Accelerating Medicine Partnership in Alzheimer’s Disease

The Accelerating Medicine Partnership for Alzheimer’s Disease Knowledge Portal is a premier repository and workspace for multi-omic data generated through the AMP-AD consortia – a public- private partnership between academic research groups, industry partners, and non-profit partners. The primary goal of the consortia is to generate and test hypotheses to identify new targets for intervention in the treatment of Alzheimer’s disease. Deposited data includes gene expression, genotype, methylation, CHiP-Seq, DNA methylation, miRNA profiles, and clinical data, among others from human participants as well as animal and cell line model systems. Data is publically released on an aggressive schedule, with data releases occurring every quarter, starting in March 2015.

Learn more about the datasets, collaborators or external research projects by visiting the AD Knowledge Portal on Synapse.


AACR GENIE is a pilot project that seeks to identify and validate genomic biomarkers relevant to cancer treatment by linking tumor genomic data from clinical sequencing efforts with longitudinal clinical outcomes. GENIE will serve as a prototype for aggregating and harmonizing next-generation sequencing data from clinical specimens from multiple national and international institutions obtained in routine medical practice. The resulting “clinical cancer genomics meta-database”, which is expected to include ~100,000 tumors within 5 years, will complement existing efforts such as TCGA and ICGC, which have focused on generating more comprehensive genomic datasets on smaller numbers of tumors using optimized samples collected and processed by select institutions under very controlled conditions.

The GENIE platform was designed to integrate and link clinical-grade cancer genomic data with clinical outcomes data for tens of thousands of cancer patients treated at multiple institutions worldwide. Sage serves as the data hosting and integration hub for Project GENIE and maintains databases on Synapse that host the sample and clinical level information and associated genomic data, including somatic variants, copy-number alterations, and fusion data. To harmonize information across eight large academic centers, Sage developed and deployed detailed data dictionaries, formats, and SOPs describing the workflow streams required of each institution as well as data processing pipelines to validate and harmonize the data.


Learn more about Project GENIE:


The MODEL-AD (Model Organism Development and Evaluation for Late-Onset Alzheimer’s Disease) consortia is a group of researchers focused on rigorous generation and characterization of fifty new mouse models of late onset Alzheimer’s disease. Alzheimer’s disease (AD) is a debilitating illness with no known disease modifying therapy.  Furthermore, 99.3% of phase III clinical trials have failed for AD drug discovery.

The goal of the MODEL-AD consortia is to improve target discovery and validation efforts in AD by creating a community resource of mouse models that closely reflect the sporadic late-onset human form of AD. As such, the consortia has focused on human AD genetics and systems biology resources such as Accelerating Medicine Partnership for AD (AMP-AD), AD Sequencing Project (ADSP), and AD Neuroimaging Initiative (ADNI) to prioritize specific variants to introduce into the mice to capture different aspects of the disease.  All data – including ‘omics, imaging, and drug treatment –  generated on the mouse models are actively distributed to the AD research community and public via the AD Knowledge Portal.

CommonMind Consortium

The CommonMind Consortium Knowledge Portal is the main distribution site for data and analysis results generated by CommonMind Consortium (CMC) members. Sage Bionetworks initiated the CMC in 2010 as a Public-Private Pre-Competitive partnership 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.

A central tenet of this project is that biological insights stemming from integrative genomic analysis are most compelling when they leverage the expertise across multiple disciplines and provide a transparent, reproducible description of analytical process. As such, the consortium has committed to making all data, analytical results, and methodological source code available to the public. The goal of this is to provide the opportunity for researchers to assess the quality of the data and results in order to (1) estimate the likelihood of our biological conclusions and (2) determine the most meaningful way of incorporating these findings into their own research.

To date, the CMC has been funded for data generation and novel analytical approaches. Data has been generated across multiple genomics modalities (RNA and DNA sequencing, genotyping, and histone modifications)across a combination of three brain regions collected from more than 1000 brain samples across four brain cohorts.

Clinical and Translational Science Award (CTSA)

Sage Bionetworks, in a broad partnership led by OHSU, has been awarded the new CTSA Program National Center for Data to Health (CD2H). This award coalesces and coordinates informatics activities across the Clinical and Translational Science Award (CTSA) Program, a network of more than 50 medical research institutions, to provide collaborative clinical and translational research infrastructure.

The CTSA will be led by Dr. Melissa Haendel (OHSU), Dr. Kristi Holmes (Northwestern University), Dr. Sean Mooney (University of Washington), Dr. Christopher Chute (Johns Hopkins University School of Medicine), and John Wilbanks (Sage Bionetworks). “The goal is to unlock the amazing wealth of technologies and innovation located within each individual CTSA and to create cohesive communities of practice founded on the fundamental premise that team science, data sharing, and collaborative innovation can advance patient care” described Dr. Melissa Haendel, the center director at Oregon Health & Sciences University.

The newly created center will focus on creating and harnessing an ecosystem for translational scientists to discover and share their software, data, and other research resources within the CTSA Program network. The CD2H also creates a social coding environment for translational science institutions, leveraging the community-driven DREAM challenges as a mechanism to stimulate innovation. Sage Bionetworks will bring community management and social engineering expertise to the program.

Dr. Justin Guinney, Sage Bionetworks Vice President of Computational Oncology and co-director of DREAM Challenges, shared, “The CTSA network is a vibrant community which can greatly benefit from a set of integrated platforms and best-practices across institutions to facilitate data sharing and method benchmarking. Our vision is that a data-driven and model-based ecosystem will have a lasting impact on patient outcomes.”

CTSA partners include Oregon Health & Science University, Northwestern University, University of Washington, Johns Hopkins University School of Medicine, and Sage Bionetworks, together with The Scripps Research Institute, Washington University in St. Louis, the University of Iowa, and The Jackson Laboratory. The program is supported by the National Center for Advancing Translational Sciences (NCATS) at the National Institutes of Health (Grant U24TR002306).

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Sage Bionetworks and the Institute for Systems Biology will partner to build the Cancer Research Institute iAtlas, an online database and web resource designed to help basic and clinical researchers navigate immunological data across multiple tumor types. The CRI iAtlas database is the first comprehensive effort in immuno-oncology to address the recent National Cancer Moonshot Blue Ribbon Panel recommendation to establish a pan-cancer immune atlas that would help catalyze new research in cancer immunotherapy.

The CRI iAtlas resource will be built on Sage’s Synapse platform for data management and sharing, while also leveraging the capabilities of ISB’s Cancer Genomics Cloud to enable immuno-oncology researchers to perform flexible data query and visualization. Its structured data repository will integrate multiple characterizations of the immune response in tumors made by a working group formed by The Cancer Genome Atlas, led by the U.S. National Institutes of Health. Data generated by the working group, which includes molecular profiling of over 10,000 tumors across 33 tumor types as well as a series of results on immune-tumor interaction and response mechanisms, will provide rich characterizations of the relationship between tumors and the immune microenvironment and its impact on patient outcomes.

“Insights derived from these data will be critical to improving the effectiveness of current cancer immunotherapy treatments and developing new immune-based treatment strategies,” said Justin Guinney, Ph.D., principal investigator, director of computational oncology and bioinformatics at Sage Bionetworks.

Read full press release.

Colorectal Cancer Subtyping Consortium (CRCSC)

The Colorectal Cancer Subtyping Consortium (CRCSC) is an international consortium of colorectal cancer (CRC) researchers, data scientists and clinicians from 15 academic, pharmaceutical, and non-profit partners which represents the first effort to generate consensus cancer subtypes, taking a major step toward precision medicine in CRC.

By comparing multiple classifiers, the CRCSC was able to identify four biologically distinct subtypes of CRC with unique clinical and molecular markers, a remarkable overlap considering different methodologies and datasets used by individual groups.

CRCSC on Synapse