Genotyping & Gene Expression Core Facility
Genotyping & Gene Expression Core FacilityThe CMMT Genotyping and Gene Expression Core Facility was established in January of 2006 to provide high-throughput genotyping and gene expression profiling services to researchers at the CMMT, CFRI, and the academic and industry research communities. The facility features the infrastructure and high-throughput methodologies of the Illumina BeadStation 500GX system that were purchased and supported by Dr. Hayden’s Genome BC-funded GATC project. Genome-wide association or linkage studies, fine mapping panels, or custom candidate gene approaches can be provided with SNPs per samples ranging from 96 to 1 million SNPs utilizing either Illumina’s Infinium or GoldenGate assays. Furthermore, gene expression services take advantage of Illumina’s 30-fold feature redundancy to provide high confidence results on up to 47,000 transcripts per sample. Since its inception, the facility has genotyped over 7,800 samples providing 46.2 million SNPs, analyzed 230 RNA samples providing data on over 8.7 million transcripts, as well as provided DNA purification services for 15 research groups. In addition to labs at the CMMT and CFRI, these groups include the labs at UBC's Dept. of Forestry, iCapture at St. Paul's Hospital, and several industry research groups.
Genotyping ServicesThe CMMT Genotyping Core Facility provides high-throughput genotyping services, gene expression profiling, and DNA purification services to researchers in the academic, industrial, and pharmaceutical communities. SERVICES Genotyping is used to identify candidate gene regions for genetic studies via genome-wide association studies (generally 10k to 500k markers), genome-wide linkage studies (6k markers) plus fine mapping panels, and custom candidate gene approaches assaying 96 to 1536 SNPs at one time. CMMT offers a range of products and services for high-confidence, cost-effective genotyping using the Illumina genotyping platform. We offer whole-genome content, focused content, and broad flexibility for custom SNP content. Content is deployed on one of two bead-based array platforms and supported by two powerful genotyping protocols: the Infinium™ Assay and the GoldenGate® Assay. CMMT’s genotyping services operation provides a full menu of SNP-based offerings that will fast-track your studies to success. We can accommodate from the smallest pilot scale projects to large scale projects, with throughput ranging from several thousand to well over one million genotypes per day. The system utilizes high-multiplex assay protocols, multi-sample microarray platforms and customer-proven software to deliver automated allele calling and industry-leading accuracy and call rates.  The key advantage of Illumina’s technology is the array of beads. Each bead type is assigned to a specific SNP locus and replicated 30 times on each array, meaning that each genotype call is the result of the mean intensity of all 30 replicates, resulting in industry-leading accuracy (>99.9%), reproducibility (99.99%), call rates (>99.7%), and low cost (as low as $0.07 per SNP custom content, and $0.01 per SNP for fixed content). Illumina offers two different array platforms for SNP genotyping: the Sentrix® Array Matrix (96 samples) and the Sentrix® BeadChip (16 samples per chip).
GENOTYPING ARRAYS AVAILABLEThe following are some of the genotyping arrays that we generally have available. Please contact us for details and to confirm availability. Human
Mouse
Custom SNP panels
DNA METHYLATION ANALYSIS
CUSTOM MARKER SELECTIONThere is an extensive and rapidly growing database of more than 1,000,000 SNP markers and informative, validated SNP assays developed for use on the Illumina genotyping platform. In addition, the International HapMap Project has made available an extensive library of mapped and validated haplotypes. This exciting project will accelerate complex genetic disease studies by providing genetic maps and assay tools for large-scale linkage disequilibrium and association studies. Learn more about the HapMap project. OUR APPROACHThe CMMT takes a highly collaborative approach to our customer relationships, maintaining strict confidentiality through the course of the study and delivery of results. The CMMT offers a complete genotyping package that includes SNP selection, primer design, data analysis and Mendelian error correction. SUBMISSION GUIDELINESANALYSIS TIMEProjects are processed on a first come, first served basis. The time needed to complete a project depends on the technology to be used and the experiment design and details. For custom SNP panels, genotyping of up to 6 plates (576 samples) with up to 1,536 SNPs per sample (0.9 million SNPs) takes about one week, and one week to analyze the results. DELIVERABLESThe genotyping results will be available through the CMMT network, secure FTP, or on disk if required. Raw data can be visualized and QC'd using Illumina GenCall Software. Processed data consists of CSV flat files to give the genotypes of each marker for each DNA sample (1), and to summarize the results of each marker (2) and each DNA sample (3):
ADDITIONAL PLATFORM INFORMATIONThe Illumina platform is designed for ultra high-throughput SNP genotyping with a capacity of over 100 million genotypes per week, making this technology is an excellent solution for large scale SNP genotyping projects. The success rate of developing a single new SNP genotyping assay varies between 80 and 95%. The call rates are typically greater than 99%. See Oliphant et al. 2002 or http://www.illumina.com/ for more details. PRICINGDNA PURIFICATIONDNA purification services may be available for the facility's genotyping clients. Please enquire for details. Gene Expression ProfilingCMMT's gene expression profiling services uses Illumina technology to deliver the latest high-performance arrays. Illumina arrays interrogate multiple whole genomes or focused sets of target genes across large sample populations with very low cost per sample. The key advantage of Illumina’s technology for RNA expression analysis is the array of beads. The 30-fold feature redundancy (30 average replicates for each transcript) delivers industry-leading high-confidence results. The high feature density reduces array-to-array variation, making single sample replicates less important than more meaningful biological sample replicates. The high feature density also enables low sample and reagent volumes, resulting in low per-sample pricing and the ability to make larger experiments feasible. In addition, the full-length 50-mer probes on each bead provide better selectivity and sensitivity and Illumina is the only company that performs quality control on every single feature on every array.  Illumina offers two different array platforms: the Sentrix® Array Matrix (96 samples) and the Sentrix® BeadChip (most commonly 6 to 8 samples per chip). For more information, please visit Illumina's gene expression profiling page. GENOME-WIDE EXPRESSION ARRAYSWe currently offer two Sentrix BeadChip configurations that provide extensive genomic coverage and the ability to process multiple samples on a single microarray. We can assay either >23,000 RefSeq genes or >46,000 genes (RefSeq + 24,000 additional transcripts). These arrays are currently available for mouse and human. PRICING (ACADEMIC RATE)
Please note: (1) prices are estimates, dependent on sample number submitted, and subject to change without notice. (2) Volume discounts are available. (3) Commercial prices are available upon request. Please contact the facility for more information. For more information, please visit Illumina's genome-wide expression analysis page. LINKS TO ASSAY SPECIFIC INFORMATION AND GENE LISTS
SUBMISSION GUIDELINESDNA Purification ServicesDNA purification services may be available for groups that utilize the CMMT genotyping core facility for genotyping of their samples. Key features
Also available...
We understand the importance of having the highest quality genomic DNA so that genotyping results can be produced for each sample. Customers use our service because of the ability to combine quality, flexibility and unmatched customer service. Downstream sequencing and genotyping require high quality DNA, free of PCR inhibitors and other contaminants. We use an organic-free, modified salt precipitation method for purifying DNA. The use of toxic organic reagents is completely avoided. The extraction methods typically produce high yields of purified genomic DNA, with a size between 100 and 200 kb and an A260/A280 ratio between 1.7 and 2.0. Our purified DNA is stable for at least 9 years at 4°C. The yield of DNA depends on the number of nucleated cells present. Yields from whole blood may vary widely, since white blood cell counts can differ by as much as 10-fold. Typical DNA yields obtained from 5 ml whole blood with a normal white blood cell count (5–7 x 10 6 cells/ml blood) are in the range of 185-210 µg DNA. (37-42 µg per ml of blood) Typical yields
Our DNA is suitable for all downstream applications, including Southern blotting, and can be amplified, for example by PCR, very efficiently. Sample TypesWe employ experts with a background in forensic DNA purification. We can purify DNA from many sample types, including old frozen blood samples, saliva samples, and buccal swabs. Please contact us for more information on these types of samples. What is the best way to store my blood samples prior to DNA purification?Whole blood samples treated with EDTA, citrate, or heparin can be used, and may be either fresh or frozen. Yield and quality of the purified DNA depend on storage conditions of the blood. Fresher blood samples yield better results.
What is the best way to store my DNA samples after purification?Our purified DNA is highly stable. Genomic DNA was purified from whole human blood and stored at 2–8°C or –20°C and no significant change in the amount of DNA was detected up to 2 years after purification. An EU workshop on Biobanks (ref. 1) recommends freezing DNA samples to prevent bacterial contamination and to minimize evaporation of the sample. Tris-EDTA (TE) buffer contains sufficient buffering capacity to prevent acid hydrolysis of DNA. Similarly, the UK Biobank (ref. 2) recommends the storage of DNA in a nuclease-inhibiting environment at a temperature of -20°C, since no significant increase in stability is observed at temperatures below -20°C. References
Pricing
Note: this academic pricing estimate is based on processing 96 samples and is subject to change without notice. Commercial prices available upon request. Please contact the facility for more information. CONTACT FORM For your convenience, we have set up a service contact form. Please feel free to use this form to contact us regarding our laboratory services. CONTACT INFORMATION
CMMT Genotyping Core Facility
Centre for Molecular Medicine and Therapeutics 950 West 28th Avenue, Room A3-194 Vancouver, BC V5Z 4H4 Canada General: +1 (604) 875-2345 ext. 4634 Fax: +1 (604) 875-2494 For more information please contact Michael Hockertz.
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