May 10, 2018

Symposium offers preview of findings from the Pan-Cancer Analysis of Whole Genomes project

PCAWG researchers pose for a group photo.

On April 13, researchers from around the world gathered at the MaRS Centre in Toronto to get a sneak peek at the findings from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. PCAWG is an ambitious international effort to comprehensively understand the non-protein coding elements of the genome, which make up 97 per cent of the genome but have been little studied in the context of cancer.

Continue reading – Symposium offers preview of findings from the Pan-Cancer Analysis of Whole Genomes project

November 18, 2015

The International Cancer Genome Consortium brings more genomic health data to researchers on the Amazon Web Services Cloud

Toronto – (November 18, 2015) The International Cancer Genome Consortium (ICGC) announced today that 1,200 encrypted cancer whole genome sequences are now securely available on the Amazon Web Services (AWS) Cloud for access by cancer researchers worldwide.

The Ontario Institute for Cancer Research (OICR), which houses the ICGC’s Data Coordination Center (DCC), copied ICGC genome data onto the AWS Cloud and is providing authorized researchers with credentials to access and analyze the data using secure mechanisms. The ICGC Data Access Compliance Office has established a framework that protects the confidentiality of research participants while working to ensure that the research will benefit future cancer patients.

The newly launched initiative means one of the world’s largest collections of cancer genome data is now more easily accessible to qualified researchers, which will enhance collaboration and potentially accelerate the development of new treatments for cancer patients.

Cloud solutions have become essential to genomics research because of the vast amount of data produced by researchers and the difficulties inherent in transferring such large datasets between sites. Projects can quickly grow to several petabytes in size, with each petabyte being the equivalent of data on 223,000 DVDs. Very few institutions around the world have the capacity to download such immense datasets for analysis, and this has limited the number of researchers who can access genome projects and the scope of what can be done with the data.

With cloud computing, researchers don’t need to download data. They can work with data and run experiments in the cloud, a flexible network of servers on the Internet, and access data in minutes rather than months. Data stored in the cloud has been shown to be as secure, if not more so, than data downloaded to local servers and hard drives. The set of 1,200 genomes now available on AWS is the first installment of ICGC data to be posted and is expected to grow several fold over the next 12 months with the addition of data from more cancer patients.

“This initiative brings together one of the world’s largest cancer genome datasets and one of the world’s leading cloud computing providers to create a powerful new resource for cancer researchers,” said Dr. Lincoln Stein, Director of the Informatics and Biocomputing Program at the Ontario Institute for Cancer Research and Director of the ICGC’s Data Coordination Center. “Now, far more researchers will have access to ICGC data, opening up the possibility of new discoveries and new breakthroughs in cancer research.”

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the ICGC and The Cancer Genome Atlas (TCGA) is coordinating analysis of more than 2,800 cancer genomes, and is making extensive use of AWS and the genomes stored on Amazon Simple Storage Service (Amazon S3). Each genome is being characterized through a suite of standardized algorithms, including alignment to the reference genome, uniform quality assessment, and the calling of multiple classes of somatic mutations. Scientists participating in the research projects of PCAWG are addressing a series of fundamental questions about cancer biology and evolution based on these data.

“Making this data available and usable will enable more researchers across the world to ask questions and get answers that were previously out of reach,” said Matt Wood, General Manager of Product Strategy at Amazon Web Services, Inc. “Researchers can now explore these large and diverse datasets in unconstrained ways, without having to manage large amounts of physical infrastructure. Instead, they can focus on driving their state-of-the-art research forward.”

“Cancer research is becoming increasingly data-heavy. Compiling the data, organizing the data, analyzing the data, making the data available to all researchers—these are fundamental to making further progress in cancer genome research, and we are excited at the possibilities of working with innovative cloud-based computing systems to achieve these advances,” said Peter Campbell, Head of Cancer Genetics and Genomics at the Wellcome Trust Sanger Institute, who is helping to lead the PCAWG project.

“In the next year, it is estimated that 14 million people worldwide will learn that they have cancer. In order to accelerate our understanding of this disease and ultimately provide better treatment, it is critical that we develop solutions able to meet the scale of this challenge. Co-localizing ICGC data as well as other cancer genomics data sets like The Cancer Genome Atlas with secure and scalable computation resources represents a major step forward for both researchers and patients. With ICGC data available on AWS, we utilized the Seven Bridges platform to perform variant calling on hundreds of genomes weeks faster than would have been possible using local infrastructure,” said Deniz Kural, CEO of Seven Bridges Genomics and Principal Investigator of one of three NCI-funded Cancer Genomics Cloud pilot projects.

“This effort to provide the ICGC datasets on AWS will lower the barriers currently associated with computing on thousands of genomes. Users will have the ability to quickly analyze datasets within the cloud on highly scalable infrastructure. This is a paradigm shift from the old model of slowly downloading data to a user’s local infrastructure before any meaningful work can commence,” said Brian O’Connor, Managing Director of Cloud Computing at the Ontario Institute for Cancer Research.

“The ICGC Data Access Compliance Office (DACO) has been a forerunner in providing controlled, secure, and efficient access to cancer genomic data to members of the research community. It now welcomes the opportunity to further advance research for the benefit of all cancer patients by enabling controlled cloud access to ICGC genomic data stored on AWS. Throughout the process, DACO will implement a robust governance framework to ensure a high degree of privacy protection to patients’ genetic and health data,” said Yann Joly, Data Access Officer, ICGC DACO, McGill University.

“This exciting collaboration and new use for cloud technology is the future of cancer research. Ontario is proud to be part of this initiative through the Ontario Institute for Cancer Research and we look forward to seeing this relationship help cancer patients around the world,” said Reza Moridi, Ontario’s Minister of Research and Innovation.

There are currently 89 ICGC projects underway at research institutes in Asia, Australia, Europe, North America, and South America. These projects seek to identify the genomic drivers of cancer 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.

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 cloud and through the ICGC Data Coordination Center at (http://dcc.icgc.org).

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

November 18, 2015

The International Cancer Genome Consortium brings more genomic health data to researchers on the Amazon Web Services Cloud

Toronto – (November 18, 2015) The International Cancer Genome Consortium (ICGC) announced today that 1,200 encrypted cancer whole genome sequences are now securely available on the Amazon Web Services (AWS) Cloud for access by cancer researchers worldwide.

The Ontario Institute for Cancer Research (OICR), which houses the ICGC’s Data Coordination Center (DCC), copied ICGC genome data onto the AWS Cloud and is providing authorized researchers with credentials to access and analyze the data using secure mechanisms. The ICGC Data Access Compliance Office has established a framework that protects the confidentiality of research participants while working to ensure that the research will benefit future cancer patients.

The newly launched initiative means one of the world’s largest collections of cancer genome data is now more easily accessible to qualified researchers, which will enhance collaboration and potentially accelerate the development of new treatments for cancer patients.

Cloud solutions have become essential to genomics research because of the vast amount of data produced by researchers and the difficulties inherent in transferring such large datasets between sites. Projects can quickly grow to several petabytes in size, with each petabyte being the equivalent of data on 223,000 DVDs. Very few institutions around the world have the capacity to download such immense datasets for analysis, and this has limited the number of researchers who can access genome projects and the scope of what can be done with the data.

With cloud computing, researchers don’t need to download data. They can work with data and run experiments in the cloud, a flexible network of servers on the Internet, and access data in minutes rather than months. Data stored in the cloud has been shown to be as secure, if not more so, than data downloaded to local servers and hard drives. The set of 1,200 genomes now available on AWS is the first installment of ICGC data to be posted and is expected to grow several fold over the next 12 months with the addition of data from more cancer patients.

“This initiative brings together one of the world’s largest cancer genome datasets and one of the world’s leading cloud computing providers to create a powerful new resource for cancer researchers,” said Dr. Lincoln Stein, Director of the Informatics and Biocomputing Program at the Ontario Institute for Cancer Research and Director of the ICGC’s Data Coordination Center. “Now, far more researchers will have access to ICGC data, opening up the possibility of new discoveries and new breakthroughs in cancer research.”

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project of the ICGC and The Cancer Genome Atlas (TCGA) is coordinating analysis of more than 2,800 cancer genomes, and is making extensive use of AWS and the genomes stored on Amazon Simple Storage Service (Amazon S3). Each genome is being characterized through a suite of standardized algorithms, including alignment to the reference genome, uniform quality assessment, and the calling of multiple classes of somatic mutations. Scientists participating in the research projects of PCAWG are addressing a series of fundamental questions about cancer biology and evolution based on these data.

“Making this data available and usable will enable more researchers across the world to ask questions and get answers that were previously out of reach,” said Matt Wood, General Manager of Product Strategy at Amazon Web Services, Inc. “Researchers can now explore these large and diverse datasets in unconstrained ways, without having to manage large amounts of physical infrastructure. Instead, they can focus on driving their state-of-the-art research forward.”

“Cancer research is becoming increasingly data-heavy. Compiling the data, organizing the data, analyzing the data, making the data available to all researchers—these are fundamental to making further progress in cancer genome research, and we are excited at the possibilities of working with innovative cloud-based computing systems to achieve these advances,” said Peter Campbell, Head of Cancer Genetics and Genomics at the Wellcome Trust Sanger Institute, who is helping to lead the PCAWG project.

“In the next year, it is estimated that 14 million people worldwide will learn that they have cancer. In order to accelerate our understanding of this disease and ultimately provide better treatment, it is critical that we develop solutions able to meet the scale of this challenge. Co-localizing ICGC data as well as other cancer genomics data sets like The Cancer Genome Atlas with secure and scalable computation resources represents a major step forward for both researchers and patients. With ICGC data available on AWS, we utilized the Seven Bridges platform to perform variant calling on hundreds of genomes weeks faster than would have been possible using local infrastructure,” said Deniz Kural, CEO of Seven Bridges Genomics and Principal Investigator of one of three NCI-funded Cancer Genomics Cloud pilot projects.

“This effort to provide the ICGC datasets on AWS will lower the barriers currently associated with computing on thousands of genomes. Users will have the ability to quickly analyze datasets within the cloud on highly scalable infrastructure. This is a paradigm shift from the old model of slowly downloading data to a user’s local infrastructure before any meaningful work can commence,” said Brian O’Connor, Managing Director of Cloud Computing at the Ontario Institute for Cancer Research.

“The ICGC Data Access Compliance Office (DACO) has been a forerunner in providing controlled, secure, and efficient access to cancer genomic data to members of the research community. It now welcomes the opportunity to further advance research for the benefit of all cancer patients by enabling controlled cloud access to ICGC genomic data stored on AWS. Throughout the process, DACO will implement a robust governance framework to ensure a high degree of privacy protection to patients’ genetic and health data,” said Yann Joly, Data Access Officer, ICGC DACO, McGill University.

“This exciting collaboration and new use for cloud technology is the future of cancer research. Ontario is proud to be part of this initiative through the Ontario Institute for Cancer Research and we look forward to seeing this relationship help cancer patients around the world,” said Reza Moridi, Ontario’s Minister of Research and Innovation.

There are currently 89 ICGC projects underway at research institutes in Asia, Australia, Europe, North America, and South America. These projects seek to identify the genomic drivers of cancer 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.

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 cloud and through the ICGC Data Coordination Center at (http://dcc.icgc.org).

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

February 4, 2015

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.