Shamini Selvarajah
Dr. Shamini Selvarajah, a clinical laboratory geneticist in the Division of Clinical Laboratory Genetics at UHN’s Laboratory Medicine Program, with the NovaSeq X Plus Sequencer. This top-of-the-line machine will enable faster, more powerful and more sustainable genome sequencing. (Photo: UHN)

Our genes are the instructions inside our cells for how our body works. That full set of instructions is unique to each person. So, the more that care and treatments can be matched to your genes, the more effective they will be.

From detecting rare gene rearrangements to personalizing cancer treatments, UHN's genomic advancements are changing patients' lives by offering more accurate diagnoses and a broader spectrum of treatment options.

Through cutting-edge technologies such as optical genome mapping (OGM) and massively parallel high-throughput sequencing, UHN's Laboratory Medicine Program (LMP) is revolutionizing patient care.

OGM is a cutting-edge technology used to assess structural and numeric changes in a patient's genome. This technique offers significantly improved resolution of up to 10,000 times higher than the traditional method of karyotyping.

This advanced technology can scan the entire genome and create a high-resolution map of an individual's DNA, making it a valuable tool for identifying specific rearrangements and abnormalities in the genome.

"This novel technology is a transformational shift in our field," says Dr. Peter Sabatini, a clinical laboratory geneticist at UHN. "Optical genome mapping can find things that we can't see under the microscope.

"It's an improved technology that complements traditional methods, allowing us to detect genetic changes we might have otherwise missed."

UHN's LMP is the first lab in Canada to offer this testing to patients.

Vincent Cha, advanced laboratory technician in UHN's LMP, unlocks the secrets of our DNA with 10,000 times higher resolution using the Bionano Saphyr System. (Photo: UHN)

Using two Bionano Saphyr machines, lab staff at UHN use OGM multiple times per day as a first line test for certain types of hematological cancers such as leukemia, lymphoma and multiple myeloma.

In August 2023, LMP became the first lab in Canada to use OGM to diagnose acute myeloid leukemia (AML). In one case, a unique genetic change that helps predict cancer outcomes was reported within a week, without needing additional tests that would normally be required in a traditional analysis.

In future, the hope is to be able to use OGM to analyze solid tumours.

Consolidating multiple tests into a single comprehensive OGM test is also beneficial to LMP staff, easing the workload and saving time. 

In June 2023, UHN became one of the first clinical sites in Canada to acquire an Illumina NovaSeq X Plus Sequencer, the newest and most powerful of next generation sequencers. This sequencer is set to accelerate patient care by offering comprehensive testing and molecular monitoring, extending its impact beyond cancer to a wide range of genetic diseases.

"It delivers an increase in capacity and faster processing time compared to previous sequencers, which translates to being able to test more patients and provide a faster turnaround time," says Dr. Shamini Selvarajah a clinical laboratory geneticist in the Division of Clinical Laboratory Genetics at UHN's LMP. "And with the scalability options offered with this advanced series of sequencers, it provides tremendous flexibility and efficiency.

"In addition, this system has a new chemistry which is more robust and generates high accuracy data compared to the previous generation of sequencers providing us with more confidence in the results."

This technology is expected to be used clinically by early 2024, and has the capability to allow for the sequencing of 128 human whole genomes in a single run. This will accelerate diagnostic processes, benefitting patients with solid tumors, hematologic malignancies and hereditary cancers.

"The more information you have about a patient's genetic alteration, the more possibilities you have to match them to a treatment," says Dr. Sabatini. "It's more personalized, and it can be beneficial for cancer patients with limited options."

Using technology to expand into other areas of care

It also opens doors for the analysis of cell-free circulating tumour DNA, a vital step in early cancer detection and monitoring of residual disease.

"So as a patient is being treated, we could tell whether that treatment is working or not," says Dr. Trevor Pugh, a cancer genomics researcher at UHN.

Beyond cancer care, the LMP is planning to expand into testing for cardiac patients.

"There are a number of genes that are relevant to familial predispositions to cardiovascular disease so there is a huge range that we could test for," Dr. Sabatini says.

Other areas where this technology can be useful include neurogenetics, neurodevelopmental genetics and pharmacogenomics.

The Novaseq X Plus in LMP is just one of the four machines that were acquired as part of a coordinated purchase between UHN clinical and research teams, as well as the Ontario Institute for Cancer Research.

"This was the single largest expansion of sequencing capacity in Canadian history," Dr. Pugh says. "The most exciting step for me is to move away from targeted sequencing and to work towards a reality where we can offer a whole genome sequence to all patients where it could inform their care.  

"There is high potential to start offering genetic testing for any disease that may have a genetic component. A whole genome strategy also comes with operational efficiencies whereby many individual assays can be consolidated into one test to increase turnaround times and decrease cost."

The integration of genetics into patient care is transformative and unfolding rapidly, with UHN at the forefront.

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