Press category: Research

Leading Cancer Research Organizations Jointly Unveil Comprehensive Immunotherapy Tool to Analyze Interactions Between Tumors and Immune Microenvironment

Cancer Research Institute iAtlas Poised to Improve Patient Outcomes by Providing Researchers Greater Access to Genomics Data

NEW YORK and SEATTLE – April 5, 2018 – The Cancer Research Institute (CRI), Institute for Systems Biology (ISB) and Sage Bionetworks – three organizations on the forefront of cancer immunotherapy, systems biology and bioinformatics –  today announced the release of the Cancer Research Institute iAtlas, a comprehensive web-based tool that allows oncologists and researchers to study and analyze interactions between tumors and the immune microenvironment.

CRI iAtlas is a bioinformatics tool that harnesses immunogenomic data, which were recently published in the journal Immunity. The data are a result of the PanCancer Atlas initiative, the final phase of The Cancer Genome Atlas (TCGA), which investigates more than 10,000 tumor samples across 33 cancer types.

“The Cancer Research Institute, having funded transformative immuno-oncology research for 65 years, decided to support the establishment of an open access database because of the potential impact this tool could have across the field. We expect that the CRI iAtlas will help to accelerate discovery and improve patient outcomes by providing researchers greater access to genomics data to better understand the immunological characteristics of the tumor microenvironment and its potential impact on patient responses to immunotherapy,” said Jill O’Donnell-Tormey, Ph.D., CEO and director of scientific affairs at CRI. “As the CRI iAtlas evolves, we would like to see it become the central repository for this crucial immunogenomics data.”

“The CRI iAtlas tool is the latest iteration of ISB’s focus on providing data resources and visualizations to the research community,” said Ilya Shmulevich, Ph.D., Professor at ISB and a core member of the TCGA and iAtlas projects. “With iAtlas, results from the new TCGA study can be harnessed to investigate the immune responses shared among different types of tumors and to explore how immune responses relate to genomic and clinical phenotypes.”

The iAtlas platform is a community resource that opens up previously difficult-to-obtain insights to research organizations of all sizes.

“We are grateful to CRI and the hundreds of researchers who have contributed to this important resource,” said Justin Guinney, Ph.D., Vice President of Computational Oncology at Sage Bionetworks. “The CRI iAtlas platform provides an intuitive and powerful set of web tools that facilitate data exploration and access to an extensive set of immune characterized samples from TCGA.”

Media contacts
For CRI: Brian Brewer, bbrewer@cancerresearch.org, 212.688.7515 x242
For ISB: Joe Myxter, joe.myxter@systemsbiology.org, 206.732.2157
For Sage Bionetworks:  Justin Guinney, justin.guinney@sagebase.org, 206.667.2102

About the CRI iAtlas

The Cancer Research Institute (CRI) iAtlas (www.cri-iatlas.org) is an interactive web-based platform and set of analytic tools for studying interactions between tumors and the immune microenvironment. These tools allow researchers to explore associations among a variety of immune characterizations as well as with genomic and clinical phenotypes. The initial version of CRI iAtlas is based on an analysis performed by The Cancer Genome Atlas (TCGA) Research Network on the TCGA data set comprising over 10,000 tumor samples and 33 tumor samples (Thorsson et al. Immunity, 2018). In this analysis, each tumor sample was scored for a variety of readouts for immune response, such as immune cell composition, adaptive cell receptor repertoire, neoantigen load, and expression of genes coding for immunomodulatory proteins. The web tool allows research to explore these data readouts, and the relation between them in TCGA tumor types and in overarching immune subtypes identified in the study. The CRI iAtlas is made possible through a collaboration between the Cancer Research Institute, Sage Bionetworks and the Institute for Systems Biology.

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 $357 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. Learn more at www.cancerresearch.org.

About Sage Bionetworks

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. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at www.sagebase.org.

About the Institute for Systems Biology

The Institute for Systems Biology is a nonprofit biomedical research organization based in Seattle. It was founded in 2000 by systems biologist Leroy Hood, immunologist Alan Aderem, and protein chemist Reudi Aebersold. ISB was established on the belief that the conventional models for exploring and funding breakthrough science have not caught up with the real potential of what is possible today. ISB serves as the ultimate environment where scientific collaboration stretches across disciplines and across academic and industrial organizations, where our researchers have the intellectual freedom to challenge the status quo, and where grand visions for breakthroughs in human health inspire a collective drive to achieve the seemingly impossible. Our core values ensure that we always keep our focus on the big ideas that eventually will have the largest impact on human health. ISB is an affiliate of Providence St. Joseph Health, one of the largest not-for-profit health care systems in the United States.

Sage Bionetworks and Celgene Corporation announce the launch of Journey PRO, a mobile health research study designed to improve the lives of patients living with chronic anemia

Smartphone-based app as a tool to collect and analyze patient-reported data leading to improved therapeutic developments and to provide study information back to the patient participants to use in managing their health.

August 14, 2017 – Seattle, WA – Sage Bionetworks, a non-profit biomedical research accelerator, together with Celgene Corporation (NASDAQ: CELG) today announced the launch of Journey PRO, a mobile health research study designed to improve the understanding of disease burden on people living with chronic anemia due to myelodysplastic syndromes (MDS), myelofibrosis, and beta-thalassemia.

This study uses mobile and wearable technologies to quantify the daily burden of chronic anemia on patients living with these diseases. The study utilizes the Apple ResearchKit framework to collect data from participants using surveys, neurological self-assessments using the BrainBaseline cognitive testing software from Digital Artifacts, health data collected from the iPhone HealthKit, and fitness tracking wearables, among others. By following participants using these quantitative assessments, we aim to develop a tool to evaluate the efficacy of new treatments for reducing the impact of these diseases on patients.

“Understanding the impact of disease on daily living is important to patients as well as researchers,” said Lara Mangravite, President of Sage Bionetworks and PI of the study. “For this reason, Journey PRO will provide direct and immediate information back to research participants to help them manage their health.”  The Journey PRO app was designed with input from members of the chronic anemia community to support patients in the management of their health.  Participants may use the app to track key health data (e.g., transfusions, lab values) and the scheduling of appointment dates. Participants will also be able to visualize their study data and may choose to download the data and share it with their healthcare team. This design was developed in consultation with patient representatives recruited through the MDS Foundation (www.mds-foundation.org), Cooley’s Anemia Foundation (www.thalassemia.org), and the Leukemia and Lymphoma Society (www.lls.org).

Journey PRO is open to participants over the age of 18 living in the United States with an iPhone model 5 or newer with iOS 8 or later. The research term encourages patients with a diagnosis of myelodysplastic syndromes (MDS), myelofibrosis, and beta-thalassemia to participate in this study. Individuals without a diagnosis of chronic anemia can also participate by providing valuable comparison data to further illustrate the difference in quality of life measures between the chronic anemia population and the general population. The Journey PRO app is available immediately for download from the App Store.

About Celgene
Celgene Corporation, headquartered in Summit, New Jersey, is an integrated global biopharmaceutical company engaged primarily in the discovery, development and commercialization of innovative therapies for the treatment of cancer and inflammatory diseases through next-generation solutions in protein homeostasis, immuno-oncology, epigenetics, immunology and neuro-inflammation. For more information, please visit www.celgene.com. Follow Celgene on Social Media: @Celgene, Pinterest, LinkedIn, Facebook and YouTube.

About Sage Bionetworks (www.sagebio2018.wpengine.com)
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. In pursuit of this Mission, Sage Bionetworks is working with others to assemble an information Commons for biomedicine that (1) is supported by an open compute space (Synapse: www.synapse.org), (2) supports open research collaborations and innovative DREAM Challenges, and (3) empowers citizens and patients with the tools to partner with researchers and share their data through Sage’s BRIDGE platform (http://sagebio2018.wpengine.com/bridge/) in order to drive the research studies that matter most to them.

Contact:
Lara Mangravite
lara.mangravite@sagebase.org
206 667-6044

Diane Gary
Diane.gary@sagebase.org
206-667-2102

Sharing Skin-Selfies for Science: melanoma study releases participant generated smartphone data to research community worldwide

Mole photos, measurements, and melanoma risk factor data contributed by over 2,500 participants are made available by Sage Bionetworks and OHSU to accelerate skin cancer research.

February 14, 2017, SEATTLE–Sage Bionetworks and Oregon Health & Science University (OHSU) today publicly released data contributed by 2,798 participants in the Mole Mapper melanoma study. The app-based research study uses Apple’s ResearchKit to enroll participants who use the phone camera to map and measure their moles over time. Abnormal or changing moles can be an indicator of the skin cancer melanoma, so remote monitoring with the possibility of early detection holds great promise for cancer prevention.

Whereas most research data are generated in a clinical or laboratory setting, Mole Mapper is crowd-sourced by individuals contributing data to the study from their own phones. Curated Mole Mapper data, consisting of mole photos and measurements together with melanoma risk factors, have been made available to qualified researchers on Sage Bionetworks’ collaborative science platform Synapse and accompanied by a publication in Nature Scientific Data. This is the second such mobile health study that has been made broadly available to qualified researchers around the world.

“In designing the study, we first wanted to know if research run remotely and entirely through an app could find the same melanoma risks as years of rigorous epidemiology and genetics research,” said lead author Dan Webster, Research Fellow at the National Cancer Institute. “We show, for instance, that Mole Mapper participants with red hair were significantly more likely to be diagnosed with melanoma. This is in alignment with previously published data showing that people with red hair caused by mutations in the MC1R gene have a higher risk for melanoma.”

The study data also touches on a frequently asked question about moles: “Is this normal?” Stanford University researchers recently demonstrated that algorithms can accurately diagnose skin conditions by training on a large database of high-quality medical skin images. The Mole Mapper team aims to create a similarly foundational database from participant-contributed data. While clinical resources will undoubtedly be important in answering this question, most moles that are measured and monitored in a clinical setting are already suspect and may already be abnormal.

“With Mole Mapper, we have a unique ability to collect thousands of measurements from ‘pre-clinical’ moles that people measure themselves at home,” said Webster. “Over time, this can provide a basis for mole size and shape distributions to serve as a new benchmark for future studies.”

The release of the Mole Mapper study data is a part of the larger mobile health ecosystem that Sage Bionetworks is cultivating. Developing open-source modules for integration into mobile applications and enabling the broad sharing of the resulting data are cornerstones of this effort.

“In the promising space of mobile health, too often data is controlled by private interests,” said study coauthor Brian Bot, Principal Scientist, Sage Bionetworks. “Shared data resources such as these will help enable the scientific community to more quickly determine what can and cannot be gleaned from these types of remote measurements.”

Additional information:

Contact: Brian Bot
brian.bot@sagebase.org
206-667-2123

About Sage Bionetworks Sage Bionetworks is a 501(c) (3) 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. It 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. More information is available at http://www.sagebio2018.wpengine.com.

Cancer Research Institute Awards Grant to Develop Powerful Genomic Data Resource for Cancer Immunotherapy Researchers

The Cancer Research Institute (CRI), a nonprofit organization established in 1953 to advance biomedical research with the goal of developing lifesaving immunotherapies for all forms of cancer, announced that is has awarded a technology innovation grant to two nonprofit research institutes, Sage Bionetworks (Sage) and the Institute for Systems Biology (ISB), for the creation of 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.

Read full press release.

The Digital Mammography DREAM Challenge

_pressrelease_DMChallenge$1.2 M Digital Mammography Challenge Aims to Improve the Accuracy of Mammograms

Contest aims to crowd-source machine learning algorithms to help reduce the false positive mammography rate

SEATTLE, WA – September 7, 2016 – A coalition of oncology and technology partners led by Sage Bionetworks and DREAM Challenges today announced the opening of the training phase for the Digital Mammography DREAM Challenge, an open-science data competition designed to improve the accuracy of mammography screening. With funding from Laura and John Arnold foundation (LJAF), the Challenge will award up to $1.2 million to data scientists, researchers, and coding experts who develop predictive algorithms that achieve milestone goals related to reducing the recall rate of mammography screening. Interested participants can sign up at https://www.synapse.org/Digital_Mammography_DREAM_Challenge.

The coalition supporting the Challenge as organizers, sponsors, partners and advisors from the health, tech, regulatory and for-profit competition sectors includes: Amazon Web Services (AWS), FDA, Group Health Cooperative, IBM, Icahn School of Medicine at Mount Sinai, Innocentive, NCI, Radish Medical, and Seattle Cancer Care Alliance.

Each year, more than 40 million women in the United States undergo routine mammogram testing to screen for breast cancer. Mammograms are widely considered to be the most accessible and cost-effective breast cancer screening method. However, the United States Preventive Services Task Force and the American Cancer Society recently issued changes to recommendations regarding start age and frequency of screening. These changes are due, in part, to the large number of false-positive mammograms. One in 10 women undergoing screening mammography are recalled for diagnostic workup, of which fewer than 5 percent will eventually be found to have cancer. Recalled patients often experience stress and additional medical costs, and some require interventions including unnecessary biopsies.

The Digital Mammography DREAM Challenge, running from June 2016 through mid-2017, will seek to attract data experts from both inside and outside the medical field to develop predictive algorithms that will reduce false-positive mammograms while maintaining or improving cancer detection. Participants will be asked to create algorithms that will help doctors determine whether a patient’s mammogram has a high or low likelihood of harboring a breast cancer, and whether or not a patient should undergo additional testing. New algorithms may allow doctors to customize screening regimens for patients and identify women who would benefit from more or less frequent screening.

“Our goal is for the Challenge to demonstrate that we can extract more information from mammograms than what meets the eye. Now that we are in an age where machines can train and learn how to recognize images, there is the possibility that machines can learn to recognize cancer-specific pixelated patterns in a digital mammogram that humans cannot detect. If highly accurate algorithms can help provide women with more clinically relevant and accurate information, then we can dramatically change the field of breast cancer screening,” Dr. Christoph Lee of the Seattle Cancer Care Alliance and clinical advisor to the challenge, explained.

To create the algorithms, participants will use anonymous patient data including nearly 650,000 digitized mammograms provided by the Group Health Cooperative through the NCI-funded Breast Cancer Surveillance Consortium and by the Icahn School of Medicine at Mount Sinai. Solvers’ algorithms will be evaluated against corresponding data on known patient outcomes, and scores will be assigned based on measures of accuracy. Algorithms that identify the fewest false positives while maintaining high rates of cancer detection will receive the highest ranking on the publicly accessible Challenge leaderboard. These medical images will be securely stored in the Amazon and IBM clouds.

“This Challenge holds great promise to improve breast cancer screening,” Group Health Cooperative Senior Investigator Dr. Diana Buist said. “It is only possible through the long-term investment the National Cancer Institute has made in the Breast Cancer Surveillance Consortium, which provides real clinical data harmonized with gold standard cancer ascertainment.”

Challenge organizers are working to maximize the level of solver participation through a targeted marketing campaign and by directly engaging the combined solver communities of DREAM and Innocentive that together include more than 370,000 registered individuals from over 200 countries.

The Challenge is also part of the Coding4Cancer initiative that was featured at Vice President Biden’s June 2016 National Cancer Moonshot Summit. Coding4Cancer seeks to drive improvements in cancer detection methods through the development of better algorithms for imaging tools. Coding4Cancer will hold a second Challenge in 2017 to improve lung cancer screening techniques.

“The Digital Mammography DREAM Challenge is the start of a larger movement focused on using prizes and Challenges to improve early cancer diagnosis,” LJAF Vice President of Science and Technology Michael Stebbins explained. “We are eager to hear more exciting ideas that will help to improve the use of medical imaging techniques to support early diagnosis.”

Due to the massive volume of data (more than 10 terabytes) and sensitivity of the Challenge’s digitized mammograms, solvers will not have direct access to the data. Rather than the usual approach of bringing the data to the algorithm, in this Challenge, organizers will bring solvers’ algorithms to the data for training and scoring. Generous sponsorships from both AWS and IBM are providing cloud computing for data hosting as well as the computational firepower needed to support solvers’ deep learning approaches for model training.

DREAM founder and IBM Research Director Dr. Gustavo Stolovitzky remarked, “We at DREAM are thrilled to be running this massive machine learning exercise on mammography data. And with Sage Bionetworks’ ability to host all the solvers’ re-runnable submissions and open source code after the Challenge, we are also creating a large resource of reproducible methods, all in a consistent, portable framework that can be run on any data set and developed further by any end-users to continue to advance the emerging opportunity to apply computer vision to medical imaging.”

Learn more and sign up at https://www.synapse.org/Digital_Mammography_DREAM_Challenge.

About Sage Bionetworks (www.sagebio2018.wpengine.com)

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. In pursuit of this Mission, Sage Bionetworks is working with others to assemble an information Commons for biomedicine that (1) is supported by an open compute space (Synapse: www.synapse.org), (2) supports open research collaborations and innovative DREAM Challenges, and (3) empowers citizens and patients with the tools to partner with researchers and share their data through Sage’s BRIDGE platform (http://sagebio2018.wpengine.com/bridge/) in order to drive the research studies that matter most to them.

About DREAM Challenges (www.dreamchallenges.org)

The Dialogue on Reverse Engineering Assessment and Methods (DREAM) Challenges pose fundamental questions about systems biology and translational medicine. A. Califano (Columbia University) and Gustavo Stolovitzky (IBM Research and the Icahn School of Medicine at Mount Sinai) founded the group in 2006. The DREAM Challenges, designed and run by a community of researchers from a variety of organizations, invite participants to propose solutions while fostering collaboration and building communities in the process. Expertise and institutional support are provided by Sage Bionetworks, along with the infrastructure to host challenges via their Synapse platform.

About Group Health Research Institute (www.grouphealthresearch.org)

Group Health Research Institute does practical research that helps people like you and your family stay healthy. The Institute is the research arm of Seattle-based Group Health Cooperative, which offers a unique health care system, care delivery, and health coverage, to achieve one goal—affordable, quality health care for all. Group Health’s innovative practices at 25 medical centers and within major Washington hospitals have earned national recognition for medical quality, disease prevention, and evidence-based treatments. These priorities have remained the same since it began serving patients in 1947. The Institute has conducted nonproprietary public-interest research on preventing, diagnosing, and treating major health problems since 1983. Government and private research grants provide its main funding. Follow Group Health research on Twitter, Facebook, Pinterest, LinkedIn, or YouTube. For more information about Group Health, visit www.ghc.org.

About IBM Research
For more than seven decades, IBM Research has defined the future of information technology with more than 3,000 researchers in 12 labs located across six continents. Scientists from IBM Research have produced six Nobel Laureates, 10 U.S. National Medals of Technology, five U.S. National Medals of Science, six Turing Awards, 19 inductees in the National Academy of Sciences and 20 inductees into the U.S. National Inventors Hall of Fame. For more information about IBM Research, visit www.ibm.com/research.

Contact: Sage Bionetworks

Thea Norman, (O) 206-667-3192
(M) 858-997-8598
thea.norman@sagebase.org

Sage Bionetworks Advocates for Open Systems in Health Research

Nature Comment: Stop the privatization of health data

SEATTLE WA (July 20, 2016)

Sage Bionetworks, a nonprofit biomedical research organization, continues its work to redefine the way in which health data is gathered, shared and used through the use of open systems, incentives and norms. In a Nature commentary published today, a set of governing principles for digital health data analysis that are designed to maximize the contribution of large-scale digital data to advancing medical care are described.  This commentary was co-authored by John Wilbanks, Chief Commons Officer at Sage Bionetworks and Eric Topol, MD, Director of the Scripps Translational Science Institute, and Chief Academic Officer of Scripps Health.   The two work together on the NIH-funded Precision Medicine Initiative that was announced earlier this month.

“Emerging technologies for sensor-based monitoring of health, including wearable trackers and smartphone apps, provide an unprecedented resource for the collection of longitudinal data from individuals,” said Lara Mangravite, PhD, President of Sage Bionetworks. “These data may enable the tailoring of disease modulators to maximize benefit on an individual basis.” The opportunities arising from the availability of large-scale digital health data have caught the attention of many technology companies including those with extensive expertise in big data management and analysis across other domains. However, these companies tend to operate in closed manners that provide little transparency into methods and little opportunity to test reliability of outcomes.  “Closed systems disable the checks and balances necessary to ensure that observations are accurate and reliable,“ said Dr. Mangravite. “This is essential when building algorithms designed to influence decisions about health.”

Harnessing these data will require large-scale efforts for data management and interoperability  – a problem that has been solved across many in other fields but remains an issue within the health space. “Many data providers offer a mechanism to return data to consumers, but not in a way that they can easily combine it with data collected across providers or shared with others,” said Mr. Wilbanks. “The digital health revolution only works if we place the patient in control of how and where their data is shared.”  Sage Bionetworks has conducted a series of clinical research studies in which more than 75% of those enrolling choose to share their data broadly, in contrast to “closed loop” systems where the data disappear into a silo for private analysis. “Over the long term, open systems are necessary to maximize the benefit derived from health data,” said Dr. Mangravite. “They promote multiple avenues of scientific progress in parallel and force a degree of scientific evaluation that can not be otherwise performed.”

A case study in Open Systems: mPower

In March 2015, Sage Bionetworks launched mPower, a smartphone application-based study to pilot the feasibility of remotely collecting frequent measurements of symptom severity and treatment sensitivity in Parkinson’s disease.  The mPower app collects data on capacities affected by Parkinson’s disease, including dexterity, balance and gait, memory, and certain vocal characteristics, through tasks that make use of iPhone sensors.  mPower launched through Apple’s ResearchKit, which helps doctors and scientists quickly gather data for medical research on an ongoing basis using iPhone apps. Unlike traditional studies, mPower participants are able to choose who to share their data with. Sharing options include only those researchers associated with mPower, or qualified researchers worldwide. So far, over 75 percent of the more than 12,000 mPower participants chose to share their data broadly with researchers.

In February 2016, Sage Bionetworks released the first six months of data donated by those mPower participants that chose to share broadly. Researchers can become qualified and access the Parkinson’s database via Synapse, a data and analysis sharing platform. From a preliminary analysis of the data, Sage has found enormous variation of symptoms within individuals, which could help researchers better pinpoint windows of intervention. Sage has also noted distinct patterns between medication intake and symptoms, insights that could eventually inform care and treatment regimes. By opening up the data and making it available to all researchers, Sage hopes to accelerate new insights that can be implemented in the clinic and lead to improvements in the lives of people with Parkinson’s disease – insights that can only be realized with a large, open community of data scientists analyzing and re-analyzing the data.

About Sage Bionetworks

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. It 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. More information is available at http://www.sagebio2018.wpengine.com.

About mPower

mPower (Mobile Parkinson’s Observatory for Worldwide, Evidence-based Research) is an iPhone app-based study notable as one of the first observational assessments of human health to rapidly achieve scale as a result of its design and execution purely through a smartphone interface. Learn more by visiting the mPower Website or download the mPower app on iTunes.

For more information on the Precision Medicine Initiative (PMI), see https://www.whitehouse.gov/precision-medicine.

Contact: Diane Gary
Diane.gary@sagebase.org
206-667-2102

TSRI Awarded $20 Million for U.S. Precision Medicine Initiative Cohort Program

Press Release issued by THE SCRIPPS RESEARCH INSTITUTE (TSRI), LA JOLLA, CA – July 6, 2016 –

STSI to Spearhead Participant Technologies Center that Leverages Smart Phone Technology

LA JOLLA, CA – July 6, 2016 – As part of the most ambitious medical research program in the history of American medicine, The Scripps Research Institute (TSRI) has received an initial award of $20 million for its role in a national Precision Medicine Initiative, the National Institutes of Health (NIH) announced today.

“We are thrilled to have the opportunity to help lead this far-reaching, transformative program of one million or more U.S. participants with long-term follow up,” said the new grant’s principal investigator Eric Topol, MD, who is director of the Scripps Translational Science Institute (STSI), professor of genomics at TSRI and chief academic officer at Scripps Health. “Our focus at STSI for the decade of its existence has been to advance individualized medicine. Using genomics, mobile apps and biosensors and providing data back to each participant, this study will set the foundation for new medical knowledge and ways of engaging people in research as citizen-scientists.”

“This grant—which will total almost $120 million over five years—is one of the largest federal grants ever awarded to TSRI,” said TSRI CEO Peter Schultz, PhD, “and it represents the expanding leadership role that Eric and TSRI will play in this new era of biomedical research.”

The five-year award is part of the Cohort Program of President Obama’s Precision Medicine Initiative (PMI); the PMI Cohort Program is a landmark longitudinal research effort that aims to engage one million or more U.S. participants to improve the ability to prevent and treat disease based on individual differences in lifestyle, environment and genetics.

“STSI already has played a pivotal role in a digital medicine revolution that is radically transforming the way we think about and provide health care,” said Chris Van Gorder, president and CEO of Scripps Health, which operates STSI in partnership with TSRI. “This grant ensures the continuation of that work for years to come on a scale that will benefit the entire nation.”

The new grant will support a Participant Technologies Center through STSI that will play a key role in enrolling participants in the study, as well as providing mobile applications. In parallel, the center will develop platforms to deliver these same functions to those without smartphones and work with various technology organizations to increase smartphone accessibility.

STSI has partnered with the NIH-funded Vibrent Health of Fairfax, Virginia, which will provide the technology platform to enroll and engage participants through mobile apps, web app, interactive voice response, feature phones and wearable sensors; Vibrent Health will develop, test, maintain and upgrade the technology platform to enroll, consent, collect data from, communicate with and retain participants throughout the grant period.

In addition, Seattle-based Sage Bionetworks, an integral partner in the design, development and data hosting for many of mobile-app-based research studies on Apple’s open source ResearchKit platform, will be responsible for developing symptom measurements from phone, wearable and other sensors, as well as community outreach and participant engagement efforts with the Participant Technologies Center.

The initiative also includes an extensive network of high-profile partners including Walgreens and PatientsLikeMe. Working collaboratively with other entities, the Scripps Participant Technologies Center will be responsible for enrollment of at least 350,000 participant-volunteers.

“These partners provide unparalleled outreach and engagement, along with data privacy and security capabilities,” Topol said.

The team aims to begin initial enrollment into the study this year, with the aim of meeting its enrollment goal by 2020.

Participants will be invited to answer questions about their health history and status, share their genomic and other biological information through simple blood and urine tests and grant access to their clinical data from electronic health records. In addition, mobile health devices and apps will provide lifestyle data and environmental exposures in real time. All of this will be accomplished with essential privacy and security safeguards. As partners in the research, participants will have ongoing input into study design and implementation, as well as access to a wide range of their individual and aggregated study results.

“This range of information at the scale of 1 million people from all walks of life will be an unprecedented resource for researchers working to understand all of the factors that influence health and disease,” said NIH Director Francis S. Collins, M.D., Ph.D. “Over time, data provided by participants will help us answer important health questions, such as why some people with elevated genetic and environmental risk factors for disease still manage to maintain good health, and how people suffering from a chronic illness can maintain the highest possible quality of life. The more we understand about individual differences, the better able we will be to effectively prevent and treat illness.”

The knowledge gained from the PMI Cohort Program will extend successes of precision medicine in some cancers to many other diseases. Importantly, the program will focus not just on disease, but also on ways to increase an individual’s chances of remaining healthy throughout life.

For more information on the Precision Medicine Initiative (PMI), see https://www.whitehouse.gov/precision-medicine. For more information on the PMI Cohort Program, see https://www.nih.gov/precision-medicine-initiative-cohort-program. For more information about NIH and its programs, visit www.nih.gov.

About The Scripps Research Institute

The Scripps Research Institute (TSRI) is one of the world’s largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs more than 2,500 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including two Nobel laureates and 20 members of the National Academy of Science, Engineering or Medicine—work toward their next discoveries. The institute’s graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. For more information, see www.scripps.edu.

About Scripps Health

Founded in 1924 by philanthropist Ellen Browning Scripps, Scripps Health is a nonprofit integrated health system based in San Diego, Calif. Scripps Health treats more than 600,000 patients annually through the dedication of 3,000 affiliated physicians and more than 15,000 employees among its five acute-care hospital campuses, hospice and home health care services, 28 outpatient centers and clinics, and hundreds of physician offices throughout the region.

Recognized as a leader in prevention, diagnosis and treatment, Scripps Health is also at the forefront of clinical research, genomic medicine and wireless health care.  With three highly respected graduate medical education programs, Scripps Health is a longstanding member of the Association of American Medical Colleges. Scripps Health has been ranked four times as one of the nation’s best health care systems by Truven Health Analytics. Its hospitals are consistently ranked by U.S. News & World Report among the nation’s best and Scripps Health is regularly recognized by Fortune, Working Mother magazine and AARP as one of the best places in the nation to work. More information can be found at www.scripps.org.

About Scripps Translational Science Institute

The Scripps Translational Science Institute aims to replace traditional one-size-fits-all medicine with individualized health care by leveraging the power of genomic medicine, wireless health sensors and mobile phone applications, and other digital medicine technologies. In a unique collaboration, STSI merges the considerable biomedical science expertise of The Scripps Research Institute with Scripps Health’s exceptional patient care and clinical research capabilities. STSI is supported in part by the National Institutes of Health Clinical and Translational Science Award. For more information, visit www.stsiweb.org.

Researchers from Mount Sinai and Sage Bionetworks Report Analysis of Nearly 600,000 Genomes for Resilience Project

Mount Sinai Press Office
(212) 241‐9200
NewsMedia@mssm.edu

Custom-built targeted sequencing panel proves essential in hunt for people naturally resistant to severe disease

NEW YORK, NY – April 11, 2016 /Press Release/ –– As part of a global collaboration, scientists from the Icahn School of Medicine at Mount Sinai and Sage Bionetworks conducted the largest genome study to date and reported the first systematic search across hundreds of Mendelian disorders in hundreds of thousands of individuals apparently not afflicted with any of these disorders to identify those carrying disease protective factors. This retrospective study of more than 589,000 genomes was a first step for the Resilience Project and was performed with researchers from 23andMe, BGI, the Ontario Institute for Cancer Research, and other institutions.

The Resilience Project launched in 2014 with a unique vision by Stephen Friend and Eric Schadt that by studying massive numbers of healthy adults, scientists might find rare individuals who are unaffected by genetic variants that should induce disease. Genome analysis of these resilient people could uncover naturally occurring, protective mechanisms that would serve as novel treatments for people affected by these diseases.

“Most genomic studies focus on finding the cause of a disease, but we see tremendous opportunity in figuring out what keeps people healthy,” said Eric Schadt, PhD, the Jean C. and James W. Crystal Professor of Genomics at the Icahn School of Medicine at Mount Sinai, and Founding Director of the Icahn Institute for Genomics and Multiscale Biology. “Millions of years of evolution have produced far more protective mechanisms than we currently understand. Characterizing the intricacies of our genomes will ultimately reveal elements that could promote health in ways we haven’t even imagined.”

In this study, researchers analyzed DNA from 12 previously collected data sets, using a newly developed targeted sequencing panel to screen 874 genes for 584 distinct genetic diseases. The diseases, which were mostly metabolic conditions, neurological diseases, or developmental disorders, present in childhood with severe symptoms. All genomes analyzed were from adults who had never been diagnosed with any of these diseases. A sophisticated, in-depth analysis process identified 13 healthy people with genetic variants associated with eight diseases.

“This study demonstrates the power of using big data to ask new biological questions,” said Anne Wojcicki, co-founder and CEO of 23andMe, which participated in the project. “More than 400,000 23andMe customers contributed to this effort, showing that engaged consumers can make a real impact on scientific research.”

In narrowing the pool of potentially resilient people from an original list of nearly 16,000 candidates, the researchers encountered two significant challenges. First, more than 75% of the candidates were eliminated due to inaccurate or low-confidence variant calls in the existing data, highlighting the need for better protocols and standards for interpreting genetic data. Second, none of the 13 final candidates could be contacted with follow-up questions due to limitations in the original studies’ informed consent policies. It will be impossible to determine whether these people are truly resistant to disease without additional information.

“There’s an important lesson here for genome scientists around the world: the value of any project becomes exponentially greater when informed consent policies allow other scientists to reach out to the original study participants,” said Stephen Friend, President of Sage Bionetworks, Professor of Genomics at the Icahn School of Medicine, and co-founder of the Resilience Project. “If we could contact these 13 people, we might be even closer to finding natural protections against disease. We anticipate launching a prospective study in the future that will include a more broadly useful consent policy.”

“While most genomics research in medicine has been disease focused, this important work exemplifies the benefit of studying health and resilience—the converse of disease—to understand the mechanism for protection in individuals with pathogenic sequence variants,” said Eric Topol, MD, Director of the Scripps Translational Science Institute, and Chief Academic Officer of Scripps Health, who was not involved in this study but has been a champion of shifting the research focus to include healthy individuals. “This makes for a standout contribution from the Icahn Institute, Sage Bionetworks, and their extensive network of collaborators.”

“This work demonstrates the power of scale in analyzing root genetic causes of human disease, but more importantly human health. Its focus on studying healthy individuals to understand the things that keep them healthy sounds obvious but actually lies at the vanguard of a movement which puts the engaged study participant at the center of scientific research,” said Vik Bajaj, PhD, Chief Scientific Officer of Verily, who was not involved in this study but has advocated for harnessing big data for improved healthcare. “This research also points to the need for more effective standardization in the generation and analysis of genetic data, a field in which the authors are pre-eminent practitioners.”

Paper cited:

Rong Chen, Lisong Shi, et al. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotechnology. DOI:10.1038/NBT.3514

For more information about the Resilience Project, visit www.resilienceproject.com

International Consortium Trailblazing the Genomic Classification of Colorectal Cancer Through Big Data

SEATTLE–(BUSINESS WIRE)–A major collaborative study carried out through an international consortium has, for the very first time, established a consensus classification for colorectal cancer (CRC) based on genomic data. The study partners collected over 4,000 samples from patients and reached a consensus on the genomic subtyping of CRC, which enabled the identification of intrinsic biological underpinnings of each subtype as well as correlative analysis with clinical behavior and prognosis of patients. The research, published inNature Medicine, was coordinated by Justin Guinney from Sage Bionetworks in Seattle, and involved a large international team including co-authors Rodrigo Dienstmann from Vall d’Hebron, Spain; Louis Vermeulen from the Amsterdam Medical Center, the Netherlands; and Sabine Tejpar from UZ Leuven, Belgium.

Combining strengths and overcoming current obstacles in collaboration

Over recent years, the classification of certain cancers has been advanced significantly thanks to the study of the genetic expression of tumors, as is the case with breast cancer. Such important insights have undoubtedly rendered cancer treatment more precise. Despite the many efforts to date, the genomic classification of CRC has struggled to reach the clinic, hampering the stratification of patients for treatment decisions. While individual groups have previously proposed classifications, they differed in both the number of subtypes and the interpretation of results. The heterogeneity of the algorithms and the small number of samples analyzed in these previous studies hindered endorsement from the wider scientific community. This impasse led researchers to join forces as an International Consortium in order to combine numbers of patient samples, and share and exchange knowledge on the biology of CRC, as well as bioinformatics expertise in the analysis of big data. “We hope our work will serve as a model for future research teams using data-driven approaches to define consensus subtypes in cancer,” said Justin Guinney.

Novel classification and correlates in CRC

There are four main groups proposed by consensus: the Consensus Molecular Subtypes (CMS). CMS1 (Microsatellite Instability Immune, 15% of tumors) is the subtype that is characterized by a prominent immunological activation, and represents the group of patients who would most likely benefit from immunotherapies. CMS2 (canonical epithelial, 40% of tumors) is the group with the highest chromosomal instability, which follows the classical carcinogenesis of CRC with activation of the WNT, MYC, and EGFR pathways. CSM3 (metabolic epithelial, 15% of tumors) is characterized by deregulation of the metabolic pathways associated with mutations in the KRAS gene. Finally, CMS4 (mesenchymal, 30% of tumors) shows a very poor prognosis with standard treatment for CRC due to an activation of the TGFB pathways, angiogenesis, and stromal invasion.

From genomics to clinical practice: an Open Access Consortium

The consensus data from this new classification represents an important first step for clinical translation of the findings. For example, knowing which subtype has the worst prognosis or which has the best response to targeted molecular therapies could better guide therapeutic strategies. “The next step will be to study the clinical applicability of this classification. Clinical trials have already been designed and their results will determine which therapies are the most beneficial for each subtype of CRC,” explains Rodrigo Dienstmann. To conduct these analyses and to facilitate clinical implementation, the Consortium has developed open-access software tools that will allow any researcher from around the globe to classify CRC tumors using gene expression data.

Press Release on BusinessWire

CORRECTING and REPLACING The Resilience Project, A New Approach to Understanding the Role of Genes in Health and Disease, Profiled in Science and TED Talk

Correction … by Sage Bionetworks

SEATTLE–(BUSINESS WIRE)–The contact information should read: Sage Bionetworks +1-206-667-2102; Thea Norman, +1-206-667-3192.The corrected release reads:

THE RESILIENCE PROJECT, A NEW APPROACH TO UNDERSTANDING THE ROLE OF GENES IN HEALTH AND DISEASE, PROFILED IN SCIENCE AND TED TALK

The Resilience Project, a collaboration between researchers at Sage Bionetworks and the Icahn School of Medicine at Mount Sinai, is pursuing an innovative and large-scale approach to identifying the role that genes and genetic mutations play in human health and disease. Rather than studying the genes of people who are sick, the Resilience Project has a goal to scan DNA samples from about one million healthy adults with the goal of identifying the small number of people who remain healthy despite carrying mutations that are known to cause rare disease in childhood. This approach provides an opportunity to identify protective genes and environmental factors that may enable the development of new therapeutics or ways to prevent disease. The May 30th issue of Scienceincludes a perspective on the Resilience Project authored by Dr. Stephen Friend of Sage Bionetworks and Dr. Eric Schadt of the Icahn School of Medicine at Mount Sinai, the Project’s lead principal investigators (http://www.sciencemag.org/content/344/6187/970.full). A related TED talk delivered by Dr. Friend is also being made available online today (http://www.ted.com/talks/2004).

“The Resilience Project inverts the traditional approach to gene-based disease research by focusing on those who are healthy rather than those who are sick,” said Dr. Friend. “While rare, our initial research looking retrospectively at approximately 500,000 DNA samples does in fact identify handfuls of individuals who harbor disease-causing mutations yet remain unaffected. We believe that these rare individuals can provide a trove of information about other factors – genetic, environmental, and others – that can be used to improve the prevention, diagnosis, and treatment of disease.”

Not only is the Resilience Project pursuing a novel path to genetic research, it is doing so through an innovative model – crowdsourcing the million DNA samples it seeks to collect from volunteers around the world. Consequently, this project has the potential not only to inform our understanding of human health and disease, but also to establish a new approach to conducting large-scale genetic studies in a highly cost-effective manner.

Additional information about the Resilience Project is available at http://resilienceproject.me/.

Press Release on BusinessWire