Click here to close now.

SYS-CON MEDIA Authors: Carmen Gonzalez, PagerDuty Blog, Liz McMillan, Elizabeth White, XebiaLabs Blog

News Feed Item

Canadian and US Leaders in Cancer Research Announce a Big Data Challenge to Develop Robust Methodologies for Predicting Cancer Mutations

Cancer research leaders from the Ontario Institute for Cancer Research (OICR) and the University of California, Santa Cruz (UCSC), in collaboration with Sage Bionetworks and IBM’s DREAM, will announce tomorrow the opening of the ICGC-TCGA-DREAM Somatic Mutation Calling (SMC) Challenge (https://www.synapse.org/#!Challenges:DREAM) at the Sixth Annual RECOMB/ISCB conference (http://www.iscb.org/recomb-regsysgen2013).

Like previous DREAM Challenges in the series, this new Challenge will engage a diverse community of scientists to solve a specific problem in a given time period by placing scientific data, tools, scoreboards and the resulting predictive models into an open Commons.

The specific problem the SMC Challenge will address is the need for accurate methods to identify cancer-associated mutations from whole-genome sequencing data. Cancer is a disease of the genome, caused by disruptions in DNA that alter specific gene functions. Although today’s DNA sequencing instruments can amass great quantities of sequence data from a patient’s normal and tumor tissues, the ability to identify DNA mutations and rearrangements accurately on the basis of those data remains elusive; current studies agree in only about 20% of their predictions.

To address this need, the Challenge will post the raw DNA sequencing data of 10 human tumor-normal pairs (5 prostate, 5 pancreatic), comprising approximately 9 terabytes of data to a high-speed distribution server. Contestants will have 6 months to optimize their predictive models. After the Challenge closes in July, 2014, at least 5,000 DNA candidate mutations predicted by different participating teams will be prospectively validated on an independent sequencing platform by the Challenge organizers. The accuracy of participants’ predictions will be ranked using the newly generated validation data based on sensitivity, specificity and balanced accuracy amongst other metrics.

To participate in the Challenge that opens tomorrow, individuals will need to register at https://www.synapse.org/ #!Challenges:DREAM. In addition, they must be approved by OICR’s ICGC Data Access Compliance Office to access the data.

As Canadian OICR researcher and Challenge organizer Professor Paul Boutros puts it, “Governments around the world have committed hundreds of millions of dollars to sequence cancer genomes to find new drug targets and to develop treatments that are personalized to each person’s cancer genome. But realizing these goals is currently blocked by scientists’ inability to identify mutations in cancer genomes. It is really tremendous that ICGC and TCGA are coming together with Sage Bionetworks and DREAM to address this problem using a DREAM Challenge that will set a gold standard that groups around the world can use to understand the cancer genome!”

To help realize this Challenge, industrial partners have stepped up. Google is making their Google Cloud Platform available to OICR-approved participants, including free access to the contest data in Google Cloud Storage and discounted Google Compute Engine cycles. Cloud processing will open the door for a whole new set of participants who do not have access to large compute clusters at their own institutions. Hitachi has provided free storage to host the data on a 1PB disk donated for cancer genomics. Annai Systems (http://www.annaisystems.com/) is providing their Annai-GNOS™ data management platform to facilitate upload, hosting and access to the data in the Hitachi store. Annai’s GeneTorrent software will provide high-speed data transfer to the Challenge participants.

Challenge participants will use the Synapse infrastructure (http://www.synapse.org), built by Sage Bionetworks, that allows collaboration by Challenge teams on an open platform. Synapse’s tools and forum will allow Challenge participants to: (1) record what processing and analysis they’ve done on the data; (2) submit their predictive models to a real-time leaderboard for scoring; and (3) share their ideas, model code and analysis results with others in the Challenge.

Publications based on the highest-ranking predictive methods from the Challenge will be considered with Nature Publishing Group. Nature Genetics editor Myles Axton will advise the Challenge on publication strategy and work with Synapse to understand the scientific quality control that can be obtained via competitive collaboration. “The exciting thing about this exercise from an editorial standpoint is that we can analyze just how much the strategies are improved during the contest and how much peer review is then needed to obtain a useful research publication at the end. The beauty of doing this on an open platform is to see the rigor, transparency and detail of each group’s approach and to be able to replay each strategy in a robust way,” Myles says. “This is a good use of editorial time since peer review improves the strategies, it improves the resulting publications and it improves the databases and journals by preparing us for the future of knowledge production. I really hope the winners combine elements of the best strategies into fuller publishable units, in that way they will get the best out of the challenge as well as our involvement with it.”

Explains UC Santa Cruz Professor Josh Stuart, “The timing of this Challenge couldn’t be better. ICGC and TCGA recently announced that they plan to jointly analyze a dataset of approximately 2,000 pairs of tumor-normal whole genomes as part of a 2014-2015 Pan-Cancer effort to elucidate comprehensively the genomic changes present in many forms of cancers. Thus, the winning algorithms selected by this DREAM Challenge will help ICGC/TCGA researchers provide the largest unified view of cancer genome variation to date.”

Cancer researcher Dr. Stephen Friend founded Sage Bionetworks out of a conviction that “…the best approach towards developing robust and accurate predictions such as those needed for mutation calling is to enable an open diverse community where data access is simple and people are incentivized to share. Sage and DREAM have already shown that in the span of several months, DREAM Challenges can attract hundreds of teams who end up submitting thousands of predictive models to a Challenge. Sage and DREAM couldn’t be more delighted to be partnered with the ICGC and TCGA research communities to provide the largest public methodology assessment for the field of somatic mutation identification.”

ABOUT ONTARIO INSTITUTE FOR CANCER RESEARCH: www.oicr.on.ca

OICR is an innovative cancer research and development institute dedicated to prevention, early detection, diagnosis and treatment of cancer. The Institute is an independent, not-for-profit corporation, supported by the Government of Ontario. OICR research supports more than 1,600 investigators, clinician scientists, research staff and trainees located at its headquarters and in research institutes and academia across the Province of Ontario. OICR has key research efforts underway in small molecules, biologics, stem cells, imaging, genomics, informatics and bio-computing. For more information, please visit the website at www.oicr.on.ca

ABOUT SAGE BIONETWORKS: http://sagebase.org/

Sage Bionetworks is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community-based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. Sage Bionetworks is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington, and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships.

ABOUT THE DREAM PROJECT: http://www.the-dream-project.org

The Dialogue on Reverse Engineering Assessment and Methods (DREAM) project is an initiative to advance the field of systems biology through the organization of Challenges to foster the development of predictive models of relevance in biomedicine. With the experience gathered by the launching of 27 successful DREAM challenges over the past seven years, the “Challenge” concept has reached a status of legitimacy and maturity. This success has triggered considerable interest by different government institutions and private organizations in working with DREAM to engage distributed teams to solve tough computational problems in biomedical research.

ABOUT ANNAI SYSTEMS INC.: (http://www.annaisystems.com)

Annai Systems Inc., located in California’s Silicon Valley, is a technology company with a core competency in big data management solutions. We are focused on applying our technology to the field of genomics to enable easier, more efficient access to genomic data. Our technology enables the producers and consumers of genomic data to achieve better results faster and at lower operating costs by providing products that overcome key data-related bottlenecks and roadblocks that are impeding progress in the growing fields of genomic research and medicine. Annai Systems offers a variety of products and services to address the “big data” challenges associated with using genomic data in personalized medicine and healthcare improvement.

More Stories By Business Wire

Copyright © 2009 Business Wire. All rights reserved. Republication or redistribution of Business Wire content is expressly prohibited without the prior written consent of Business Wire. Business Wire shall not be liable for any errors or delays in the content, or for any actions taken in reliance thereon.

Latest Stories
SYS-CON Events announced today that the DevOps Institute has been named “Association Sponsor” of SYS-CON's DevOps Summit, which will take place on June 9–11, 2015, at the Javits Center in New York City, NY. The DevOps Institute provides enterprise level training and certification. Working with thought leaders from the DevOps community, the IT Service Management field and the IT training market, the DevOps Institute is setting the standard in quality for DevOps education and training.
Plutora provides enterprise release management and test environment SaaS solutions to clients in North America, Europe and Asia Pacific. Leading companies across a variety of industries, including financial services, telecommunications, retail, pharmaceutical and media, rely on Plutora's SaaS solutions to orchestrate releases and environments faster and with integrity. Products include Plutora Release Manager, Plutora Test Environment Manager and Plutora Deployment Manager.
SYS-CON Events announced today the DevOps Foundation Certification Course, being held June ?, 2015, in conjunction with DevOps Summit and 16th Cloud Expo at the Javits Center in New York City, NY. This sixteen (16) hour course provides an introduction to DevOps – the cultural and professional movement that stresses communication, collaboration, integration and automation in order to improve the flow of work between software developers and IT operations professionals. Improved workflows will res...
When it comes to building applications, one database definitely does not fit all. Traditional SQL databases are great for storing highly structured, normalized data and performing analytics and reporting. NoSQL has attracted developers with its awesome flexibility, and JSON-centric document stores like Cloudant make web developers incredibly productive by offering a JavaScript environment from end-to-end. Recent Big Data challenges have driven the need for a distributed approach to analytics e...
Containers and microservices have become topics of intense interest throughout the cloud developer and enterprise IT communities. Accordingly, attendees at the upcoming 16th Cloud Expo at the Javits Center in New York June 9-11 will find fresh new content in a new track called PaaS | Containers & Microservices Containers are not being considered for the first time by the cloud community, but a current era of re-consideration has pushed them to the top of the cloud agenda. With the launch ...
The WebRTC Summit 2014 New York, to be held June 9-11, 2015, at the Javits Center in New York, NY, announces that its Call for Papers is open. Topics include all aspects of improving IT delivery by eliminating waste through automated business models leveraging cloud technologies. WebRTC Summit is co-located with 16th International Cloud Expo, @ThingsExpo, Big Data Expo, and DevOps Summit.
Modern Systems announced completion of a successful project with its new Rapid Program Modernization (eavRPMa"c) software. The eavRPMa"c technology architecturally transforms legacy applications, enabling faster feature development and reducing time-to-market for critical software updates. Working with Modern Systems, the University of California at Santa Barbara (UCSB) leveraged eavRPMa"c to transform its Student Information System from Software AG's Natural syntax to a modern application lev...
SOA Software has changed its name to Akana. With roots in Web Services and SOA Governance, Akana has established itself as a leader in API Management and is expanding into cloud integration as an alternative to the traditional heavyweight enterprise service bus (ESB). The company recently announced that it achieved more than 90% year-over-year growth. As Akana, the company now addresses the evolution and diversification of SOA, unifying security, management, and DevOps across SOA, APIs, microser...
Even though it’s now Microservices Journal, long-time fans of SOA World Magazine can take comfort in the fact that the URL – soa.sys-con.com – remains unchanged. And that’s no mistake, as microservices are really nothing more than a new and improved take on the Service-Oriented Architecture (SOA) best practices we struggled to hammer out over the last decade. Skeptics, however, might say that this change is nothing more than an exercise in buzzword-hopping. SOA is passé, and now that people are ...
The webinar, hosted by XebiaLabs, will feature 4 experts including Special Host Gene Kim, author of The Phoenix Project, along with IT thought leaders Gary Gruver, Randy Shoup and XebiaLabs' Andrew Phillips. The panel brings more than 30 years of collective experience surrounding microservices transformations at major companies including Google, eBay and Tripwire. "The story around microservices and containers is pretty compelling and the attraction of more flexibility is obviously alluring,"...
SYS-CON Events announced today that Creative Business Solutions will exhibit at SYS-CON's 16th International Cloud Expo®, which will take place on June 9-11, 2015, at the Javits Center in New York City, NY. Creative Business Solutions is the top stocking authorized HP Renew Distributor in the U.S. Based out of Long Island, NY, Creative Business Solutions offers a one-stop shop for a diverse range of products including Proliant, Blade and Industry Standard Servers, Networking, Server Options and...
WHOA.com has announced the newest addition to its data center footprint with the expansion into Equinix's newest state-of-the-art facility: DC-11 Washington, DC IBX+. Located in Ashburn, VA, this data center expands Whoa.com's presence to meet rapidly expanding customer demand for secure cloud solutions. Equinix, Inc. operates International Business Exchange™ (IBX®) data centers in 32 markets across 15 countries in the Americas, EMEA, and Asia-Pacific. Equinix is committed to operating faciliti...
SYS-CON Events announced today that FierceDevOps will exhibit at SYS-CON's 16th International Cloud Expo®, which will take place on June 9-11, 2015, at the Javits Center in New York City, NY. FierceDevOps keeps software developers and IT operations personnel updated on the latest news and trends around the rapidly evolving role of the traditional IT worker.
The Open Compute Project is a collective effort by Facebook and a number of players in the datacenter industry to bring lessons learned from the social media giant's giant IT deployment to the rest of the world. Datacenters account for 3% of global electricity consumption – about the same as all of Switzerland or the Czech Republic -- according to people I met at the recent Open Compute Summit in San Jose. With increasing mobility at the edge of the cloud and vast new dataflows being pre...
GENBAND has announced that SageNet is leveraging the Nuvia platform to deliver Unified Communications as a Service (UCaaS) to its large base of retail and enterprise customers. Nuvia’s cloud-based solution provides SageNet’s customers with a full suite of business communications and collaboration tools. Two large national SageNet retail customers have recently signed up to deploy the Nuvia platform and the company will continue to sell the service to new and existing customers. Nuvia’s capabili...