DNA sequence to verify the integrity of a gene inserted into an expression vector or to re-sequence targeted regions of a genome with the purpose of finding genetic variations. Sanger sequencing is most suitable for small to medium range sequencing projects. For large scale sequencing projects, please contact the Client Management Office to help select the most suitable Next-Generation sequencing technology.
The Centre d’expertise et de service Génome Québecoffers services for DNA extraction and sample preparation to academic and industrial researchers. Genomic DNA extraction* Centre d’expertise et de service Génome Québec offers a genomic DNA isolation service from blood, saliva, buffy coat, bacteria and cultured cells. DNA can be isolated from a range of sample volumes of 0.2 to 2 mL, and can be used for various types of genetic analyses including genotyping and sequencing.
Among others, the Centre d’expertise et de service Génome Québec NGS fleet included MiSeq, HISeq 4000 and NovaSeq 6000 instruments. Various library types are available for Illumina sequencing, including:
- Shotgun DNA libraries for the sequencing of large size genomes - de novo assemblies and SNP calling
- ChIP-Seq libraries
- Whole genome bisulfite libraries - identification of methylation sites
- Reduced genome libraries - Exome captures (Agilent SureSelect; Roche Nimblegen SeqCap)
- Custom panels (Roche Nimblegen SeqCap)
- Methylation (Roche Nimblegen SeqCapEpi)
- Custom Amplicons, 16S
- RNA-Seq Most library preparation pipelines have been automated to increase robustness and cost efficiency. Libraries can be sequenced in either single-read of paired-end formats and for read lengths of 50, 100, 150, or 250 bases (up to 300 bases for the MiSeq). On average, 15M reads can be obtained on the MiSeq and 300M reads can be obtained on a single lane of HiSeq 4000 flowcell . NovaSeq 6000 outputs are 375M reads per lane of SP flowcell to 2500M reads per lane S4 flowcell. Sequences are downloadable directly from Nanuq. Sequence reads will be delivered as bam files for human, rat and mouse and as fastq for the other species.
This technology performs genotyping of microsatellite markers for Genome-Wide Scans and Fine Mapping. Both methods are powerful options for mapping genes of Mendelian-type inheritance due to the highly informative nature of these markers compared to SNPs.
Genome-Wide Scan: A set of 400 highly polymorphic microsatellite markers spaced at an average distance of 8.7 cM throughout the human genome is currently used. Each marker is amplified individually followed by pooling of 8 markers together in a panel. The genotyping results are obtained using an ABI-3730XL DNA Analyzer.
Fine-Mapping: The personnel of the service is available to facilitate in the choice, panel design and ordering of microsatellite markers to suit the chromosomal region and density requirements.
Note that the optimization and the production of PCR reactions is no longer supported since January 2009, except for markers already validated or from the genome-wide scan set. Detailed information on the design of the labelled PCR primers can be obtained by contacting the Client Management Office.
Clariom™ D assays (Human)
Clariom™ D assays (Mouse)
Clariom™ D assays (Rat)
The number of known transcribed genes has expanded rapidly in recent years providing more sources for actionable biomarkers, such as transcript variants and lncRNA, that can be used for clinical utility and advancing our understanding of disease mechanisms. Such biomarkers can be missed by lengthy, complex, and costly sequencing and targeted expression approaches, leading to irreproducible signatures and wasted time and money.
With full coverage of the transcribed genome including all known coding and non-coding splice variants, compatibility with clinical sample types, and flexible data analysis software, Clariom D assays are the premier tools for translational researchers performing complex expression biomarker discovery studies and wanting the fastest path to robust, clinically relevant, and actionable results.
Rapidly identify complex disease signatures from >540,000 transcripts sourced from the largest number of public databases, the most comprehensive coverage of the human transcriptome available, to ensure biomarkers are not missed.
Confidently detect genes, exons, and alternative splicing events that give rise to coding RNA and lncRNA isoforms.
Detect rare and low-expressing transcripts otherwise not detected by common sequencing approaches.
Go from data to insight in minutes with intuitive, highly visual, free analysis software.
Download the free Affymetrix software.
Sequencing Data Analysis Services
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Centre d’expertise et de service Génome Québec has not received any endorsements.