- February 16, 2010
Next -generation sequencing symposium - December 7, 2009
Affymetrix User Group Meeting
The Genetic Analysis Facility provides microsatellite and SNP genotyping on a variety of hardware platforms. Assays are customized to each user's needs and include capabilities for genomewide linkage or association, regional localization and fine mapping, custom panels, candidate gene analysis or individual genetic markers. Complementary technologies from Illumina, Applied Biosystems, Affymetrix and Pyrosequencing are available. Although our main focus is on human and mouse genotyping, we also provide genotyping for a variety of other organisms.
The facility also supports gene expression analysis on the Illumina system. For other gene expression technologies, see the Microarray Analysis and Gene Expression Facility.
The Statistical Analysis Facility provides high-level consulting services and analytical support for projects using data either generated within TCAG, or provided by the client.
Please see our acknowledgment policy.
- Genetic Analysis Overview
- Genetic Analysis Technologies
- Mouse Genotyping
- Genetic Analysis Pricing
- Facility Contact
The Genetic Analysis Facility provides genotyping in support of a wide variety of genetic studies. These services include genome wide scans, fine mapping and regional localization, candidate gene analysis, marker and assay development, and mutation analysis. Human genome wide microsatellite scans are provided by the TCAG node at the Ottawa Health Research Institute (OHRI). Please contact us for information. The facility also provides gene expression analysis on the Illumina platform as well as genotyping services tailored for researchers working on transgenic mice or murine genetics. Genotype data can also be generated from other organisms.
The facility generates genotype data from a variety of platforms. The platform used for each specific project is selected in accordance with project scope, cost-effectiveness, and client preference.
- Illumina BeadStation 500G
- GoldenGate® custom SNP panels (96 SNPs or 384 - 1,536 SNPs)
- iSelect® custom SNP panels (6,000 to 60,800 SNPs)
- Human genome-wide Infinium® SNP chips (1M-Duo, 610-Quad or CNV370-Quad)
- Human and mouse linkage panels
- Human cancer, MHC and DNA test panels
- Human, mouse and rat whole-genome expression chips (48K and 24K)
- Human whole-genome expression panels for degraded (eg. FFPE) RNA samples
- Human and mouse whole-genome microRNA panels
- NEW - High-throughput gene expression analyses for human samples - do 96 samples in one experiment for both whole-genome expression and miRNA profiling using the same RNA sample! Reduce batch effects!
- Applied Biosystems 3730xl and 3100 capillary sequencers
- Human genome-wide microsatellite genotyping
- UPD testing or fine-mapping human samples using microsatellite markers. Please see our list of available markers here. Primers for other markers can be custom-ordered.
- Electrophoresis and size-calling of microsatellite fragments from any species
- Electrophoresis of AFLP, RFLP and t-RFLP fragments
- Other speciality polymorphism testing (ie SLC6A4 (5-HTTLPR), DRD2 TaqI A, DRD4 exon III, MAOA)
- SNaPshot™ multiplexed SNP genotyping
- Applied Biosystems 7900HT real-time PCR system
- TaqMan® SNP genotyping
- Use of 7900HT instrument for gene expression experiments
- Affymetrix GeneChip® genotyping microarrays and custom MegAllele SNP assays are supported by the Microarray Analysis and Gene Expression Facility.
Illumina Genotyping order form
Illumna Gene Expression order form
Pricing for Illumina chips
Instructions for preparing DNA or RNA samples for Illumina experiments
Microsatellite and ABI SNP genotyping order form
Pricing for microsatellite and ABI SNP genotyping services
The facility also provides training on various instrumentation platforms. Please contact the facility for details.
Additionally, the facility performs gene expression analysis using the Illumina system. For other gene expression technologies, see the Microarray Analysis and Gene Expression Facility.
The facility performs genotyping for the following applications:
- Genome wide analysis using Illumina Mouse Linkage panels
- Modifier and QTL mapping
- Genotyping of progeny from genetic crosses
- Transgene identification
- Mutation analysis
A variety of technologies are employed, including microsatellite genotyping, heteroduplex analysis, PCR-RFLP and Illumina GoldenGate® genotyping. For more information, please contact us for details.
All projects are custom-priced depending on the number of samples and number of markers to be employed. TCAG staff select the most cost-effective solution for each project. Please contact the facility for free initial consultation, project design assistance and a quotation.
Illumina DNA Analysis
Note: Prices shown are per sample, in Canadian dollars. Includes all reagents and processing fees.
| Whole-genome Genotyping | 8-24 samples | 24-96 samples | ≥ 96 samples |
| Human 1M-Duo | $755 | $725 | $690 |
| 16-48 samples | 48-96 samples | ≥ 96 samples | |
| Human Omni1-Quad | $540 | $515 | $490 |
| Human 660W-Quad | $500 | $475 | $450 |
| Linkage | 48 samples | ≥ 96 samples | |
| Human Linkage-12 (6,090 SNPs) | $200 | $175 | |
| ≥ 16 samples | |||
| Mouse Low Density Linkage panel (344 SNPs) | $60 | ||
| Mouse Med Density Linkage panel (1,441 SNPs) | $100 | ||
| Custom and Focused content SNP genotyping | # SNPs | # samples | Price |
| iSelect custom genotyping panel | 7,600-60,800 | ≥ 1152 | Please enquire |
| Custom SNP genotyping panels (any species) | 96 or 384-1,536 | ≥ 96 | Please enquire |
| 48 samples | ≥ 96 samples | ||
| CVD SNP55 | $200 | $190 | |
| Canine SNP20 | $350 | $335 | |
| Bovine SNP50 | $350 | $335 | |
| MHC Panel (Mapping and/or Exon-centric) | Please enquire | ||
| African-American admixture panel | Please enquire | ||
| Cancer SNP panel | Please enquire | ||
| DNA test panel | Please enquire | ||
| DNA Methylation profiling | 24 samples | ≥ 24 samples | |
| Human Methylation27 | $375 | $325 | |
| 16 samples | 96 samples | ||
| Methylation Cancer Panel I | $105 | $95 | |
| Custom methylation panel | please enquire | ||
| Illumina RNA Analysis | # transcripts | Per sample | |
| Human HT-12 Beadchip | 48,000 | $200 | 12 sample minimum |
| Human WG-6 v3 Beadchip | 48,000 | $305 | 6 sample minimum |
| Human Ref-8 v3 | 24,500 | $220 | 8 sample minimum |
| Mouse WG-6 v2 Beadchip | 45,200 | $305 | 6 sample minimum |
| Mouse Ref-8 v2 | 25,600 | $220 | 8 sample minimum |
| Rat Ref-12 | 22,000 | $200 | 24 sample minimum |
| miRNA profiling (1,135 human or 656 mouse miRNA) |
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| Beadchip format (multiples of 12 samples) | $175 | 12 minimum sample |
Genetic Analysis
The Hospital for Sick Children
MaRS Centre - East Tower
101 College Street, Room 14-701
Toronto, Ontario
M5G 1L7, Canada
Tel.: (416) 813-7654 ext.1358 Fax: (416) 813-8319
Email:
The Centre for Applied Genomics
The Hospital for Sick Children
MaRS Centre - East Tower
101 College Street, Room 14-601
Toronto, ON
M5G 1L7
Tel.: (416) 813-7654 ext 3579 Fax: (416) 813-8319
Email: