Greg Beier, Bagooba’s Chief Evangelist, has a thoughtful post on the value of sharing information where he highlights Stephen Friend and Sage Bionetworks’ efforts to encourage and facilitate the sharing of research data. He notes, “This movement is so interesting on so many levels and could find application in so many other areas where poor incentives are leading to stakeholders withholding information for private advantage.”
Press Release: CommonMind Consortium Launched as a Public-Private Effort to Generate and Broadly Share Molecular Data on Neuropsychiatric Disease.
Date: April 9th, 2012
Contact: Jonathan Derry, Vice-President, Sage Bionetworks
Tel: (206) 667-2101 email: info@CommonMind.org
SEATTLE, WA. 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.
Sage Bionetworks is offering 10 travel awards to the 2012 Commons Congress in San Francisco to grad students, postdocs and early stage investigators. Details and an on line application form are available on the Congress website. This is a fantastic opportunity for young clinicians, biologists, software engineers and computational scientists who are passionate about open science and data-intensive science to participate and contribute.
Application deadline is February 29, so act quickly. Please forward this information on to outstanding candidates!
One of Sage Bionetworks’ primary activities is the creation of a computational platform, called Synapse, that will facilitate open, reproducible data-driven science and support the reusability of information by ontology-based services and applications directed at scientific researchers and data curators. Dr. Michael Kellen, Director of Technology at Sage Bionetworks provided a demonstration of an alpha version of the Synapse platform to the National Center for Biomedical Ontology and discussed its application to clinical science. A recorded webinar of his presentation and the discussions is available on line: http://www.bioontology.org/Sage-Bionetworks-Synapse-Project
One important outcome from the April Commons Congress in San Francisco was the Commons Principles. This charter for open, contributor-driven genomic research and progressive community engagement was developed to define behaviors and processes for those working in the Commons computational environment as well as for researchers interested in cooperative, data-intensive science and patient advocacy.
The Principles are an aspirational guide rather than a detailed roadmap (which will come from the activities of Community of Interest D over the next year.) This vision for the Commons is described in six principles emphasizing the; healthcare focus, open platform, respect for all stakeholders, proper attribution, transparent standards, and absence of IP barriers.
Starting with a draft prepared by Robert Cook-Deegan, the Principles were revised and approved by Congress attendees and after further revision and condensation the Principles were approved by the Sage Bionetworks Board of Directors. A public endorsement has now begun and we invite you to raise your voice and support for open science and the Sage Bionetworks Commons concept by adding your name or comments to the Principles at http://sagebase.org/WP/com.
Sage Bionetworks has built a strong program in neuroscience with partnerships to build advanced computational models of disease with CHDI Foundation and Takeda Pharmaceutical Company. The analyses and the resulting models will be deposited in the Sage Bionetworks repository and will be valuable public resources available to all interested researchers.
CHDI Foundation is continuing to support Sage Bionetworks in a project to apply advanced computational modeling to the discovery and development of biomarkers and therapies for Huntington’s disease (HD). Initially, Sage Bionetworks and CHDI will work with Massachusetts General Hospital colleagues to conduct a worldwide inventory of HD tissues available for research purposes.
“Even though HD is caused by mutations in a single gene, there are unexplained variations in disease onset and progression,” explained Jonathan Derry PhD, Project Leader and Vice President of Research at Sage Bionetworks. ”We believe that genomic network analysis that uses both genetic and phenotypic data will help identify the factors underlying this complexity and provide insights into new models and therapies for the disease.” Robi Blumenstein, President of CHDI Management said, “We are particularly excited to bring HD to Sage Bionetworks’ open-access infrastructure. This shared platform will allow investigators to freely build and compare their network models using Sage Bionetworks’ sophisticated tools, to the benefit of the entire HD research community.”
Schizophrenia and other CNS Diseases
Takeda Pharmaceutical Company and Sage Bionetworks have began a four-year research alliance focusing on therapeutic targets for central nervous system (CNS) disease. Using its integrated genomics methods, Sage Bionetworks scientists will build predictive computational models and identify key regulatory genes and predictive biomarkers in patients with CNS diseases including schizophrenia. Scientists at the two companies will then collaborate to discover and prioritize the targets holding the greatest potential for molecular intervention. Under the terms of the agreement, Takeda will provide more than $3.6 million over four years in research funding and fees.
“Sage Bionetworks’ leading-edge technology and world-wide reach offers the potential for Takeda to understand currently unknown disease mechanisms. This represents a key strategy for meeting Takeda’s challenge for innovation,” said Dr. Paul Chapman, General Manager, Head of Pharmaceutical Research Division of Takeda Pharmaceutical Company Limited. Dr. Stephen Friend, President of Sage Bionetworks noted, “We believe this project, which is our first in central nervous system area, creates an opportunity for new therapeutic insights.”
Sage Bionetworks and AstraZeneca have begun an exciting cancer collaboration using advanced computational modeling. The goal is to develop a deeper understanding of cancer to help better match patients with appropriate treatments and might one day lead to new cancer therapeutics.
Cancer is a major cause of mortality globally; accounting for 7.4 million (or 13%) of all deaths in 2004. The World Health Organization estimates the incidence of cancer to continue rising to reach an estimated 9.2 million deaths in 2015, driving the critical need for novel therapies to reach patients quickly and efficiently as well as better ways to match patients with treatments.
The partnership will combine Sage Bionetworks’ expertise in computer models of disease genetics with AstraZeneca’s extensive knowledge and expertise of oncology including access to data on AstraZeneca’s compounds. It will focus on investigating regulatory pathways among different cancers using large coherent cancer genomic datasets and predictive disease models developed at Sage Bionetworks. This will potentially provide data-driven rationales for prioritizing therapeutic targets for developing new insights to improve cancer treatments, as well as potentially helping to identify cancer patient subpopulations that will most likely benefit from such treatments. Dr. Jonathan Derry, Vice President of Research at Sage Bionetworks noted, “This is an exciting opportunity to combine what we have learned about complex genetic networks with the outstanding resources and scientists at AstraZeneca.”
Dr. Susan Galbraith, Vice President and Head of Oncology Innovative Medicines Unit at AstraZeneca said: “We are looking forward to collaborating with Sage Bionetworks to build realistic, predictive models of cancers to expand our current understanding of these diseases and potentially harness that knowledge into new target identification, portfolio positioning and patient selection all of which we hope will lead to new treatment options for patients.”
“Everyone truly wins in this project,” noted Dr. Stephen Friend, President of Sage Bionetworks. “Sage Bionetworks gets to work with an industry innovator and the resultant computational models will be placed in our public repository and available to all researchers following the completion of the project. Most importantly, we hope patients will gain better drugs.”
Ingenuity Systems (www.ingenuity.com), a leading provider of information solutions for life science researchers, has begun a new collaboration with Sage Bionetworks. Under the collaboration, Sage Bionetworks will leverage IPA®, Ingenuity’s industry-leading analysis software, and the Ingenuity® Knowledge Base of structured biomedical Findings, to inform and enhance Sage’s predictive disease networks. Additionally, Sage Bionetworks’ web portal will provide links to the Ingenuity Knowledge Base and to IPA, to help visitors access timely, context-rich biomedical information and better understand it in a biological context. Sage Bionetworks’ content, algorithms, and predictive disease networks will also be made available within Ingenuity products like IPA®.
The Ingenuity-Sage collaboration will support therapeutic area researchers who are working to understand the complex developments in the diagnosis, treatment, and etiology of diseases. Researchers will be able to use the content and algorithms from Sage Bionetworks within IPA to analyze molecular data, generate testable hypotheses, and build and visualize predictive disease models. These models will enable researchers to more rapidly identify and prioritize therapeutic targets for drug development and assess toxicity of potential drug candidates.
“We’re very excited about our collaboration with Ingenuity Systems”, stated Stephen Friend MD, PhD, President, Sage Bionetworks. “Leveraging their high-quality, expert-reviewed Ingenuity Knowledge Base Findings and their powerful pathway analytics in our research will enhance and add functionality to our predictive disease networks and algorithms.”
“This represents a rare and precious opportunity to fundamentally advance the field of predictive disease networks,” said Doug Bassett, Chief Science and Technology Officer at Ingenuity, “We’re thrilled to be working with Sage in this context, and excited at the value this can bring to Sage and Ingenuity customers and partners. We are committed to providing researchers with the very best predictive disease content and analytics within Ingenuity’s products.”