Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone

TORONTO, ON (June 15, 2015) Researchers in Canada and the U.K. have for the first time sequenced and assembled de novo the full genome of a living organism, the bacteria Escherichia Coli, using Oxford Nanopore’s MinIONTM device, a genome sequencer that can fit in the palm of your hand.

The findings, which were published today in the journal Nature Methods, provide proof of concept for the technology and the methods lay the groundwork for using it to sequence genomes in increasingly more complex organisms, eventually including humans, said Dr. Jared Simpson, Principal Investigator at the Ontario Institute for Cancer Research and a lead author on the study.

“The amazing thing about this device is that it is many times smaller than a normal sequencer – you just attach it to a laptop using a USB cable,” said Simpson. “And while our work is a demonstration of the capabilities of the technology, the most significant advance is in the methods. We were able to mathematically model nanopore sequencing and develop ways to reconstruct complete genomes off this tiny sequencer.”

While standard sequencing platforms can either generate vast amounts of data, or read long enough stretches of the genome to allow complete reconstruction, the Nanopore device has the potential to achieve both goals according to Simpson. “Long reads are necessary to assemble the most repetitive parts of genomes but we need a lot of reads if we want to sequence human genomes. The small size of the MinION suggests there is room to scale up and sequence larger and more complex samples,” Simpson said.

A drawback of the technology is that the single reads it produces are currently much less accurate than the reads produced by larger devices. Strong bioinformatics tools are needed to correct errors. The methods Simpson and colleagues developed are able to overcome the error rate and compute a more accurate final sequence.

“This was a fantastic example of a successful long distance research collaboration between Canada and the U.K.,” said Dr. Nicholas Loman, a co-lead author on the paper and an Independent Research Fellow from the Institute of Microbiology and Infection at University of Birmingham. “We explored new ways of working, including hosting a hackathon to explore new algorithm development and using shared computing resources on the Medical Research Council funded Cloud Infrastructure for Microbial Bioinformatics (CLIMB) based in the U.K. Midlands and Wales.”

The method of assembly the authors devised had three stages. First, overlaps between sequence reads are detected and corrected using a multiple alignment process. Then the corrected reads are assembled using the Celera assembler and finally the assembly is refined using a probabilistic model of the electric signals caused by DNA moving through the nanopore.

“This work has incredible potential,” said Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research. “Scaled up, this technology could one day be used to sequence tumour genomes. The device’s portable nature would allow for sequencing to become far more accessible, bringing the option of more personalized diagnosis and treatment to more patients.”

Global Alliance for Genomics and Health Marks Two Years of Progress

Over 250 Leaders Convene at Third Plenary Today to Build on Efforts and Drive Results

LEIDEN, the Netherlands (June 10, 2015) – The Global Alliance for Genomics and Health (GA4GH), an international coalition dedicated to improving human health by maximizing the potential of genomic medicine, marked its second anniversary this month. Today, more than 250 GA4GH Members are coming together in the Netherlands to collaborate on the development of innovative, integrated solutions that promote genomic and clinical data sharing, and the creation of a global learning system in genomic medicine.

Since its inception in June 2013, GA4GH has grown to include over 320 organizations across 32 countries and made important progress to unite and guide the field. Members include world leaders in healthcare, research, patient and disease advocacy, life science, and information technology. More than 700 individuals around the globe are actively developing dozens of tools, methods, and approaches to facilitate effective, responsible data sharing.

“Two years ago, we set out to engage a diverse set of leaders around the need to enable responsible sharing of genomic and clinical data. This has developed into a vibrant international effort beyond what we could have imagined when we first came together,” said David Altshuler, MD, PhD, Chair of the GA4GH Steering Committee. “In 2015 our mission is more critical than ever, as we increasingly see genomic information having positive impact on diagnosis, targeting, and development of new medicines.”

At today’s third Plenary Meeting, GA4GH Members are sharing progress on priority tools and projects and discussing ways to promote the use of these interoperable methods to encourage data sharing. Members are focusing on work being done to link existing solutions, emerging areas of interest like e-Health, and issues such as big data challenges and how best to align with major national and institutional efforts arising in genomic medicine.

“The future of medicine requires a collective commitment to developing scalable and interoperable approaches to sharing data,” said Francis S. Collins, MD, PhD, Director of the National Institutes of Health. “GA4GH has made important early progress by uniting critical communities, identifying challenge areas, and collaborating on efforts to help the world realize the benefits of genomic data sharing.”

GA4GH Working Groups have already developed products that lay a technical and regulatory foundation for data sharing, including:

A regulatory Framework to guide the responsible sharing of genomic and health-related data;
A GA4GH Genomics API to enable the interoperable exchange of data in DNA sequence reads; and
A Security Infrastructure that recommends policy and technology options for the ecosystem.

“The world is on the verge of an explosion in genomic data. If we fail to effectively navigate this rocky terrain, we will miss a tremendous opportunity to enable a new era of medical discovery and delivery,” said Tom Hudson, newly announced Chair-Elect of the GA4GH Steering Committee and President and Scientific Director of the Ontario Institute for Cancer Research. “GA4GH has not only brought critical communities to the table, but is showing the results of what happens when these diverse leaders combine their experiences and work together.”

“Health systems around the world must turn into learning systems that responsibly share information—we owe it to every citizen in the world to do this right,” said Eric Lander, Founding Director of the Broad Institute of MIT and Harvard. “GA4GH has taken critical steps to ensure that we unlock the transformational power of genomic medicine.”

GA4GH Members are now building off early foundational products. New Consent and Privacy and Security Policies released this week follow the guidelines and principles of the regulatory Framework. GA4GH recently developed a catalogue of current activities in eHealth and in April, a beta Reference Implementation for the Genomics API was released. Finally, a “data sharing start-up kit” is underway which will include downloadable APIs and reference implementations, as well as polices and standards necessary to implement them responsibly.

“GA4GH tools facilitate interoperability and allow researchers and clinicians to tap the power of genomic data on a global scale, while ensuring participants feel secure that their interests are protected,” explained David Haussler, Chair of the GA4GH Data Working Group and Scientific Director of the Genomics Institute at UC Santa Cruz. “No one of our Member organizations is in the position to provide every tool that is needed, but together we can really move the needle.”

“We started the Global Alliance two years ago to address current barriers to genomic and clinical data sharing before they became entrenched,” said Bartha Knoppers, Chair of the GA4GH Regulatory and Ethics Working Group and Director of the Centre of Genomics and Policy at McGill University. “We are working to guide the responsible sharing of genomic and health-related data around the world based on a human rights approach.”

Several projects advanced by GA4GH act as testing grounds and demonstrate immediate, real-world value:

A global BRCA Challenge to merge and accelerate efforts to interpret BRCA 1 and 2 variants, holding its inaugural meeting June 12-13 at UNESCO in Paris co-organised by the Human Variome Project;
Matchmaker Exchange, a project designed to help patients and doctors grappling with rare genotypes and phenotypes to find one another through a federated network of databases; and
The Beacon Project, which tests the willingness of institutions to share data internationally and now includes over 250 datasets across 15 institutions, including the GA4GH Beacon Network.

“Right now consortia around the world are collecting genomic sequence data, but many efforts are happening in parallel, not in concert,” said Michael Stratton, Director of the Wellcome Trust Sanger Institute. “The Global Alliance is providing packaged, workable solutions and engaging with large-scale data collection and sharing programs around the world.”

“If we don’t ensure data interoperability now, within a few years it’s going to be too late,” said Kathryn North, Vice-Chair of the GA4GH Steering Committee and Director of the Murdoch Childrens Research Institute. “We must all work together to realize the potential of genomic research, reveal the underlying causes of genetic disorders, and transform the way individuals are treated and diagnosed.”

A Road Map produced in early 2015 lays out specific near-term goals for GA4GH. These goals align with the Global Alliance’s vital initial mission and will guide today’s Plenary Meeting.

The Global Alliance for Genomics and Health is an international, non-profit alliance formed to help accelerate the potential of genomic medicine to advance human health. Bringing together over 300 leading organizations working in healthcare, research, disease and patient advocacy, life science, and information technology, GA4GH Members are working together to create a common framework of tools, methods, and harmonized approaches and supporting demonstration projects to enable the responsible, voluntary, and secure sharing of genomic and clinical data. Learn more at: http://genomicsandhealth.org.

The Ontario Institute for Cancer Research invests $4.6 million to support pancreatic cancer research

TORONTO, ON (June 1, 2015) – Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research (OICR) today announced OICR is investing $4.6 million over two years in PanCuRx, an initiative that seeks solutions to the high fatality rate of pancreatic cancer. The multidisciplinary program brings together researchers from the fields of genomics, pathology, cancer biology and informatics, as well as clinician scientists, who will collaboratively work to better understand pancreatic cancer on a molecular level and use this understanding to develop better, more personalized diagnostics and therapies for patients. The research will focus on pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer.

“There have been huge scientific advances over the past few decades on many types of cancer, but statistics on pancreatic cancer have remained largely unchanged,” said Dr. Tom Hudson, President and Scientific Director of OICR. “OICR is proud today to announce support for PanCuRx and help to improve these statistics and bring new solutions to patients.”

Initial funding for the initiative was provided last spring by Sylvia M. G. Soyka, director, and the Board of Trustees of the SMGS Family Foundation to the Canadian Friends of the Hebrew University (CFHU). The focus of this funding is to find and identify the molecular drivers behind metastatic pancreatic cancer. Researchers at the Institute for Medical Research Israel-Canada (IMRIC) at the Hebrew University of Jerusalem and Sheba Medical Center in Israel and at OICR in Toronto are currently working collaboratively to achieve this goal.

“This new funding will help tackle one of the least understood types of cancer. Ontario’s innovative and collaborative research community, together with our partners in Israel, are well suited for this challenge to discover new solutions and treatments that will benefit patients worldwide,” said Reza Moridi, Ontario Minister of Research and Innovation.

PanCuRx’s unique, collaborative design will allow teams of researchers to pursue research and clinical questions in parallel, with a tight link between clinical practice and lab research. The research will also be highly integrated with the Princess Margaret Cancer Centre’s translational PDAC program, ensuring that in addition to increasing understanding of the disease more generally, the research will directly inform the treatment strategy of patients who participate.

“The focus of PanCuRx is to ensure we bring the patients closer to the research and the research closer to the patients,” said Dr. Steven Gallinger, Surgical Oncologist and Head, Hepatobiliary/Pancreatic Surgical Oncology Program at University Health Network, Senior Investigator, Samuel Lunenfeld Research Institute of Mount Sinai Hospital and leader of the PanCuRx initiative. “By working together among disciplines and between the research and clinical components we feel much more can be accomplished and we have a real chance of making an impact on improving outcomes for PDAC patients.”

“I am alive today because of the groundbreaking treatment I received from Dr. Gallinger, Dr. Malcolm Moore and their team,” said Libby Znaimer, a prominent Canadian journalist and pancreatic cancer survivor. Znaimer received therapy targeted at the molecular level to the specific subtype of pancreatic cancer she was diagnosed with, an avenue of diagnosis and treatment that this new funding will further explore. “This summer I will celebrate seven years since diagnosis. We need more research to ensure that outcomes like mine become the norm, rather than a rare exception.”

Pancreatic ductal adenocarcinoma (PDAC) makes up approximately 85 per cent of pancreatic cancer cases. In 2014, an estimated 4,700 Canadians were diagnosed with PDAC and 4,400 died from the disease. It is the fourth leading cause of cancer death in Canada and the current five-year survival rate of 7.7 per cent is the lowest of all cancers. While the number of people dying from common cancers such as breast and colon cancer has dropped dramatically over the past 30 years, there have been only slight improvements for PDAC. It is estimated that PDAC will be the second leading cause of cancer death in North America within 10 years.

Groundbreaking Research Moves One Step Closer to Personalizing Prostate Cancer Treatment

Movember Foundation, Prostate Cancer Canada and the Ontario Institute for Cancer Research funded research breakthrough published in Nature Genetics

TORONTO, ON (May 25, 2015) The results of groundbreaking genetics research in Canada, funded by the Movember Foundation, the Ontario Institute for Cancer Research (OICR) and Prostate Cancer Canada, has identified a unique sub-type of prostate cancer that will help clinicians develop more personalized treatments for their patients, ensure that fewer men undergo unnecessary treatments and improve their chances of survival. The research has been published today in a paper, titled, Spatio-genomic heterogeneity and within localized, multi-focal prostate cancer in Nature Genetics.

Currently, tests that predict whether a patient’s cancer will progress or will respond to specific treatments are limited and existing tests can miss areas of aggressive prostate cancer meaning that men could be “understaged” and given treatments which do not work appropriately for the severity of their specific disease. Researchers at the University Health Network and OICR identified for the first time, a new gene involved in prostate cancer, which, when mutated, leads to unique sub-type of prostate cancer that is associated with DNA damage and a more aggressive type of cancer. The researchers also demonstrated that a single man could have multiple, genetically distinct prostate cancers, and outlined how this variability would impact the delivery of personalized therapy for prostate cancer patients.

“This work is a wonderful example of what happens when a multi-disciplinary team of researchers applies cutting-edge technology to ask clinically-relevant questions,” said Dr. Paul Boutros, a principal investigator at the Ontario Institute for Cancer Research, who co-led the research, “The discovery of a new oncogene in prostate cancer opens a brand-new field for researchers to try to understand prostate cancer biology and treatment. Meanwhile the characterization of the way mutations in prostate cancer vary spatially from one region of a tumour to another will facilitate the development and application of personalized therapies by helping researchers understand why new diagnostic tests fail.”

“The discoveries are a further step along the road to personalizing prostate cancer medicine,” said Dr. Robert Bristow, a clinician-scientist at Princess Margaret Cancer Centre who co-led the research with Dr. Boutros. “Our research shows how prostate cancers can vary from one man to another – despite the same pathology under the microscope – as well as how it can vary within one man who may have multiple tumour types in his prostate.”

“This is a significant development and one that will positively impact the treatment for many men around the world. As a strategic funder of men’s health programs, our prostate cancer goal is for men living with the disease to have the treatment and care needed to be physically and mentally well,” said Paul Villanti, Movember Foundation, Executive Director, Programs. “This piece of work is an important step in helping to achieve our goals in this space. This research demonstrates the considerable impact that Movember funds are having, the results of which have the potential to benefit hundreds of thousands of men and their families around the world.”

“A significant number of prostate cancer cases involve more than one type of cancer cell, and this is a discovery that will provide profound insights into the future of prostate cancer detection and treatment,” said Dr. Stuart Edmonds, Vice-President, Research, Health Promotion & Survivorship with Prostate Cancer Canada. “Breakthroughs such as this are a testament to the comprehensive work being done within the CPC-GENE Network, and Prostate Cancer Canada is proud to be a part of such a large-scale, cohesive collaboration.”

The study is part of a larger initiative called the Canadian Prostate Cancer Genome Network (CPC-GENE) that has brought together a team of multidisciplinary researchers from across Canada to crack the genetic code of prostate cancer. CPC-GENE researchers are identifying mutations in the DNA sequences of prostate cancer to develop better ways of detecting tumours, determining tumour aggressiveness and identifying the best treatment needed to personalize prostate cancer medicine for individual patients. CPCGENE is funded by the Movember Foundation with an investment of $15 million, the largest donation ever made by the Foundation to a single research project, Prostate Cancer Canada and OICR, which has contributed $5 million to the Network. This study was conducted with assistance from the Princess Margaret Cancer Centre.

Research community comes together to provide new “gold standard” for genomic data analysis

TORONTO, ON (May 18, 2015) – Cancer research leaders at the Ontario Institute for Cancer Research, Oregon Health & Science University, Sage Bionetworks, the distributed DREAM (Dialog for Reverse Engineering Assessment and Methods) community and The University of California Santa Cruz published the first findings of the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge (The Challenge: https://www.synapse.org/#!Synapse:syn312572) today in the journal Nature Methods. These results provide an important new benchmark for researchers, helping to define the most accurate methods for identifying somatic mutations in cancer genomes. The results could be the first step in creating a new global standard to determine how well cancer mutations are detected.

The Challenge, which was initiated in November 2013, was an open call to the research community to address the need for accurate methods to identify cancerassociated mutations from whole-genome sequencing data. Although genomic sequencing of tumour genomes is exploding, the mutations identified in a given genome can differ by up to 50 per cent just based on how the data is analyzed.

Research teams were asked to analyze three in silico (computer simulated) tumour samples and publicly share their methods. The 248 separate analyses were contributed by teams around the world and then analyzed and compared by Challenge organizers. When combined, the analyses provide a new ensemble algorithm that outperforms any single algorithm used in genomic data analysis to date.

The authors of the paper also report a computational method, BAMSurgeon (developed by co-lead author Adam Ewing, a postdoctoral fellow in the lab of Dr. David Haussler at UC Santa Cruz), capable of producing an accurate simulation of a tumour genome. In contrast to tumour genomes from real tissue samples, the Challenge organizers had complete knowledge of all mutations within the simulated tumour genomes, allowing comprehensive assessment of the mistakes made by all submitted methods, as well as their accuracy in identifying the known mutations.

The submitted methods displayed dramatic differences in accuracy, with many achieving less than 80 per cent accuracy and some methods achieving above 90 per cent. Perhaps more surprisingly, 25 per cent of teams were able to improve their performance by at least 20 per cent just by optimizing the parameters on their existing algorithms. This suggests that differences in how existing approaches are applied are critically important – perhaps more so than the choice of the method itself.

The group also demonstrated that false positives (mutations that were predicted but didn’t actually exist) were not randomly distributed in the genome but instead they were in very specific locations, and, importantly, the errors actually closely resemble mutation patterns previously believed to represent real biological signals.

“Overall these findings demonstrated that the best way to analyze a human genome is to use a pool of multiple algorithms,” said co-lead author Kathleen Houlahan, a Junior Bioinformatician at the Ontario Institute for Cancer Research working with the Challenge lead, Dr. Paul Boutros. “There is a lot of value to be gained in working together. People around the world are already using the tools we’ve created. These are just the first findings from the Challenge, so there are many more discoveries to share with the research community as we work through the data and analyze the results.”

“Science is now a team sport. As a research community we’re all on the same team against a common opponent,” said Dr. Adam Margolin, Director of Computational Biology at Oregon Health & Science University and co-organizer of the challenge. “The only way we’ll win is to tackle the biggest, most challenging problems as a global community, and rapidly identify and build on the best innovations that arise from anywhere. All of the top innovators participated in this Challenge, and by working together for a year, I believe we’ve advanced our state of knowledge far beyond the sum of our isolated efforts.”

“Paul and the whole team have done something truly exceptional with this Challenge. By leveraging the SMC Challenge to establish a living community benchmark, the Challenge organizers have made it run more like an “infinite game” where the goal is no longer one of winning the Challenge but instead of constantly addressing an everchanging horizon,” said Dr. Stephen Friend, President of Sage Bionetworks. “And given the complex heterogeneity of cancer genomes and the rapid rate with which next generation sequencing technologies keep changing and evolving, this seems like an ideal approach to accelerate progress for the entire field.”

“We owe it to cancer patients to interpret tumour DNA information as accurately as we can. This study represents yet another great example of harnessing the power of the open, blinded competition to take a huge step forward in fulfilling that vision,” said Josh Stuart, professor of biomolecular engineering at UC Santa Cruz and a main representative of The Cancer Genome Atlas project among the authors. “We still have important work ahead of us, but accurate mutation calls will give a solid foundation to build from.”

Ontario Institute for Cancer Research scientist wins 2014 Roger Cotton Prize for Histopathology.

TORONTO, ON (March 9, 2015) — Dr. Tom Hudson, President and Scientific Director of The Ontario Institute for Cancer Research (OICR) today congratulated Mary Anne Quintayo, recipient of the 2014 Roger Cotton Prize for Histopathology for her paper on virtual tissue microarrays. The prize is awarded annually to the best paper published the previous year in the journal Histopathology.

The paper demonstrates that virtual tissue microarrays have many benefits over traditional physical microarrays and constitute an important new tool in digital pathology for both research and clinical settings. Testing was performed on breast cancer samples but the results would be replicable across a broad range of cancers.

“I congratulate Mary Anne Quintayo on this award,” said Dr. Hudson. “Her innovative work has the potential for significant applications to pathology research worldwide, for many different types of cancer. OICR is proud to support this research and delighted with the international recognition it has received.”

“This is an elegant solution to a pathology question and an important new technique for histopathology,” said Dr. John Bartlett, Program Leader of OICR’s Transformative Pathology Program. “This technique provides the opportunity for researchers to perform validation faster, move toward the research environment much more efficiently and to improve the validity of research findings. This allows for more flexibility to analyze many more samples and for researchers to ask more questions of interest.”

“It is contributions from individuals like Mary Anne Quintayo that make Ontario a world leader in cancer research. Her work with virtual tissue microarrays has the potential to significantly impact the lives of patients living with cancer here in Ontario and around the globe. I want to congratulate Quintayo on her award and everyone at OICR for the ground breaking research they do each and every day,” said Reza Moridi, Ontario Minister of Research and Innovation.

This study forms part of an ongoing collaboration addressing challenges relating to early cancer, a key OICR strategic objective. The Improved Management of Early Cancer initiative links multiple research projects to seek to accurately diagnose early cancers, such as ductal carcinoma in situ (DCIS), to avoid overtreatment. This study links researchers at OICR and Sunnybrook Health Sciences Centre in a collaborative network targeting this challenging disease.

Tissue microarrays (TMAs) are an excellent research tool for high throughput analysis of large patient cohorts because they are both economical and rapid. They act as tiny tumour banks on a slide, assisting researchers in analyzing hundreds of samples simultaneously. The challenge for researchers is in knowing how many cores are needed in a particular section to be certain the samples accurately represent the tumour as a whole. The conventional way of doing this is to create and then analyze real microarrays with multiple cores. This can be time consuming for researchers.

Quintayo’s new technique allows researchers to drop virtual cores onto a single slide, representing a computer simulation of multiple TMA cores. It then uses an image analysis system to “mirror” the same cores on sequential sections to assess the impact of creating TMAs across multiple biomarkers using a computer. It does the same work, but faster and more economically than researchers manually constructing multiple replicate TMAs and staining them individually.

The work was published in the January 2014 issue of the journal Histopathology. Histopathology is published on behalf of the British Division of the International Academy of Pathology (BDIAP). The society aims to advance pathology through improving methods of teaching pathology, coordination of pathology with allied sciences and techniques, promoting pathology research and convocation of meetings and congresses to facilitate the exchange of ideas.

OICR extends collaboration with Janssen Inc. to develop clinical trials for prostate cancer

TORONTO, ON (February 25, 2015) — The Ontario Institute for Cancer Research (OICR) is extending its collaborative research partnership with Janssen Inc. to develop more multi-centre clinical trials and other translational research projects that address important clinical questions in prostate cancer, announced Dr. Tom Hudson, President and Scientific Director of OICR.

The new funds will be made available to qualifying researchers at cancer centres across Canada who are addressing important clinical questions in prostate cancer. The funding will be dispersed to researchers through the Canadian Cancer Clinical Trials Network, which is based at OICR, through an open application process.

“We are proud to extend this successful collaboration with our partners at Janssen,” said Dr. Hudson. “Our work together is already supporting some of the most promising translational prostate cancer research in Canada. The continuation of this partnership will help extend this collaboration further, and ultimately help bring the discoveries made in research to patients sooner.”

Janssen Inc. is a leading healthcare company that offers innovative products in areas of high unmet medical need like oncology, immunology, neuroscience, infectious diseases and vaccines, and cardiovascular and metabolic diseases.

“Prostate cancer places a significant burden upon the men who are diagnosed with the disease and their loved ones,” said Dr. Janet Dancey, Scientific Director of 3CTN. “Working with Janssen to identify and support the most promising translational research in Canada for prostate cancer will help us to find improved treatment for these men with fewer and less serious side effects.”

“OICR’s partnership with Janssen is an exciting example of how collaborative, innovative research has the ability to bring very tangible benefits for Ontarians. The Ontario government is proud to support this partnership, which not only leads to critical advances in prostate cancer treatment, but also spurs economic growth in the province,” said Reza Moridi, Minister of Research and Innovation.

OICR and Janssen first entered into partnership in 2012 and first extended the agreement in 2013. There are currently three projects underway as part of the collaboration. These projects are studying ways to better predict the development of castrate resistant prostate cancer in hopes of providing more targeted treatment with fewer side effects for patients.

Utility of miRNA signatures to predict rapid versus delayed onset of castrate resistance in prostate cancer
Dr. Christina Addison, Ottawa Hospital Research Institute

Dr. Addison’s lab is validating the use of miRNA expression to help doctors to better monitor disease progression and target treatment for patients.

Assessment of CRPC response through comprehensive characterization using novel biomarkers
Dr. Eric Winquist, Lawson Health Research Institute

Dr. Winquist is leading a multicentre clinical trial studying novel blood and imaging biomarkers that can be used prior to therapy to better guide treatment and evaluate how patients respond.

Assessment of new molecular imaging strategies for prostate cancer
Dr. Katherine Zukotynski, Sunnybrook Health Research Institute

Dr. Zukotynski is running a clinical study examining novel imaging biomarkers that could provide a more accurate early measure of response to therapy and have a higher prognostic value than standard imaging.

The new agreement announced today extends the initiative through 2015 and opens the eligibility for funding beyond Ontario to cancer sites across Canada.

Prostate cancer is the most common cancer among Canadian men, excluding non-melanoma skin cancer. An estimated 26,500 men are diagnosed with prostate cancer and 4,000 will die of the disease each year.

ICGC launches six new projects from Australia, France, Germany, Japan and Singapore

Toronto – (February 4, 2015) Today, World Cancer Day, the International Cancer Genome Consortium (ICGC) announced six new projects from Australia, France, Germany, Japan and Singapore. These projects seek to identify the genomic drivers in melanoma, uterine, lung, bile duct, gastric and blood cancers and will help to lay the foundation for developing treatments tailored to patients’ individual needs.

The Consortium leads worldwide efforts to map the genomes of both common and rare cancers and has the goal of identifying cancer-causing mutations in more than 25,000 tumours representing more than 50 types of cancer of clinical and societal importance across the globe.

There are now 85 ICGC projects underway at research institutes in Asia, Australia, Europe, North America and South America.

“On World Cancer Day I am pleased to announce that the ICGC continues to expand and is making a real contribution to the development of personalized cancer treatments and prevention strategies,” said Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research and a co-founder of the ICGC. “It is exciting to see the ICGC continue to grow and I am pleased to welcome the researchers working on these six new projects to the Consortium.”

The Consortium also announced the scheduled release of new datasets that will provide new genomic data to researchers worldwide. This includes 55 different cancer types or subtypes from 18 different primary sites, including bladder, blood, bone, brain, breast, cervical, colorectal, esophageal, head and neck, liver, lung, ovarian, pancreatic, prostate, renal, skin, stomach, and uterine cancers. These datasets are used by researchers in their search for, and identification of, the mutations that drive cancer and can be used as targets for the development of new treatments and therapies. Cancer genome data are available on more than 12,807 donors through an Internet portal at www.icgc.org.

More than 220 ICGC researchers will come together for the 10th ICGC Scientific Workshop in Verona, Italy from February 15 to 17, 2015. Attendees will discuss what has been discovered so far and develop strategies for the future direction of the Consortium. Each ICGC member project is conducting a comprehensive, highresolution analysis of the full range of genomic changes in at least one specific type or subtype of cancer, with studies built around common standards of data collection and analysis. The ICGC has conducted benchmarking exercises to improve sequencing and analysis results.

In Italy, the researchers will report on progress on a number of fronts, including:

The PanCancer Analysis of Whole Genomes (PCAWG) project – the ICGC and The Cancer Genome Atlas (TCGA) are committing to study the socalled “dark matter” of the human genome, with more than 2,000 tumournormal whole genome pairs from 23 different tumour types. Progress in the past five years focused on the two per cent of DNA that make human proteins. PCAWG will be the first international project to systematically analyze the other 98 per cent of the genome. This work is expected to identify new classes of cancer mutations that coordinate cancer specific processes. This is a very exciting milestone in human cancer research. More than 600 researchers are contributing to the interpretation of the data and writing of papers that will focus on specific analyses. Because the projected size of the pan-cancer dataset for 4,000 whole genome sequences is very large, PCAWG is using a distributed compute cloud environment, using computing centres in the U.S.A., Europe and Asia that meet technical requirements of the project and the bioethical framework of the ICGC and its member projects.
ICGC2 – the objective of ICGC2 is to link genomic data to clinical data. In order to make further progress, researchers require a more thorough description of the tumour beyond genomic analysis, including how the tumour was diagnosed, the patient’s clinical response, toxicology and outcomes as well as more complex scientific data such as patient phenotype and exposome. Researchers have to think about how to implement genomic tests and use genomics to improve patients’ treatments. Researchers must demonstrate that the expense of genomic testing provides diagnostic and prognostic information that actually allows for better care and longer life expectancy for cancer patients.

“The cancer challenge is immense and the only way to meet it head on is through collaboration,” said Dr. Aldo Scarpa, Director of the ARC-NET Research Centre for Applied Research on Cancer and Chair of the Department of Pathology and Diagnostics at the University and Hospital Trust of Verona, Italy. “The ICGC meeting in Verona, Italy will bring together the best minds from around the world in an effort to address this challenge and find new solutions for cancer patients. I look forward to an informative and productive meeting.”

The ICGC develops policies and quality control criteria to help harmonize the work of member projects located in different jurisdictions. Data produced by ICGC projects are made rapidly and freely available to qualified researchers around the world via the ICGC Data Coordination Centre (http://dcc.icgc.org) housed in Toronto, Canada.

For more information and updates about ICGC activities, please visit the website at: www.icgc.org.

Canadian Cancer Clinical Trials Network receives new funding, launches online service to connect patients to clinical trials

TORONTO, ON (January 13, 2015) – Dr. Janet Dancey, Scientific Director of the Canadian Cancer Clinical Trials Network (3CTN), today announced that 3CTN has received funding support from the Ontario Institute for Cancer Research (OICR), the Canadian Partnership Against Cancer (the Partnership), the Canadian Breast Cancer Foundation (CBCF) and CancerCare Manitoba. These contributions are the first from 3CTN’s coalition of cancer research funding organizations. 3CTN is in the process of finalizing additional funding commitments.

The funding will be used to establish the Network’s sites at cancer centres conducting clinical trials across Canada. Network sites will receive financial support and other resources to be able to increase trials available to patients. Dancey also announced that 3CTN has also launched a new online service that will assist patients and clinicians in finding cancer clinical trials that may be of benefit.

“This funding is great news for Canada’s cancer clinical trials infrastructure, which is essential for bringing the most promising therapies and technologies to the clinic,” says Dr. Tom Hudson, President and Scientific Director of OICR. “Connecting patients to clinical trials is important in moving the science forward, but also allows us to provide avenues of treatment for those patients who have exhausted standard treatment options.”

3CTN is a pan-Canadian initiative to improve patient access to trials and the efficiency and quality of clinical trials activities in Canada. Its aim is to provide support and coordination for a network of teams at cancer treatment centres and hospitals and enable the sites to increase their capacity and capability to conduct academic trials and increase access for patients to participate in trials.

Seven Network Regional Coordinating Centres and 15 Network Cancer Centres will be established by 3CTN with the funding. In the future 3CTN will expand to include many Network Affiliated Cancer Centres. Currently 3CTN has 229 clinical trials in its portfolio including 60 pediatric trials, with more to be added as they are ready to be opened for patients. These academic trials supported by 3CTN reflect the priorities of clinicians, researchers, patients, ministries of health and funders.

“Connecting cancer patients with clinical trials may help to improve their chances of better treatment and outcomes, two key elements of Canada’s national cancer strategy. By strengthening the environment for cancer clinical trials in our country, 3CTN will improve the quality of cancer care for all Canadians,” says Ms. Shelly Jamieson, CEO of the Canadian Partnership Against Cancer.

“With approximately 24,000 individuals diagnosed with breast cancer each year, the investment by CBCF to 3CTN reflects our commitment to bring new breast cancer treatments to patients sooner. Supporting the breast cancer clinical research community is critical for ensuring that innovative Canadian research has an opportunity to improve outcomes and the quality of life for all Canadians affected by breast cancer,” says Ms. Sandra Palmaro, Co-CEO Canadian Breast Cancer Foundation.

The funding contribution from CancerCare Manitoba comes as the Government of Manitoba highlighted supporting academic clinical trials as a priority in its Speech from the Throne on November 20, with the specific goal of increasing patient participation in clinical trials.

“Ontario is thrilled that organizations from across Canada have come together to fund this important initiative. This network will give researchers the ability to bring life-saving innovations into cancer centres sooner and offer more patients the opportunity to join clinical trials. Both may lead to better treatments and healthier outcomes for people in Ontario and around the world,” says Reza Moridi, Ontario’s Minister of Research and Innovation.

Fluorinov Pharma and FACIT Announce Investment in Breakthrough Bromodomain Inhibitors for the Treatment of Cancers

TORONTO, ON (January 07, 2015) – FACIT and Fluorinov Pharma announced today an investment in the development of highly potent inhibitors of key bromodomain targets. Targeting drugs to epigenetic modifications to DNA is an exciting new strategy in the fight against cancer. Bromodomain inhibitors have shown profound preclinical efficacy in models of leukemia, multiple myeloma, solid tumours and other non-oncology indications. However, first-generation inhibitors such as JQ-1 have poor drug-like properties that may limit their utility in patients.

Jeff Courtney, FACIT’s Chief Commercial Officer noted “Fluorinov’s one-of-a-kind technology platform is expanding the boundaries of medicinal chemistry, and FACIT is pleased to advance these important therapeutics towards clinical development. We believe this investment is key to unlocking the value of Fluorinov’s technologies for industry and patients alike, and is another example of FACIT’s work to strengthen innovative networks for worldclass cancer drug development in Ontario and Canada.”

Fluorinov’s oncology drugs have been developed through a broad collaborative network including the Ontario Institute for Cancer Research (OICR), U.S. National Cancer Institute, and the laboratories of Drs. Sam Weiss and Artee Luchman at the University of Calgary. FACIT, together with Fluorinov, is exploring partnerships with investors and pharmaceutical companies and also pathways for clinical development for these and other innovative Ontario based cancer therapies.

“Fluorinov is very pleased to have FACIT’s support in further developing this important program. While we anticipated our proprietary technology would give rise to exceptional bioavailability, we were delighted to identify preclinical candidates with potencies and activity superior to competitor drugs” remarked Malik Slassi, President and Chief Scientific Officer at Fluorinov. “Clinical candidates from this class have a promising future with our hematology-oncology development partners at Princess Margaret Cancer Centre.”

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