Genomics Technology Seeding
The technology seeding program was created to support and develop Ontario science and technology service platforms. The objectives of the program include acquiring novel and/or leading edge technologies and tools for genomics platforms in the province, catalyzing capacity-building activities in Ontario, ascertaining the potential of new technologies and enhancing the breadth and quality of services available to researchers in the province.
Six GTS investments have been made to date since the program's launch in 2009:
OGI received three project proposal to the Genomics Technology Seeding program. The competition was strong, but the two projects that were funded were:
A comparative genomic analysis of costs, coverage, sensitivity and specificity among leading and new alternative exome capture methods using high throughput sequencing
Investigators: Dr. Stephen Scherer and Dr. Sergio Pereira, The Centre for Applied Genomcics at the Hospital for Sick Children.
Illumina TruSeq and Life Tech TargetSeq Exome Enrichment methods offer alternative ways to capture the human exome that differ from the current leading method (Agilent SureSelect). Neither of these two new methods are currently being offered as a service in Ontario. Moreover, TCAG is the only facility in Ontario publicly offering whole exome sequencing (WES) using Agilent SureSelect. Comparative studies of the performance of different capture methods as proposed here will place TCAG in the forefront on national and international competition by allowing us to provide well informed guidance in the selection of the appropriate method depending on the genes of interest and performance of the capture methods in terms of coverage, sensitivity and specificity. TCAG currently runs six newly launched Life Tech 5500xl instruments, being the 5500xl instrument available as a service to Ontario scientists. Within the next few month Life Tech will release nanobeads to replace the current microbeads used during sample preparation for 5500xl sequencing. This will increase our capacity for processing multiple samples in the same sequencing run and increase data throughput. Therefore, a further decrease in WES cost at TCAG is anticipated.
Optimization of ChIP-Seq Library Construction for Illumina Next Generation Sequencing)
Investigator: Dr. Pearl Campbell, Director, StemCore Laboratories, Ottawa Hospital Research Institute
The proposed study will undertake a systematic examination of the ChIP-Seq library construction protocol to optimize the amount of usable data that can be obtained from each experiment. The ChIP-Seq protocol supported by Illumina has not undergone revision since 2007, despite this company's aggressive approach to improvement of its NGS hardware and of other applications for this technology. Notably, there have been a limited number of publications dealing with optimization of ChIP-Seq library construction (Park, 2009; Quail et al., 2008) although much anecdotal evidence exists indicating that this should be an intensive area of study. Our study therefore may assist in development of standard operating procedures (SOPs) and clarify best practices for bioinformatic handling of clonal duplications observed in SE ChIP-Seq Data.
Using the Nanostring nCounter system to determine the fidelity, reproducibility and utility of popular RNA amplification methodologies.
Collaborators: Drs. Neil Winegarden (University Hospital Network (UHN) Microarray centre) and Paul Rasmussen (Nanostring)
The UHN Microarray Centre is examining which RNA amplification method works best in combination with the nCounterâ„˘ technology, allowing for decreased sample input requirements, potentially down to a single cell â€“ increasingly desirable, for example, in the ncontext of analyzing disease tissue â€“ and thus enabling new and valuable research constrained by limited sample amounts.
Read the OGI news announcement here
Development and validation of targeted genome sequencing approach for BRCA1 and BRCA2 sequence analysis
Collaborators: Dr. Kathy Siminovichâ€™s group at Princess Margaret Hospital
This project is aimed at capitalizing on next-generation sequencing (NGS) to provide a new level of cost effectiveness, speed and accuracy for targeted sequencing in clinical diagnostics. The project focuses on two of the most highly-demanded gene sequence tests in the cancer diagnostics area, BRCA1 and BRCA2, so as to provide the â€śproof-of-principleâ€ť data for incorporation of NGS strategies into the clinical diagnostic arena. The ultimate goal is to demonstrate the utility of this technology and to then provide a validated NGS diagnostic test for BRCA1 and BRCA2 and ultimately other clinically-relevant genes to the clinical and research communities.
Neuromuscular disease genetic testing using SureSelect and RainDance enrichment technologies in Next Generation Sequencing
Collaborators: Dr. Peter Ray, Head, Molecular Genetics, SickKids Hospital
The team is investigating the sensitivity and specificity of available methodologies for targeted enrichment of selected regions of the genome for use both in research and as a clinical diagnostic molecular genetic test. These technologies provide an efficient and cost-effective approach to target specific regions of the genome, and can substantially lower the sequencing costs of a project by providing a high sequencing coverage of targeted region in a single sequencing experiment. These technologies offer an unprecedented opportunity to isolate specific regions of the genome in a relatively short period. Although the sequence capture will represent a considerable portion of the total costs of the clinical diagnostic test, it will provide major cost advantages over whole genome sequencing both in terms of sequencing costs and in the time and cost of sequence assembly and analysis of genomic regions that are not relevant to the disease. Having these technologies available to Ontario scientists will widen the scope of medical and non-medical genomics research to both research and clinical scientists. These technologies have not been tested in a diagnostic setting as yet, providing a unique opportunity to pioneer in this field of research.technologies.
The project is investigating the use of this technology to develop a comprehensive clinical diagnostic test for neuromuscular disease. The current diagnostic method for targeted re-sequencing is PCR amplification of the genes followed by Sanger sequencing. This procedure is labour intensive, expensive and time consuming, thus it is not economically feasible as a diagnostic test for diseases where many genes need to be analyzed.
Formalin Fixed Parfin Embedded (FFPE) Technology Development
Collaborators: Andrew Seto (PI: Irene Andrulis, Hospital for Sick Children) and The Centre for Applid Genomics (TCAG)
TCAG is measuring the accuracy and improvement in call rate of FFPE samples on Affymetrix/ Illumina Whole Genome Genotyping (WGG) chips after processing with Qiagenâ€™s Repli-g FFPE Kit, compared to untreated FFPE samples. Affymetix and Illumina are currently processing the samples. This project is ongoing and results so far appear promising. Results have demonstrated that TCAG at the Hospital for Sick Children can obtain greater than 70% genotype calls for an FFPE sample, and the data is high quality. The next step is to improve the call rate of the FFPE sample by selection of fragments of greater size. Work is on-going to increase Single Nucleotide Polymorphism(SNP) and Copy Number Variant CNV) call rates.
Please contact the Genetic Analysis facility manager at The Centre for Applied Genomics www.tcag.ca/geneticAnalysis.html for more information.