The Centre for Applied Genomics (TCAG) is a Canadian centre dedicated to supporting genomic applications in biomedical research and other areas of genomic research. TCAG maintains Core Facilities for (i) Informatics and Biostatistics, (ii) DNA Sequencing, (iii) Microarrays and Genotyping, (iv) Cytogenomics and (v) Biobanking. These facilities are supported by an on-site Administrative Group. The Scientific Director of TCAG is Dr. Stephen Scherer, the Assistant Director is Dr. Richard Wintle and there are seven Scientific Co-Directors who form the Scientific Management Committee, with expertise in various related disciplines (Drs. Bader, Brudno, Danska, Paterson, Ray, Strug and Wilson).
TCAG serves as the Genome Canada Science and Technology Innovation Centre for Ontario, supporting large-scale Genome Canada projects, dozens of other large-scale projects and over 700 additional laboratories each year. Facility users represent 33 different countries. There are approximately 80 staff operating on a multi-million dollar annual budget, including significant grant support from Genome Canada, the Canada Foundation for Innovation (CFI), the Ontario Ministry of Economic Development and Innovation, SickKids Foundation, and other stakeholders. TCAG services are open to all users in the academic, public, government/NGO or private sectors, on a fee-for-service, cost-recovery basis. TCAG is embedded within the Genetics and Genome Biology Program at SickKids. Samples and processes are tracked within TCAG by comprehensive Laboratory Information Management Systems (LIMS).
The fully integrated Informatics facility provides sophisticated analysis including mapping, assembly, variant identification and annotation pipelines, network and pathway analysis, analysis of structural variation (CNV, indels) and other approaches, using TCAG's integrated high-performance computing facility and data storage. All experiments are tracked through the LIMS and data provided either via secure ftp or on physical storage media (e.g., portable or cartridge hard disks). The Biostatistics group assists with all phases of a project's lifecycle, from experimental design and power calculations through to post-experimental data analysis.
TCAG's Sequencing facility operates instruments including those from Life Technologies (Ion Torrent Proton and PGM, SOLiD 5500xl), Illumina (HiSeq 2500 and HiScan SQ) and Roche (GS-FLX "Titanium"). TCAG also acts as a Core Lab for Complete Genomics, Inc., allowing for high-coverage, whole-genome sequencing of human constitutional and cancer samples. This suite of technologies enables sequencing of whole-genome de novo or re-sequencing using either single fragments or paired-end approaches, whole exome or other targeted regions or gene panels, ChIP- and other antibody pulldowns (e.g. methylated DNA or MeDIP), transcriptome, epigenetics, metagenomic samples, sequencing of specialized samples such as ancient DNA or polyploid organisms, bacterial or viral genomes and many other applications. The centre also provides conventional capillary sequencing using Applied Biosystems instruments and Beckman Coulter BioMek NX robotics. A supporting DNA synthesis service provides conventional, long and modified oligonucleotides and a portal for the purchase of oligos from IDT, one of the world's leading suppliers.
Microarray and genotyping analysis is performed on microarray systems from Affymetrix, Illumina and Agilent, quantitative PCR instruments, and by fragment analysis on either capillary or gel electrophoresis systems. Either off-the-shelf (e.g. Taqman) or custom marker panels can be run, as required. Significant areas of focus include qPCR validation of genomic copy number changes, insertions and deletions, as well as mouse linkage and transgenic progeny genotyping, and forensic panels for cell line and stem cell culture identification.
The Cytogenomics facility includes imaging microscopes for applications including Spectral Karyotyping (SKY), mFISH (MetaSystems), metaphase FISH, sequential G-to-FISH mapping (for mapping transgene insertion sites), breakpoint and inversion testing (by interphase FISH) and karyotyping of human, mouse and other species. The facility also performs significant karyotyping and analysis of oncology and stem cell lines, and provides fluorescently-labeled FISH probes to clients including many of Canada's clinical cytogenetics laboratories. The Genome Resources component also supports the other facilities, including genomic clone and cDNA library resources and repositories of human genomic DNA samples.
All of these facilities are supported by the Biobanking and tissue culture facility, which processes blood and fibroblast cultures for DNA, transforms white blood cells to create permanent lymphoblastoid cell lines and banks white cell pellets. This facility also includes the Ontario Population Genomics Platform (OPGP) collection of over 2,500 cell lines and DNA from healthy controls, as a resource for the scientific community.
The TCAG group has provided data, analysis and consultative assistance for hundreds of client publications in the leading scientific journals such as Science, Nature, Nature Genetics, PNAS and PLoS, among others.