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 is part of a consortium of universities and research groups which has received a five-year, $25 million grant from the National Center for Advancing Translational Science

Bringing a Team Science Approach to Research Informatics

November 3, 2017 – Healthcare Informatics recently published a news item about the creation of a new National Center for Data to Health (CD2H). A consortium of universities and research groups has received a five-year, $25 million grant from the National Center for Advancing Translational Science to coalesce and coordinate informatics activities across the Clinical and Translational Science Award (CTSA) Program, a network of more than 50 medical research institutions.

In a follow-up interview, Melissa Haendel, Ph.D., an associate professor in the Department of Medical Informatics and Clinical Epidemiology at Oregon Health & Science University, one of the project leaders, discussed the new center’s approach and goals in more detail.

One area of focus involves data sharing and interoperability, which means advancing work on ontologies, phenotypes and data standards plays a role.

Another goal is to foster a spirit of collaborative innovation and a “social coding” environment for the informatics teams working in the CTSAs. “We want to understand what tools and algorithms are being developed at each site and to see where there are overlaps, gaps and opportunities to benchmark those,” Haendel said. “We also want to see how we can create a coding community across sites.”

The consortium members have always been committed to sharing successes and knowledge transfer across CTSAs, she said, but it has proved challenging. “We are all at different institutions, with different environments, clinical infrastructure and policies. There are a lot of innovations within each CTSA that are not necessarily easy to discover or transfer to another site, so this is an effort to bust those open a bit and learn from each other a little more than we have.”

Haendel noted that CD2H would build upon some of the successes in sharing across CTSAs but in a more innovative and open-ended way.

“I come more from the intersection of basic research informatics and clinical informatics and do a lot of open science,” she said. “We are trying to bring some of those perspectives to the consortium. We can create a more welcoming environment so that it is not just people in the CTSAs that can participate. Anybody in the community, including commercial interests, pharma, other universities and medical centers that might not have a CTSA can participate, too”.

Another area of focus is making it easier to find people with specific expertise and how attribution is given for contributions, she said. “If someone creates an algorithm or shares a data set, we should have mechanisms to track those contributions and value those in the context of the informatics work we do,” Haendel said. “We should also be able to identify experts to help us with specific problems. We have enormous expertise in clinical and basic research informatics across the CTSAs but if you need to do something very specific, we don’t have the easiest way of searching for that person.”

Traditional methods have involved looking for someone who has published a paper, but it takes six to nine months to publish a paper. The content related to informatics is not well represented in the literature anyway, she added. “People are writing code, making clinical instruments and doing analytics, not writing papers. We want to improve the ability to find collaborators and experts for particular areas in computational science.”

The shift to open data, open software, and open resources, is changing the way people work in biomedical informatics, she said. One of Haendel’s colleagues on the project is John Wilbanks, chief commons officer at Sage Bionetworks, who has spent his career advocating for open data innovation systems.

“One of the reasons it takes so long for a drug to get to market, or any finding to lead to a change in clinical care is because of this lengthy cycle we go through of hording our data and hiding our algorithms in order to publish a paper so we can be first and get tenure and promotion. The patients deserve better than that,” Haendel said. “If we can address the attribution and contribution problem, you can be first just by posting it on GitHub or the web.”

As it builds up the team science approach and governance, the CD2H will focus on two thematic areas: rare disease and human health across the lifespan.

CD2H also plans to create an inventory of its training materials to help train the next generation of informaticians to participate in a more open way, she said. Read more.

First Analysis of AACR Project GENIE Data Published, demonstrating potential of data-sharing initiatives to accelerate the pace of progress against cancer

First Analysis of AACR Project GENIE Data Published


June 1, 2017 – The first analysis of nearly 19,000 de-identified genomic records from the American Association for Cancer Research (AACR) international data-sharing initiative known as AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) was published today in Cancer Discovery, a journal of the AACR.

In addition to the genomic analysis, the report includes examples of how the AACR Project GENIE genomic data can be used to facilitate clinical research, including:

  • Analysis showing that more than 30 percent of the samples had mutations that are clinically actionable, meaning that they are suggestive of a specific treatment that is either already approved by the U.S. Food and Drug Administration or is being tested in clinical trials.
  • Analysis showing that the rate at which patients with samples in the AACR Project GENIE registry would match with arms of the NCI-MATCH trial reflected the actual accrual rates for the trial.
  • Details of two additional studies underway that are linking certain genetic characteristics of metastatic breast cancer with clinical and pathological features of the tumors, as well as with patient outcomes.

“There has been a lot of discussion about the potential of data-sharing initiatives to accelerate the pace of progress against cancer,” said Charles L. Sawyers, MD, FAACR, who is the AACR Project GENIE Steering Committee chairperson and an author on the paper. “This paper shows that AACR Project GENIE has made the first steps to delivering on this promise.

“We are particularly excited by the clinical actionability analysis,” continued Sawyers, who is also chairperson of the Human Oncology and Pathogenesis Program at Memorial Sloan Kettering Cancer Center in New York, and a Howard Hughes Medical Institute investigator. “Prior studies looking at how often tumor genome sequencing identifies a clinically actionable mutation have yielded variable results, leading some to question its clinical utility. The huge number of samples in our study and the high rate of clinical actionability give us confidence that tumor genome sequencing can have an important role in clinical care.”

AACR Project GENIE is a multi-phase, multi-year, international data-sharing project that was launched by the AACR in partnership with eight global academic leaders in clinical cancer genomics in November 2015. Just over a year later, in January 2017, the AACR Project GENIE consortium made public nearly 19,000 de-identified genomic records collected from patients who were treated at the eight international institutions participating in the first phase of the project.

“This paper describes the AACR Project GENIE consortium and provides a landscape overview of the first public GENIE data release,” said Ethan Cerami, PhD, director of the Knowledge Systems Group and lead scientist in the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute in Boston, and an author on the paper. “By showing that we can share data across multiple institutions in the United States, Canada, and Europe to obtain results none of the institutions could have obtained alone, we have put AACR Project GENIE at the forefront of data-sharing efforts to accelerate scientific discovery and ultimately improve patient care.”

The paper provides detailed information about the data collected at the different institutions, highlighting that even though the types of sequencing and size of the gene panels used at the individual institutions differ and are evolving over time, the data can be compared across institutions. The high-level analysis of the nearly 19,000 de-identified genomic records made public by the consortium also shows many similarities with the data in The Cancer Genome Atlas (TCGA). The paper also highlights several differences with TCGA data, which the authors speculate are a result of a greater proportion of the AACR Project GENIE records coming from patients with recurrent or relapsing disease.

The eight institutions who participated in AACR Project GENIE phase 1 are: Dana-Farber Cancer Institute, Boston; Gustave Roussy Cancer Campus, Paris-Villejuif, France; The Netherlands Cancer Institute, Amsterdam, on behalf of the Center for Personalized Cancer Treatment, Utrecht, The Netherlands; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore; Memorial Sloan Kettering Cancer Center, New York; Princess Margaret Cancer Centre, Toronto; University of Texas MD Anderson Cancer Center, Houston; and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.

This study was supported by funds from the AACR, Genentech, Boehringer Ingelheim, Pfizer, Eli Lilly, the Howard Hughes Medical Institute, the National Institutes of Health, the National Cancer Institute, the Princess Margaret Cancer Foundation, the Ontario Ministry of Health, Susan G. Komen, the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, the T.J. Martell Foundation, the Commonwealth Foundation, the Cancer Prevention and Research Institute of Texas, the Dutch Ministry of Health, and the Dutch Cancer Society. Sawyers serves on the board of directors of Novartis. Cerami declares no conflicts of interest.