SYS-CON MEDIA Authors: Pat Romanski, Elizabeth White, Yeshim Deniz, Glenn Rossman, Cynthia Dunlop

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.

@CloudExpo Stories
Once the decision has been made to move part or all of a workload to the cloud, a methodology for selecting that workload needs to be established. How do you move to the cloud? What does the discovery, assessment and planning look like? What workloads make sense? Which cloud model makes sense for each workload? What are the considerations for how to select the right cloud model? And how does that fit in with the overall IT tranformation? In his session at 15th Cloud Expo, John Hatem, head of V...
Cloud services are the newest tool in the arsenal of IT products in the market today. These cloud services integrate process and tools. In order to use these products effectively, organizations must have a good understanding of themselves and their business requirements. In his session at 15th Cloud Expo, Brian Lewis, Principal Architect at Verizon Cloud, will outline key areas of organizational focus, and how to formalize an actionable plan when migrating applications and internal services to...
SAP is delivering break-through innovation combined with fantastic user experience powered by the market-leading in-memory technology, SAP HANA. In his General Session at 15th Cloud Expo, Thorsten Leiduck, VP ISVs & Digital Commerce, SAP, will discuss how SAP and partners provide cloud and hybrid cloud solutions as well as real-time Big Data offerings that help companies of all sizes and industries run better. SAP launched an application challenge to award the most innovative SAP HANA and SAP ...
SYS-CON Events announced today that ElasticBox is holding a Hackathon at DevOps Summit, November 6 from 12 pm -4 pm at the Santa Clara Convention Center in Santa Clara, CA. You can enter as an individual or team of up to 10 developers. A New Star Is Born Every Month! All completed ElasticBoxes will then be sent to a judging panel - 12 winners will be featured on the ElasticBox website in 2015. All entrants will receive five full enterprise licenses for one year + ElasticBox headphones + Elasti...
Ixia develops amazing products so its customers can connect the world. Ixia helps its customers provide an always-on user experience through fast, secure delivery of dynamic connected technologies and services. Through actionable insights that accelerate and secure application and service delivery, Ixia's customers benefit from faster time to market, optimized application performance and higher-quality deployments.
SYS-CON Events announced today that Calm.io has been named “Bronze Sponsor” of DevOps Summit Silicon Valley, which will take place on November 4–6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Calm.io is a cloud orchestration platform for AWS, vCenter, OpenStack, or bare metal, that runs your CL tools puppet, Chef, shell, git, Jenkins, nagios, and will soon support New Relic and Docker. It can run hosted, or on premise and provides VM automation / expiry, self-service portals,...
In her General Session at 15th Cloud Expo, Anne Plese, Senior Consultant, Cloud Product Marketing, at Verizon Enterprise, will focus on finding the right mix of renting vs. buying Oracle capacity to scale to meet business demands, and offer validated Oracle database TCO models for Oracle development and testing environments. Anne Plese is a marketing and technology enthusiast/realist with over 19+ years in high tech. At Verizon Enterprise, she focuses on driving growth for the Verizon Cloud pla...
SYS-CON Events announced today that Aria Systems, the recurring revenue expert, has been named "Bronze Sponsor" of SYS-CON's 15th International Cloud Expo®, which will take place on November 4-6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Aria Systems helps leading businesses connect their customers with the products and services they love. Industry leaders like Pitney Bowes, Experian, AAA NCNU, VMware, HootSuite and many others choose Aria to power their recurring revenue bu...
The Internet of Things (IoT) is going to require a new way of thinking and of developing software for speed, security and innovation. This requires IT leaders to balance business as usual while anticipating for the next market and technology trends. Cloud provides the right IT asset portfolio to help today’s IT leaders manage the old and prepare for the new. Today the cloud conversation is evolving from private and public to hybrid. This session will provide use cases and insights to reinforce t...
As Platform as a Service (PaaS) matures as a category, developers should have the ability to use the programming language of their choice to build applications and have access to a wide array of services. Bluemix is IBM's open cloud development platform that enables users to easily build cloud-based, creative mobile and web applications without having to spend large amounts of time and resources on configuring infrastructure and multiple software licenses. In this track, you will learn about the...
Blue Box has closed a $10 million Series B financing. The round was led by a strategic investor and included participation from prior investors including Voyager Capital and Founders Collective, as well as the Blue Box executive team. This round follows a $4.3 million Series A closed in December of 2012 and led by Voyager Capital. In May of this year, the company announced general availability of its private cloud as a service offering, Blue Box Cloud. Since that release, the company has dem...
SYS-CON Events announced today that Verizon has been named "Gold Sponsor" of SYS-CON's 15th International Cloud Expo®, which will take place on November 4-6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Verizon Enterprise Solutions creates global connections that generate growth, drive business innovation and move society forward. With industry-specific solutions and a full range of global wholesale offerings provided over the company's secure mobility, cloud, strategic network...
SimpleECM is the only platform to offer a powerful combination of enterprise content management (ECM) services, capture solutions, and third-party business services providing simplified integrations and workflow development for solution providers. SimpleECM is opening the market to businesses of all sizes by reinventing the delivery of ECM services. Our APIs make the development of ECM services simple with the use of familiar technologies for a frictionless integration directly into web applicat...
The only place to be June 9-11 is Cloud Expo & @ThingsExpo 2015 East at the Javits Center in New York City. Join us there as delegates from all over the world come to listen to and engage with speakers & sponsors from the leading Cloud Computing, IoT & Big Data companies. Cloud Expo & @ThingsExpo are the leading events covering the booming market of Cloud Computing, IoT & Big Data for the enterprise. Speakers from all over the world will be hand-picked for their ability to explore the economic...
Cloudwick, the leading big data DevOps service and solution provider to the Fortune 1000, announced Big Loop, its multi-vendor operations platform. Cloudwick Big Loop creates greater collaboration between Fortune 1000 IT staff, developers and their database management systems as well as big data vendors. This allows customers to comprehensively manage and oversee their entire infrastructure, which leads to more successful production cluster operations, and scale-out. Cloudwick Big Loop supports ...
To manage complex web services with lots of calls to the cloud, many businesses have invested in Application Performance Management (APM) and Network Performance Management (NPM) tools. Together APM and NPM tools are essential aids in improving a business’s infrastructure required to support an effective web experience… but they are missing a critical component – Internet visibility. Internet connectivity has always played a role in customer access to web presence, but in the past few years use...
SAP is delivering break-through innovation combined with fantastic user experience powered by the market-leading in-memory technology, SAP HANA. In his General Session at 15th Cloud Expo, Thorsten Leiduck, VP ISVs & Digital Commerce, SAP, will discuss how SAP and partners provide cloud and hybrid cloud solutions as well as real-time Big Data offerings that help companies of all sizes and industries run better. SAP launched an application challenge to award the most innovative SAP HANA and SAP ...
Software AG helps organizations transform into Digital Enterprises, so they can differentiate from competitors and better engage customers, partners and employees. Using the Software AG Suite, companies can close the gap between business and IT to create digital systems of differentiation that drive front-line agility. We offer four on-ramps to the Digital Enterprise: alignment through collaborative process analysis; transformation through portfolio management; agility through process automation...
What are the benefits of using an enterprise-grade orchestration platform? In their session at 15th Cloud Expo, Jeff Tegethoff, CEO of Appcore, and Kedar Poduri, Senior Director of Product Management at Citrix Systems, will take a closer look at the architectural design factors needed to support diverse workloads and how to run these workloads efficiently as a service provider. They will also discuss how to deploy private cloud environments in 15 minutes or less.
Headquartered in Santa Monica, California, Bitium was founded by Kriz and Erik Gustavson. The 1,500 cloud-based application using Bitium’s analytics, app management, and single sign-on services include bug trackers, customer service dashboards, Google Apps, and social networks. The firm states website administrators can do multiple tasks online without revealing passwords. Bitium’s advisors include Microsoft’s former CMO and the former senior vice president of strategy, the founder and CEO of Li...