Press category: Research

Collaborating in Real Time: Sage Bionetworks’ Open Software Platform Enables First Round of Collaborative Cancer Projects on Large Genomic Data Sets

SEATTLE–(BUSINESS WIRE)–Four open access papers issued in Nature Genetics today highlight the benefits of making large biomedical research data sets open as a community resource and equipped with cloud-based tools that facilitate rapid learning and future discovery.

http://dx.doi.org/10.1038/ng.2761

http://dx.doi.org/10.1038/ng.2762

http://dx.doi.org/10.1038/ng.2760

http://dx.doi.org/10.1038/ng.2764

The papers report on the genetic profiles of 12 cancer types, describe the collaborative approach taken by The Cancer Genome Atlas (TCGA) Pan-Cancer Project researchers and highlight the new bioinformatics tools that Sage Bionetworks provided to the effort. TCGA includes 250 researchers spread across 30 institutions and running a total of 60 different research projects, all affiliated with the same set of nearly 2000 biomedical data files covering 12 different cancer types. For the duration of the Pan-Cancer project, TCGA members agreed to pilot Synapse (www.synapse.org), Sage Bionetworks’ software platform, for managing the myriad interdependencies of these projects and for facilitating the sharing and evolving of data and findings in real time.

The non-profit Sage Bionetworks was founded in 2009 with a vision to accelerate biomedical research by developing open systems, incentives and standards that allow an open commons of research to flourish. Sage Bionetworks’ Director of Computational Biology, Dr. Adam Margolin likens Synapse to “…a computational researcher’s sandbox where open data aggregates and can be used continuously by researchers. We intentionally embedded tools of collaboration into Synapse. These are things like automated data versioning and real time ‘provenance’ records that detail how a researcher processed his/her data. With these tools in place, Synapse ends up transforming efforts like these first reported findings of the Pan-Cancer project into an open resource: where any stage of the work can serve as the starting point for additional exploration by the greater scientific community.”

The TCGA community piloted the Synapse software platform for its ability to support three different requirements of their collaborative work: providing data freezes and data versioning controls, conducting and sharing multistep data analysis workflows and collaboratively evolving novel analytical methods. Today’s four TCGA papers in Nature Genetics are the first of 18 papers already in press that showcase a range of discoveries all emerging from a common set of data managed in Synapse. In addition, the resulting TCGA data freezes, analysis results and evaluation framework for survival predictions are a new publicly available resource released on Synapse in conjunction with this work.

Judging from the impressions of two TCGA researchers, the way in which Synapse supported the Pan-Cancer project could very well become a working model to guide aspects of future large-scale collaborative studies on biomedical data.

Kyle Ellrott, a UCSC software developer and heavy user of Synapse for the TCGA projects, notes, “Synapse empowers data providers and analysts to share their work while at the same time providing a common framework everyone can use. It is the YouTube of scientific data.”

Professor Josh Stuart (Biomolecular Engineering, UCSC) concludes, “Synapse was indeed the connecting data framework that held the entire project together. It represents an important milestone for collaborative science that so many groups around the country and world were able to work together on a common set of scientific problems. The beauty of it is that it will only improve as we scale to even larger projects in the near future.”

Press Release on BusinessWire

CommonMind Consortium Expands Public-Private Effort to Generate and Broadly Share Molecular Data on Neuropsychiatric Disease

SEATTLE–(BUSINESS WIRE)–The CommonMind Consortium (CMC), launched in April 2012, is pleased to announce that its membership has expanded to include five academic groups (Icahn School of Medicine at Mount Sinai – MS; University of Pennsylvania – Penn; National Institute of Mental Health – NIMH; University of Pittsburgh – Pitt; and University of Texas Southwestern – UTSW), two pharmaceutical companies (Takeda Pharmaceuticals Company Limited – TAKEDA; and F. Hoffmann-La Roche Ltd – Roche) and one nonprofit group (Sage Bionetworks). The new additions to the founding members include Pitt, UTSW and Roche.

CMC is a Public-Private Pre-Competitive Consortium that brings together disease area expertise, large-scale and well-curated brain sample collections, and data management and analysis expertise with a goal to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. Phase I of this project will generate whole genome transcriptome data on the prefrontal cortex as well as high-density SNP genotypes from >700 postmortem brain samples from Schizophrenia and control tissue collections at MS, Penn, Pitt and UTSW using funding provided by TAKEDA, Roche and the NIMH. The consortium benefits from synergies created from the combined expertise of all contributors. Currently it is envisaged that this data will become available to the public through Synapse (synapse.sagebio2018.wpengine.com) in 2014. Subsequent phases of the project will expand the molecular data for the brain collection to include new brain regions and new types of information beyond transcriptomic data (exome sequencing, epigenetic, etc).

Dr. Jonathan Derry, Vice President of Research at Sage Bionetworks, noted, “We are happy to welcome our new members who will provide both additional samples to our collection and valuable experience that can guide our studies.” Dr. Enrico Domenici, Molecular Biomarker Lead, Neuroscience Discovery and Translational Area, Roche, added, “We are fully committed as a pharmaceutical company to identifying and developing new therapeutic approaches for neuropsychiatric disease and we see this type of public-private collaboration as an important part of our strategy.”

The addition of Pitt and UTSW to the consortium has significantly expanded the brain tissue collection available for data generation. Dr. Carol Tamminga, Professor and Chair of Psychiatry, UTSW, commented, “CMC is a natural partner for us in our efforts to better understand the molecular underpinnings of these devastating mental health diseases. There is no doubt that we will make faster progress to this common goal as a group than if we worked independently.”

The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info@CommonMind.org.

Press Release on BusinessWire

H3 Biomedicine Announces Strategic Collaboration with Sage Bionetworks to Advance Cancer-Genomics Research

Cambridge, MA, December 19, 2012 — H3 Biomedicine Inc., a biopharmaceutical company specializing in the discovery and development of oncology treatments, announced today that it has forged a partnership with Sage Bionetworks to jointly develop software platforms that advance critical components of H3’s cancer genomics research. Sage will pair its advanced predictive modeling capabilities and collaboration platform with H3’s assimilation of genomic and pharmacology data to identify and predict associations between specific human genomic alterations and pharmacological drug responses. As part of an ongoing commitment to an open data-sharing environment, H3 Biomedicine and Sage Bionetworks intend to make the data and tools resulting from this partnership freely accessible to other organizations pursuing cancer research.

“Our partnership with Sage is symbiotic on several fronts: we are able to bring together our technical expertise to advance critical needs in cancer genomic research, and we share a dedication to the philosophy of open access,” stated Markus Warmuth, M.D., President and Chief Executive Officer of H3 Biomedicine. “Unfortunately, there is no shortage of urgent needs in cancer treatment. We hope that making our collaborative results publicly accessible will advance the field of translational research in oncology, ultimately bringing more personalized medicines to patients with many types of cancers, especially those for whom there are limited effective treatment options.”

Translating data from the cancer genome into potential therapeutic drugs is largely dependent on the systematic genetic and pharmacological profiling of the increasingly large collection of preclinical cancer genomic models. The H3/Sage partnership aims to develop a robust analytical pipeline of pharmaco-genomic profiling data, which is required to efficiently verify and identify drug response biomarkers. These can be used to determine patients for whom a particular drug may have the largest likelihood for positive therapeutic results, an important step to bring “personalized medicine” to cancer patients.

Dr. Stephen Friend, President and Founder of Sage Bionetworks, remarked, “H3 is a visionary company. While H3’s focus on deep interrogations of biology and commitment to open data-sharing is unusual in the biotech world, we believe it will be trendsetting. Sage’s fully curated, open-compute platform is nicely positioned to host H3’s drug response and cancer genomic data, and the results of this collaboration hold potentially enormous benefits for the cancer research community as a whole.”

Press Release

CommonMind Consortium Launched as a Public-Private Effort to Generate and Broadly Share Molecular Data on Neuropsychiatric Disease

Press Release | Mon Apr 9, 2012 5:30pm EDT

CommonMind Consortium Launched as a Public-Private Effort to Generate and Broadly Share Molecular Data on Neuropsychiatric Disease

Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions.

As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering.

Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr. Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented “this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease”, while Dr Raquel Gur, Professor of Psychiatry from Penn observed “this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture.”

Dr. Jonathan Derry, Vice President of Research at Sage Bionetworks noted, “We are truly thrilled to be partnering with some of the best brain researchers to generate an unprecedented scale of molecular data that we will make broadly available as a resource to the community through our data analysis and management platform Synapse.” Dr Thomas Lehner, Chief Genomics Research Branch at NIMH added, “The NIMH is particularly excited about this partnership that will leverage resources and expertise in both the public and the private sector to accelerate research into the causes and treatments of major mental illness.”

TAKEDA has provided seed funding for the effort that will look to expand in the future. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info@CommonMind.org.

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