MODEL-AD

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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iAtlas

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.

Tumor neoantigEn SeLection Alliance (TESLA)

The Parker Institute for Cancer Immunotherapy, started by Napster founder Sean Parker, and the Cancer Research Institute have joined together to launch a global research alliance with 30 public and private groups to advance the development of more effective personalized cancer treatments.

Seattle-based bioinformatics nonprofit Sage Bionetworks, is among the participants and will be playing a key role.

The research will focus on tumor neoantigens. These unique cancer cell markers are specific to each patient and present only on cancer cells, making them excellent potential targets for immunotherapy treatments such as cancer vaccines that can energize the body’s own defense system to fight tumors.

For this project, participating scientists will use algorithms to mathematically predict which neoantigens coded in a patient’s genes can both be recognized by the immune system and stimulate it to destroy tumor cells. The results of this research could pave the way to developing longer-lasting cancer vaccines tailored to a patient’s genetic makeup, with fewer side effects.

Parker Institute for Cancer Immunotherapy and Cancer Research Institute Launch Collaboration on Cancer Neoantigens

Researchers at 30 organizations to test algorithms that predict tumor markers from DNA in hunt for new personalized cancer treatments

SAN FRANCISCO – Dec. 1, 2016 – The Parker Institute for Cancer Immunotherapy and the Cancer Research Institute (CRI) today announced a major collaboration focused on neoantigens. The search for these unique cancer markers has become a robust area of research as scientists believe they may hold the key to developing a new generation of personalized, targeted cancer immunotherapies.

This new collaboration, the Tumor neoantigEn SeLection Alliance (TESLA), includes 30 of the world’s leading cancer neoantigen research groups from both academia and industry. Because these tumor markers are both specific to each individual and unlikely to be present on normal healthy cells, neoantigens represent an optimal target for the immune system and make possible a new class of highly personalized vaccines with the potential for significant efficacy with reduced side effects.

“Bringing together the world’s best neoantigen research organizations to accelerate the discovery of personalized cancer immunotherapies is exactly the type of bold research collaboration that I envisioned when launching the Parker Institute,” said Sean Parker, Silicon Valley entrepreneur and founder of the Parker Institute for Cancer Immunotherapy. “This alliance will not only leverage the immense talents of each of the researchers but will also harness the power of bioinformatics, which I believe will be critical to driving breakthroughs.”

The goal of the initiative is to help participating groups test and continually improve the mathematical algorithms they use to analyze tumor DNA and RNA sequences in order to predict the neoantigens that are likely to be present on each patient’s cancer and most visible to the immune system. In support of this, Parker Institute and CRI have partnered with renowned open science nonprofit, Sage Bionetworks, to manage the bioinformatics and data analysis.

Initially, the project is expected to focus on cancers such as advanced melanoma, colorectal cancer and non-small cell lung cancer that tend to have larger numbers of mutations and thus more neoantigens. Over time, the initiative will seek to broaden the relevance of neoantigen vaccines to a wide range of cancers.

Participants come from universities, biotech, the pharmaceutical industry and scientific nonprofits. The researchers represent a wide swath of scientific fields, including immunology, data science, genomics, molecular biology, and physics and engineering.

“This project embodies the spirit of collaboration and partnership between academia, industry and nonprofits that the Parker Institute strives to foster,” said Jeffrey Bluestone, Ph.D., president and CEO of the Parker Institute for Cancer Immunotherapy. “It is a great example of how we are breaking down traditional barriers to conduct groundbreaking, multidisciplinary science to get cancer treatments to patients faster.”

“The Cancer Research Institute and the Parker Institute share a belief that the immune system is a platform technology that can be harnessed to turn all cancers into a curable disease,” said Adam Kolom, Parker Institute vice president of business development and strategic partnerships and CRI’s Clinical Accelerator program director. “We believe that by bringing together the top laboratories in the world that are developing neoantigen prediction software, we will be able to unlock the promise of this next generation of personalized cancer immunotherapies sooner.”

This marks the first major collaboration between the San Francisco-based Parker Institute for Cancer Immunotherapy, launched in April 2016, and the Cancer Research Institute, founded in 1953 in New York City.

“We’re proud to join the Parker Institute in this collaboration, which demonstrates the vital role that nonprofits can play in bringing together stakeholders from across sectors to work alongside one another to advance the field of cancer immunotherapy,” said Jill O’Donnell-Tormey, Ph.D., Cancer Research Institute CEO and director of scientific affairs.

Participating researchers said they looked forward to working collaboratively through the alliance to solve one of immunotherapy’s most complex problems.

“This experiment is truly remarkable because of its potential to help us more precisely identify abnormal proteins in an individual’s tumor that can be used as targets for personalized cancer immunotherapy,” said professor Robert D. Schreiber, Ph.D., director of the Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs at Washington University School of Medicine in St. Louis. “We believe that this type of precision medicine, used alone or with other forms of immunotherapy, will significantly improve our capacity to treat cancer patients more effectively and with fewer side effects than current treatments.”

About Neoantigens
Neoantigens are markers present on the surface of cancer cells but absent on normal tissue, making them attractive drug target candidates. They commonly arise from mutations that occur as tumor cells rapidly divide and multiply. The immune system can recognize these markers as “foreign,” and as a result, target the cancer cell for destruction. In order to predict which neoantigens will be present on a patient’s tumor, researchers have developed software programs to analyze tumor DNA and output the unique set of markers that the immune system is most likely to recognize.

What the Alliance Will Do
Participating research groups will receive genetic sequences from both normal and cancerous tissues. Using each laboratory’s own algorithms, each group will output a set of predicted neoantigens that are anticipated to be present on the tumor cells and recognizable by the immune system. The predictions will then be validated through a series of tests to assess which predictions are most likely to be correct and recognizable by T-cells. Through this effort, each participant will be provided with data to inform and to further improve their algorithms and therefore the potential effectiveness of personalized neoantigen vaccines for cancer.

Participating Organizations
Currently, the research institutions taking part include the Broad Institute of MIT and Harvard, Caltech, the Dana-Farber Cancer Institute, the La Jolla Institute for Allergy and Immunology, the Ludwig Institute for Cancer Research, Roswell Park Cancer Institute, The Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai, the University of California, Santa Cruz, The Carole and Ray Neag Comprehensive Cancer Center at UConn Health and Washington University School of Medicine. Internationally, scientists from the Fondazione Network Italiano per la Bioterapia dei Tumori, National Cancer Centre Singapore, the National Center for Tumor Diseases at Heidelberg University Hospital and the Netherlands Cancer Institute have also stepped forward to join the project.

Participants from industry include Advaxis; Agenus; Amgen; BioNTech; Bristol-Myers Squibb; Genentech, a member of the Roche Group; ISA Pharmaceuticals; MedImmune, the global biologics research and development arm of AstraZeneca; Neon Therapeutics and Personalis, Inc.

The six academic research centers that make up the core of the Parker Institute are also expected to participate, including: Memorial Sloan Kettering Cancer Center, Stanford Medicine, the University of California, Los Angeles (UCLA), the University of California, San Francisco, the University of Pennsylvania and The University of Texas MD Anderson Cancer Center. Initial tissue samples are expected to be provided by Memorial Sloan Kettering Cancer Center, National Cancer Centre Singapore, Roswell Park Cancer Institute, UCLA, the University Hospital of Siena in Italy and the John Theurer Cancer Center at Hackensack University Medical Center, a member of Hackensack Meridian Health. As the project progresses, the alliance will add to its growing roster of participants.

About the Parker Institute for Cancer Immunotherapy
The Parker Institute for Cancer Immunotherapy brings together the best scientists, clinicians, and industry partners to build a smarter and more coordinated cancer immunotherapy research effort.

The Parker Institute is an unprecedented collaboration between the country’s leading immunologists and cancer centers: Memorial Sloan Kettering Cancer Center, Stanford Medicine, the University of California, Los Angeles, the University of California, San Francisco, the University of Pennsylvania and The University of Texas MD Anderson Cancer Center. The Parker Institute was created through a $250 million grant from The Parker Foundation.

The Parker Institute’s goal is to accelerate the development of breakthrough immune therapies capable of turning cancer into a curable disease by ensuring the coordination and collaboration of the field’s top researchers, and quickly turning their findings into patient treatments. The Parker Institute network brings together six centers, more than 40 industry and nonprofit partners, more than 63 labs and more than 300 of the nation’s top researchers focused on treating the deadliest cancers.

About the Cancer Research Institute
The Cancer Research Institute (CRI), established in 1953, is the world’s leading nonprofit organization dedicated exclusively to transforming cancer patient care by advancing scientific efforts to develop new and effective immune system-based strategies to prevent, diagnose, treat, and eventually cure all cancers. Guided by a world-renowned Scientific Advisory Council that includes three Nobel laureates and 26 members of the National Academy of Sciences, CRI has invested $336 million in support of research conducted by immunologists and tumor immunologists at the world’s leading medical centers and universities, and has contributed to many of the key scientific advances that demonstrate the potential for immunotherapy to change the face of cancer treatment. To learn more, go to cancerresearch.org.

In the News:

Sean Parker’s I/O group teams up with CRI for cancer neoantigens R&D deal – Fierce Biotech

ICGC-TCGA Whole Genome Pan-Cancer Analysis Working Group

In 2013, Sage assisted with the coordination of The Cancer Genome Atlas (TCGA) pan-cancer analysis by hosting and coordinating the outputs of 65 different analytical workflows using the open source software platform developed by Sage, called Synapse, which data scientists can use to carry out, track, and communicate their research in real time. Since then, all TCGA working groups have been using Synapse to coordinate their analysis outputs during the research process and preparation of manuscripts.

In 2015, the International Cancer Genome Consortium  (ICGC) and TCGA partnered for a joint analysis of over 800 terabytes of data from 1,350 cancer whole genomes. The group used infrastructure and techniques developed by Sage Bionetworks to coordinate distribution of data and analytical results of the more than 400 researchers involved in the project.