The Genetic Analysis Core Facility, part of The John and Jennifer Ruddy Canadian Cardiovascular Genetics Centre, provides genotyping services, specialized equipment and technical expertise to researchers throughout the University of Ottawa Heart Institute, the Ottawa region and to external researchers internationally and to the Statistical Genetics Services.
A major focus of the core has been large-scale genome-wide association studies (GWAS) to identify genes associated with common cardiovascular diseases and risk factors, including coronary artery disease, hypertension, and obesity.
We are a high throughput genotyping and sequencing core facility and are currently involved in multiple national and international collaborative projects that leverage our technology.
- advice on study design
- sample size and power calculations
- statistical analysis of study data
- compile and interpret results
- association studies of quantitative and discrete traits
- genome-wide association analysis
- determination of population stratification
- single marker or multi-marker associations
- family-based control design
- case-control design
- haplotype analysis
Gene Expression Analysis
- advice on experimental design such as sample size and power calculations
- analysis of data from microarray platforms including pre-processing and QC metrics
- identification of differentially expressed genes
- gene set enrichment, pathway and gene function analysis
Statistical Analysis Tools
- SNAP: https://www.broadinstitute.org/mpg/snap/
- Gene Ontology: http://www.geneontology.org/
- PLINK: http://pngu.mgh.harvard.edu/~purcell/plink/
- R version 3.1.0 – “Spring Dance” ( http://www.R-project.org/)
- gDB v3.1: http://www.broadinstitute.org/gsea/msigdb/index.jsp
- i-GSEA4GWAS: http://gsea4gwas.psych.ac.cn/inputPage.jsp
- ReactomeFI Cytoscape plugin: http://chianti.ucsd.edu/cyto_web/plugins/displayplugininfo.php?name=Reactome%20FIs
- Cytoscape (v 2.8.2): http://www.cytoscape.org/
Statistical Analysis Pricing
- hourly rate: $70 per hour
- weekly or monthly basis: Please contact Dr Majid Nikpay firstname.lastname@example.org for details.
Education and Training
We provide training in genotyping and phenotyping for single gene and multigene disorders. Extensive training in genetic statistics is provided in conjunction with the Cardiovascular Research Methods Centre. Our education and training activities occur at the undergraduate, graduate, postgraduate and fellowship levels.
We are a designated Affymetrix Core laboratory, offering large-scale whole-genome single nucleotide polymorphism genotyping based on the Affymetrix Gene Chip 6.0 platform.
Equipped with 20 fluidics stations and 6 high-capacity, top-loading GeneChip scanners, we have a maximum capacity to genotype 576 samples per week. The latest generation in genotyping from Affymetrix, the Gene Titan platform (pictured) and Axiom genotyping solution allows high throughput GWAS and customized genotyping of as many as 750 samples per week.