The Centre for Applied Genomics (TCAG) is a Canadian centre dedicated to supporting genomic applications in biomedical and other areas of genomic research. TCAG maintains Core Facilities for (i) DNA Sequencing and Synthesis, (ii) Cytogenomics and Genome Resources, (iii) Microarray Analysis and Gene Expression, (iv) Genetic and Statistical Analysis, and (v) Biobanking and Databases. These activities are supported by an on-site Administrative Group.
TCAG occupies approximately 12,000 square feet of space in the Toronto Medical Discovery Tower of the MaRS Discovery District, within the Division of Genetics and Genome Biology of The Hospital for Sick Children Research Institute. Samples and processes are tracked within TCAG by the GeoSpiza Finch Suite Laboratory Information Management System (LIMS), which covers the capillary sequencing service, and the Genologics Geneus LIMS, which is being implemented across the other Core Facilities. Each Core Facility is managed by a dedicated Director.
TCAG's Next-Generation Sequencing (NGS) facility operates eight instruments, including five SOLiD instruments from Applied Biosystems/Life Technologies, Illumina HiSeq 2000 and HiScan SQ, and a Roche/454 GS-FLX running long-read "Titanium Chemistry." 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.
A fully integrated Informatics team provides sophisticated analysis including mapping, assembly, and variant identification and annotation pipelines, using TCAG's integrated high-performance computing facility and data storage. All experiments are tracked through the NGS component of TCAG's Genologics Geneus Laboratory Information Management System (LIMS) and data provided either via secure ftp or on physical storage media (e.g., portable or cartridge hard disks).
For genotyping and conventional capillary sequencing, the centre uses three ABI 3730xl DNA sequencers, one ABI 3100 sequencer, an ABI 7900HT quantitative thermocycler for qPCR analysis and Taqman genotyping, two Illumina BeadStations with an autoloader and associated liquid handling robotics. Custom SNP genotyping by PCR-RFLP or single-base extension is also performed. The Illumina systems are used for genome-wide and targeted genotyping, as well as gene expression, microRNA and methylation analyses. The capillary sequencing facility performs mutation screening, clone verification, and BAC end-sequencing. All of these applications are assisted by automated liquid handling using two Beckman BioMek NX and one BioMek FX robots.
Other microarray technologies include four Affymetrix systems and one Agilent system. The Affymetrix systems are used for both gene expression and genome-wide SNP analysis; one is also upgraded with four-colour MegAllele custom genotyping capability and all are equipped with autoloaders. The Agilent system is used for oligonucleotide array-CGH and other applications, including processing of custom arrays from Agilent or other providers. This microarray facility is by far the most productive in Canada, processing over 5,000 arrays in 2008.
The Cytogenomics Core 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.
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 1,700 cell lines and DNA from healthy controls, as a resource for the scientific community. The Genome Resources facility also supports the other facilities, including genomic clone and cDNA library resources and repositories of human genomic DNA samples. Finally, a DNA synthesis service provides conventional, long and modified oligonucleotides. For users requiring large numbers of oligonucleotides, TCAG also provides a portal for the purchase of oligos from IDT, one of the world's leading suppliers.
The Statistical Analysis Core provides experimental design and power calculations, and a wide variety of analytical approaches, including analysis of genotype, microarray, genomic copy number, epidemiological, and pathway data. TCAG maintains multiple suites of analysis software packages including those from InforSense, SpotFire, Stratagene/Iobion Informatics, Partek, Golden Helix, Ingenuity Pathways Analysis, and a variety of open-source and in-house developed tools. These are also available for clients to use on site for their own data analysis. The Bioinformatics team is active in developing new analytical algorithms and assisting in genome mapping and assembly, annotation, and project design, and is responsible for maintaining TCAG's databases, including the Database of Genomic Variants (http://projects.tcag.ca/variation).
In order to support all data generation, storage, analysis and bioinformatics activities associated with the Centre's activities, TCAG has a variety of computing hardware, including turnkey workstations controlling lab instrumentation, personal and analytical workstations (including several multi-core machines for microarray analysis), web and database servers, and the High-Performance computing Facility (HPF). This cluster consists of symmetric-multi-processing (SMP) computational nodes, and now includes nearly 1,200 predominantly Intel Xeon quad-core processors, three Terabytes of RAM, and over 50 Terabytes of disk space for high throughput computational, bioinformatic and genomic research projects. The computing infrastructure at TCAG is managed by Research Information Technology (RIT) and forms a flexible and capable high performance back end to the centre's 'wet-lab' activities. The TCAG group has supported numerous publications in the leading scientific journals such as Science, Nature, Nature Genetics, PNAS and PLoS, among others.