May 10, 2019

An innovative way to look at genome rearrangements leads to new insights about ovarian cancer

Dr. Paul Krzyzanowski, Director of Genome Technology Translation at OICR.

Researchers look beyond an obvious hypothesis to connect patterns in gene expression with genome rearrangements, drawing attention to often-overlooked regions of the genome

If two different genes come together, the resulting gene fusion can have a new function that can cause or contribute to cancer. The discovery of cancer-causing gene fusions has led to the development of new therapies for many cancer types and sparked efforts to identify rearrangements that might yield new treatment targets. Often, however, researchers discover fusions with no effect on a cell, but a recent study has shown that the regions around these ‘fusions of unknown significance’ may be just as important to study as the fusion itself.

In their investigation into high grade serous ovarian cancer (HGSOC) – which has a five-year survival rate of only 20 per cent – the Genomics Program at OICR identified thousands of gene fusions and investigated the regions around these key points. As described in Scientific Reports, they found that the neighbouring regions are overexpressed – in essence, overactive – which may contribute to the cancerous nature of cells.

“Often, we find evidence of rearranged DNA without a clear picture of how rearrangements drive cancer,” says Dr. Paul Krzyzanowski, Director of Genome Technology Translation at OICR and primary author of the publication. “In this study, we found that the regions around gene fusions – in addition to the fusions themselves – are very active in cancer cells. This observation hints at the idea that we can look at broader genetic regions, and not just the location of a fusion by itself, to better understand how genomic rearrangements wreak havoc in cancer cells.”

In this study, we found that the regions around gene fusions – in addition to the fusions themselves – are very active in cancer cells

The observed overexpression of regions around fusions could be used to differentiate diseased cells from normal cells and lead to new cancer treatment approaches. The observations in this study are consistent with findings from the Pan-Cancer Analysis of Whole Genomes network, which identified patterns of overexpression in disturbed genomic regions across many cancer types.

Krzyzanowski says this work highlights a non-intuitive analytical approach for analyzing cancer-related gene fusions which will continue to be employed as OICR’s Ovarian Cancer Translational Research Initiative investigates how DNA rearrangements in ovarian cells drive cancer.

Read more about OICR’s Ovarian Cancer Translational Research Initiative or learn more about Genomics at OICR.

June 5, 2017

OICR donates sequencer to Fleming College for high-tech training

Individuals from OICR and Fleming College pose for a photo in front of the sequencer.

Fleming’s Biotechnology-Advanced students have received a significant boost to their career preparation with the help of The Ontario Institute for Cancer Research (OICR). Their investment in people is recognized through a very generous donation of an Illumina HiSeq DNA Sequencer to the Biotechnology-Advanced program, a benefit to Fleming College valued at $600,000. This new equipment will provide students with hands-on experience using cutting-edge automated instruments that are utilized widely across the biotechnology industry.

“Some of the best technicians in OICR’s genomic labs are Fleming College graduates. We are proud to pay-it-forward by helping the College give future life sciences researchers in Ontario hands-on training opportunities on real genomics equipment.” says Paul Krzyzanowski, Program Manager of Genome Technologies, OICR. “Illumina equipment is the backbone of most sequencing labs and it’s essential for today’s students to become familiar with the complexity around these machines with hands-on experience.”

The remarkable relationship between OICR and Fleming College has flourished over the last nine years. With its state of the art facilities and research, OICR has become a highly sought after internship agency for Fleming students since the first placement student in 2008. The support from OICR and Illumina helps Fleming College to lead the way in biotechnology training; contributing to excellence in academic programming that includes relevant experiences. The hands-on learning creates a positive impact towards the future of Fleming students and alumni, the success of employers and especially those who benefit from cancer research.

“We are very grateful for the Ontario Institute of Cancer Research for their investment in our students,” says Biotechnology Program Coordinator Ashvin Mohindra. “OICR provides a practical training component through their in-kind gifts and placement opportunities for our students. With their help, we are also pleased to meet OICRs employment needs which is proven with the hiring of more than 18 Fleming College graduates to fill their high-tech positions.”

The in-kind donation would have not been possible without the tireless effort of OICR and Illumina, the sequencer manufacturer and third party liquid handler software provider. The College would like to specifically recognize and thank everyone at OICR who made these donations possible (Lee Timms, Jessica Miller, Paul Krzyzanowski, Tom Hudson, Mike Kostiuk, Susan Hockley, Jeremy Johns, and Howard Simkevitz) and the staff at Illumina for their tireless help and expertise in setting up the equipment (Lisa Lock, Peter Ayache and Mike Ramsey).

OICR, a global leader in healthcare, research and innovation, is dedicated to exploring the prevention, early detection, diagnosis and treatment of cancer. Their commitment to exploring cancer extends beyond the lab; OICR invests in people who can make novel discoveries.

Note: This story originally appeared in the Spring 2017 edition of Fleming Ties magazine and has been reproduced with the permission of Fleming College. The original can be found here (PDF): https://flemingcollege.ca/PDF/FlemingTies/fleming-ties-spring-2017.pdf

March 29, 2017

New approach improves sensitivity of DNA sequencing, producing more reliable results

A lab technician works at a bench

Polymerase chain reactions (PCR) are one of the most common tools used in molecular biology labs worldwide. This technique allows researchers to amplify, or increase, the amount of DNA in a sample so that they have more to work with. To keep track of the original molecules from a sample, chemical ‘barcodes’ are added. While barcodes serve an important purpose they can lead to errors and interfere with results. To prevent these cross-reactions a small team of international researchers have devised an ingenious method to ‘hide’ the barcodes when needed, leading to increased sensitivity and more reliable results.
Continue reading – New approach improves sensitivity of DNA sequencing, producing more reliable results

March 9, 2017

Innovative technique greatly increases sensitivity of DNA sequencing

Dr. Paul Krzyzanowski

New molecular barcode technology reduces error rate in genomic sequencing to 1 in 10,000

Toronto (March 9, 2017) – Researchers at the Ontario Institute for Cancer Research (OICR), together with international collaborators, have invented a technique to avoid a major problem with common laboratory techniques and improve the sensitivity of important cancer tests.

Continue reading – Innovative technique greatly increases sensitivity of DNA sequencing