February 9, 2018
The Global Alliance for Genomics and Health (GA4GH) has laid out its plans for the next five years as it continues to align its activities with meeting the key needs of the genomics data community. The Strategic Roadmap encompasses the standards and frameworks that will be developed by GA4GH and will be updated with new deliverables annually. OICR is a GA4GH Host Institution.
January 12, 2018
Endocrine therapy uses hormone antagonists to greatly reduce the risk of disease recurrence in women with early-stage, estrogen-receptor (ER) positive breast cancer. However, the treatment can come with severe side effects. Around 30 per cent of women stop taking the therapy after three years largely due to these negative impacts. Usually patients receive the hormone therapy for five years following initial treatment (e.g., chemotherapy, surgery), but it can also be taken longer-term. A central question facing patients and clinicians is how to balance, in their decision making, the side effects of long-term treatment with the potential reduction in recurrence risk. In short, they want to know: ‘is it worth it?’
October 18, 2017
Orlando, Florida (October 17, 2017) – The Global Alliance for Genomics and Health (GA4GH) has struck formal collaborations with 15 international genomic data initiatives as 2017 Driver Projects, including Genomics England, Australian Genomics and the U.S. All of Us Research Program. The announcement, made at the GA4GH 5th Plenary Meeting, comes as part of the launch of GA4GH Connect: A 5-year Strategic Plan. GA4GH Connect aims to drive uptake of standards and frameworks for genomic data sharing within the research and healthcare communities in order to enable responsible sharing of clinical-grade genomic data by 2022.
October 17, 2017
The Global Alliance for Genomics and Health (GA4GH) has launched a new five-year strategic plan to develop international standards that will enable the responsible and secure sharing of genomic data for both scientific and clinical purposes. The plan, known as GA4GH Connect, was launched at the organization’s 5th Plenary Meeting in Orlando, Florida.
May 3, 2017
The advent of genomic sequencing and targeted therapies has opened the door to new ways of diagnosing and treating cancer. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) program is a new, province-wide initiative supported by OICR that will allow more patients to benefit from these innovations while also helping to advance cancer research in Ontario.
January 10, 2017
The Global Alliance for Genomics and Health’s (GA4GH) Beacon Project has partnered with ELIXIR, the body that organizes Europe’s infrastructure for life science data, to make genomic data in that continent more easily discoverable by researchers. The Beacon Project is a demonstration project that enables genomic data centres to make their data more easily discoverable to users by allowing them to use simple queries to explore a dataset’s contents.
December 9, 2015
- A study published in the prestigious journal Nature Communications revealed a high degree of heterogeneity in how cancer genome sequencing is done at different institutions across the globe;
- This result lays the foundation for the coming era of cancer genomics by creating guidelines and providing new tools for achieving higher quality data, for better diagnosis and precision medicine;
- The Centro Nacional de Analisis Genómico (CNAG-CRG) and the German Cancer Research Center (DKFZ) took leading roles in this international effort by 78 different institutions.
BARCELONA, Dec. 9, 2015 /CNW/ – An eye-opening article from the International Cancer Genome Consortium (ICGC) was published today in the prestigious journal Nature Communications. It lays a foundation for the coming era of research in cancer genomics. The project, led by the Centro Nacional de Analisis Genómico (CNAG-CRG) and the German Cancer Research Center (DKFZ) is the result of an effort to create reliable standards to obtain accurate results in the detection of somatic mutations, which are a hallmark of cancer genomes. Somatic mutations are genetic alterations spontaneously acquired by a cell that can be passed to the progeny of the mutated cell in the course of cell division and tumour growth. Somatic mutations differ from germline variants, which are inherited from parents to children.
The study, involving 83 researchers from 78 research institutions participating in the International Cancer Genomics Consortium, identified big differences in procedures and quality of cancer genome sequencing between sequencing centers. This led to dramatic discrepancies in the number and types of gene mutations detected when using the same cancer genome sequences for analysis. Out of >1,000 confirmed somatic single-base mutations in the cancer genome analyzed, only 40 per cent were unanimously identified by all participating teams. Small insertions or deletions in the DNA sequence were even more challenging – only a single somatic insertion/deletion mutation out of 337 was identified in all centres (0.3 per cent). As a consequence, the Consortium has established a reference mutation dataset to assess analytical procedures. The ‘gold-set’ reference database has helped the ICGC community to improve procedures for identifying more true somatic mutations in cancer genomes while making fewer false positive calls.
As whole genome sequencing of cancer genomes is increasingly being used as a clinical tool, full understanding of the variables affecting sequencing analysis output quality is required. The key points to consider and the necessary tools for improvement are provided here. “The findings of our study have far-reaching implications for cancer genome analysis. We have found many inconsistencies in both the sequencing of cancer genomes and the data analysis at different sites. We are making our findings available to the scientific and diagnostic community so that they can improve their systems and generate more standardized and consistent results,” says Ivo Gut, senior author of the publication and director of the CNAG-CRG in Barcelona.
David Jones, a Senior Scientist at the DKFZ who co-led the study, commented that “as the latest technological advances in cancer genome analysis become more widely available to support personalized cancer medicine, it is vitally important that rigorous quality testing is applied to ensure accuracy and consistency of results. We hope that our study can provide a framework for this process, to help researchers in providing the best possible analysis of patients’ samples.”
Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research (OICR) declared that “At the founding of the ICGC, members of the Consortium agreed that the guidelines for “best practices” could be revised as needed to adapt to new technologies and knowledge. This benchmarking exercise gives the research community gained confidence in calling and verifying somatic mutations – a step forward to improve clinical decisions based on genomic analyses.”
“The promise of cancer genomics relies on accurate and robust detection of mutations affecting DNA,” said Dr. Jared Simpson, Principal Investigator in OICR’s Informatics and Bio-computing Program. “This paper helps us track progress on this important problem by both identifying the strengths of our current approaches and where further work is needed.”
“This project really demonstrates that while new technologies can bring challenges in data quality and data analysis, when the international community comes together in a collaborative way these can rapidly become results,” said Dr. Paul Boutros, Principal Investigator in OICR’s Informatics and Bio-computing Program. “The results of this collaboration are going to significantly improve the quality of sequencing and data analysis we do here at OICR, for example as part of the Canadian Prostate Cancer Genome Network.”
The International Cancer Genome Consortium is an international effort to establish a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumour types and/or subtypes which are of clinical and societal importance across the globe. The ICGC is characterizing over 25,000 cancer genomes from many forms of cancer. There are 78 projects supported by different national and international funding agencies. For this project, two different types of cancer genomes were studied: chronic lymphocytic leukemia and medulloblastoma (a malignant pediatric brain tumour arising in the cerebellum). Spain’s contribution to the ICGC is on chronic lymphocytic leukemia (CLL) with a consortium led by Dr. Elías Campo and Dr. Carlos López-Otín from the Hospital Clínic de Barcelona, and the University of Oviedo, respectively, with other partners including the Hospital of Salamanca, the Barcelona Supercomputing Center, the Catalan Institute of Oncology, the National Cancer Research Center and the CNAG-CRG. The genomic research on medulloblastoma and pilocytic astrocytoma (another common pediatric brain tumour), is being conducted by the “PedBrain Tumor Research Project”, the first German contribution to the ICGC. In this research project, where the German Cancer Research Center (DKFZ) plays a key role, the entire tumour genome of a patient is analyzed and compared to the normal genome of the same patient to decipher the molecular causes for these types of cancer. The PedBrain Tumor Research Project started in early 2010 and is a collaborative effort between the DKFZ, the NCT, Heidelberg University, the University Clinics in Heidelberg and Düsseldorf, the EMBL and the Max-Planck Institute for Molecular Genetics.
The Centro Nacional de Analisis Genómico (CNAG-CRG) was created on 2009 as a centre of reference for genomics and a key part of the scientific infrastructure required to advance biomedical and genomics research in Catalonia and Spain. Its mission is to carry out genome projects aimed at improving the health and quality of life for people, in collaboration with national and international scientists, to promote Spanish genomics and to ensure its competitiveness in the areas of biomedicine and biology as well as the agrofood sector. With its legal incorporation into the Centre for Genomic Regulation (CRG) on July 1, 2015, these two centres have joined forces to go even further in genome research.
The German Cancer Research Center
The German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) with its more than 3,000 employees is the largest biomedical research institute inGermany. At DKFZ, more than 1,000 scientists investigate how cancer develops, identify cancer risk factors and endeavor to find new strategies to prevent people from getting cancer. They develop novel approaches to make tumor diagnosis more precise and treatment of cancer patients more successful. The staff of the Cancer Information Service (KID) offers information about the widespread disease of cancer for patients, their families, and the general public. Jointly with Heidelberg University Hospital, DKFZ has established the National Center for Tumor Diseases (NCT)Heidelberg, where promising approaches from cancer research are translated into the clinic. In the German Consortium for Translational Cancer Research (DKTK), one of six German Centers for Health Research, DKFZ maintains translational centers at seven university partnering sites. Combining excellent university hospitals with high-profile research at a Helmholtz Center is an important contribution to improving the chances of cancer patients. DKFZ is a member of the Helmholtz Association of National Research Centers, with ninety per cent of its funding coming from the German Federal Ministry of Education and Research and the remaining ten percent from the State of Baden-Württemberg.
The Ontario Institute for Cancer Research
OICR hosts the ICGC’s Secretariat and Dr. Tom Hudson, OICR’s President and Scientific Director, chairs both its Executive Committee and its International Scientific Steering Committee. The data produced by the ICGC project teams are housed on the ICGC website at www.icgc.org and the Data Coordination Centre is based at OICR. More than 14,000 cancer genomes are currently in the ICGC database and are made rapidly available to qualified investigators around the world. As of December 2015, there are commitments from funding organizations in Asia,Australia, Europe, North America and South America for 89 project teams in 17 jurisdictions to study more than 25,000 tumour genomes. OICR has two projects, one on pancreatic cancer and one being conducted on prostate cancer in partnership with Prostate Cancer Canada.
Tyler S. Alioto, Ivo Buchhalter, Sophia Derdak, Barbara Hutter, Matthew D. Eldridge,Eivind Hovig, Lawrence E. Heisler, Timothy A. Beck, Jared T. Simpson, Laurie Tonon,Anne-Sophie Sertier, Ann-Marie Patch, Natalie Jäger, Philip Ginsbach, Ruben Drews, Nagarajan Paramasivam, Rolf Kabbe, Sasithorn Chotewutmontri, Nicolle Diessl, Christopher Previti, Sabine Schmidt, Benedikt Brors, Lars Feuerbach, Michael Heinold, Susanne Gröbner, Andrey Korshunov, Patrick S. Tarpey, Adam P. Butler,Jonathan Hinton, David Jones, Andrew Menzies, Keiran Raine, Rebecca Shepherd,Lucy Stebbings, Jon W. Teague, Paolo Ribeca, Francesc Castro Giner, Sergi Beltran, Emanuele Raineri, Marc Dabad, Simon C. Heath, Marta Gut, Robert E. Denroche, Nicholas J Harding, Takafumi N. Yamaguchi, Akihiro Fujimoto, Hidewaki Nakagawa, Víctor Quesada, Rafael Valdés-Mas, Sigve Nakken, Daniel Vodák, Lawrence Bower,Andrew G. Lynch, Charlotte L. Anderson, Nicola Waddell, John V. Pearson, Sean M. Grimmond, Myron Peto, Paul Spellman, Minghui He, Cyriac Kandoth, Semin Lee,John Zhang, Louis Létourneau, Singer Ma, Sahil Seth, David Torrents, Liu Xi, David A. Wheeler, Carlos López-Otín , Elías Campo, Peter J. Campbell, Paul C. Boutros, Xose S. Puente, Daniela S. Gerhard, Stefan M. Pfister, John D. McPherson, Thomas J. Hudson, Matthias Schlesner, Peter Lichter, Roland Eils, David T. W. Jones, Ivo G. Gut.(2015). A comprehensive assessment of somatic mutation detection in cancer using whole genome sequencing. Nature Communications.
Centro Nacional de Analísis Genómico (CNAG-CRG, Barcelona, Spain), German Cancer Research Center (DKFZ, Heidelberg, Germany), Cancer Research UK Cambridge Institute (UK), Norwegian Cancer Genomics Consortium (Oslo, Norway),Oslo University Hospital (Norway), University of Oslo (Norway), Ontario Institute for Cancer Research (Canada), Synergie Lyon Cancer Foundation (France), Queensland Centre for Medical Genomics (Australia), QIMR Berghofer Medical Research Institute (Australia), Stanford University (USA), Heidelberg University Hospital (Germany), Wellcome Trust Sanger Institute (Cambridge, UK), RIKEN Center for Integrative Medical Sciences (Tokyo, Japan), Universidad de Oviedo (Spain), The University of Melbourne (Australia), Wolfson Cancer Research Centre (Glasgow, Scotland), Knight Cancer Institute (Portland, USA), BGI-Schenzhen (China), The Genome Institute (St. Louis, USA), Harvard Medical School (Boston, USA), MD Anderson Cancer Center (Houston, USA), McGill University (Quebec, Canada), Institut de Recerca Biomèdica (IRB, Barcelona, Spain) & Barcelona Supercomputing Center (BSC-CNS, Spain), Human Genome Sequencing Center, Hospital Clínic (UB, Barcelona, Spain) & Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS, Barcelona, Spain),University of Toronto (Canada), National Cancer Institute (Bethesda, USA).
For further information: Centro Nacional de Análisis Genómico (CNAG-CRG), Dr. Ivo G. Gut, Director of the CNAG-CRG, +34 934020580, email@example.com
November 20, 2015
On October 6, at the 2015 Annual Meeting of the American Society of Human Genetics, Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research, assumed the role of Chair of the Global Alliance for Genomics and Health (GA4GH) Steering Committee, succeeding Dr. David Altshuler. Altshuler has served as Chair since GA4GH was established in 2013, and will remain as a member of the Steering Committee.
“Just over two years ago, a group of leaders from around the globe came together to enable the responsible sharing of genomic and clinical data. Tom was a key contributor from the start, and with his help, GA4GH has made substantial progress,” Altshuler said. “I cannot think of a better person to lead the Steering Committee.”
The role of the Steering Committee is to make high-level decisions about the direction, values, and working products from the GA4GH. GA4GH is a community of individuals and world-leading organizations working together to create interoperable tools and approaches to enable genomic and clinical data sharing. More information about GA4GH can be found at www.genomicsandhealth.org.
June 10, 2015
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.
May 18, 2015
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.”