Research Lab Spin-Off Company Uses HPC To Develop Improved Method for Diagnosing Childhood Cancers

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Access to powerful computing resources supported by Compute Canada and WestGrid has enabled a Vancouver-based research lab to launch a spin-off company that is devising more cost-effective and timely testing techniques for childhood cancers.

Childhood sarcomas are aggressive cancers that affect the bones and soft tissues of children and adolescents. These cancers are often very challenging, time-consuming and costly to diagnose accurately, typically involving the use of more than one testing method. Successful treatment of these cancers requires accurate and early diagnosis, which is often hindered by existing clinical methods.

Partial funding from Genome BC’s Proof of Concept program enabled researchers led by Dr. Poul Sorensen, Senior Scientist at the BC Cancer Agency and Professor of Pathology and Laboratory Medicine at the University of British Columbia, to develop a novel diagnostic assay called ChildSeq-RNA. This assay is the first diagnostic tool to employ next-generation sequencing (NGS) technology to produce highly sensitive results (at the DNA level) in a fraction of the time. The success of ChildSeq-RNA prompted Dr. Sorensen and several other members of the research team to found Fusion Genomics, a NGS assay development and bioinformatics company.

“We were confident that our diagnostic kit would be valuable to clinical institutions that diagnose patients with childhood sarcomas,” says Dr. Mohammad Qadir, Chief Scientific Officer at Fusion Genomics. “Furthermore, our team has developed laboratory and computing expertise which could be used to develop kits for other diseases that could benefit from our technology. We realized that we could start a new viable company which could address important unmet needs in the clinical diagnostic industry.”

The ChildSeq-RNA assay would not have been possible without recent advances in DNA sequencing technology and high-performance computing. Whereas the first human genome project took more than 10 years to complete at a cost of nearly $3 billion USD, today, a human genome can be sequenced using NGS technology in 2 to 3 days for less than $5,000. This is possible thanks to high-performance computing clusters, like those supported by Compute Canada and WestGrid, which have accelerated the analysis of the extremely large data sets produced by NGS technology.

Fusion Genomics is using high-performance computing resources hosted by WestGrid and Compute Canada at Simon Fraser University to develop and refine their diagnostic assays. Their analysis requires the use of a secure environment which Compute Canada and WestGrid are able to provide.

“The choice of WestGrid and Compute Canada was an easy one,” says Dr. Qadir. “They have an excellent and secure infrastructure. And we have first-hand knowledge of the administrators at the Simon Fraser University’s Burnaby site. Their solid reputation gave us the confidence that we will be working with a well equipped and effective organization.”

Dr. Dugan O’Neil, Chief Science Officer with Compute Canada, says the opportunity to collaborate with Fusion Genomics was a natural fit.

“By harnessing the power of these advanced computing resources, these researchers can conduct more efficient and effective analysis of their data. Paired with this new diagnostic tool, it is an exciting advancement in the field of cancer research, with direct and beneficial impacts on Canadians’ lives,” says Dr. O’Neil. “We are proud to support the work of this team and we look forward to exploring additional ways our computing resources can help them succeed.”

While existing molecular techniques used to diagnose childhood sarcomas can take several weeks to complete and analyze, Fusion Genomic’s technology generates a diagnosis in just two to three days. Dr. Qadir says that ChildSeq-RNA is not only accurate and reproducible, it is also both time and cost effective.

“Our technology allows the sequence data to be assembled and analyzed as it is generated,” he says. “The rapid turnaround time for diagnosis allows clinicians to make quicker decisions regarding therapeutic options and ultimately provide better quality care for patients.”

ChildSeq-RNA is projected to be widely adopted by clinical laboratories worldwide and is being evaluated in a clinical setting at the renowned Texas Children’s Hospital at the Baylor College of Medicine. The research team has also published its results in the Journal of Molecular Diagnostics.

“At this time, we are unaware of any other company of academic intuition that is close to developing a kit similar to the assay that Fusion Genomics has developed,” says Dr. Qadir.

It is expected that the clinical evaluations at Baylor will be completed by the end of 2014. Once finished, Fusion Genomics hopes that Baylor, which currently tests a large number of childhood sarcoma cases in North America, will purchase the assay for routine use in their clinic. The company is also currently in negotiations with other reference diagnostic laboratories to adopt ChildSeq-RNA, and is in the process of developing diagnostic assay kits for a variety of other diseases.

“We are developing assays for resistant forms of tuberculosis, among others,” says Dr. Qadir. “These diseases together infect millions of people worldwide. We have developed partnerships with world-leading infectious disease testing facilities to develop the technology.

Other members of Fusion Genomics include Brian Kwok – Technology Development, Greg Stazyk – Chief IT Officer and COO, Dr. Vikram Chopra – Business Development and Regulatory Affairs and Shing Zhan – Computational Biologist. Current bioinformatics efforts at Fusion Genomics are also supported by grants from the National Research Council-Industrial Research Assistance Program. In the long term, the company aims to lead the hybridization-based NGS assay development market for not only the medical sector, but also the agriculture and environmental sustainability sectors.

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