In May 2018, Providence Cancer Institute of Oregon and Swedish Cancer Institute were invited to join an international data-sharing consortium of leading cancer centers working on a groundbreaking registry of publicly accessible genomic data.
The registry, known as the American Association for Cancer Research (AACR) Genomics Evidence Neoplasia Information Exchange, or Project GENIE, is designed to boost oncology research by making high quality, de-identified (anonymous) genomic sequencing data and clinical outcomes from cancer patients accessible to the global cancer research community.
Initially, the Project GENIE consortium consisted of eight cancer centers in the U.S., Canada and Europe, then in 2017, the group launched an open call to institutes worldwide. By inviting more participants, the consortium anticipated the project would greatly accelerate, thereby benefiting more patients sooner. Today, there are 18 members of the consortium, and more cancer centers are expected to join this year.
Providing high-quality data, together
Providence Cancer Institute and Swedish Cancer Institute work collaboratively within the consortium to provide data to the GENIE registry. The Providence team is led by Walter J. Urba, M.D., Ph.D., chief medical officer, Providence Cancer Institute. Dr. Urba is principal investigator and a member of the Project GENIE executive and screening committees. Philip J. Gold, M.D., medical oncologist, director of clinical research and the program leader for the Gastrointestinal Oncology Program at Swedish Cancer Institute, leads the Swedish GENIE team.
Brady Bernard, Ph.D., director of bioinformatics at Providence Cancer Institute, and assistant member of the Computational Immuno-oncology Laboratory at Earle A. Chiles Research Institute, a division of Providence Cancer Institute, is an instrumental member of the team and served as senior author, with other contributing members of the consortium, on the article, AACR Project GENIE: 100,000 Cases and Beyond, published in Cancer Discovery in 2022. Providence Molecular Genomics Laboratory’s Carlo Bifulco, M.D., medical director, and Brian Piening, Ph.D., technical director, also play key roles on the GENIE team.
More data accelerates discovery
Over the past decade, advances in genomic sequencing have contributed to more data about cancer cells and mutations that drive cancers. But researchers need large populations of patients to draw conclusions about the role mutations play in the development of cancers and how they respond to treatment.
Project GENIE can help by providing greater breadth and depth of cancer types and driver mutations from a large population of patients. Currently, the repository contains genomic data from more than 148,000 people from six countries and more than 167,000 tumors. Non-small cell lung cancer, breast, colorectal and pancreatic cancers, glioma and melanoma make up the top 50% of all cancer types in the repository.
“This large sample of cancer types is a powerful tool in improving clinical trial matching and targeted therapies for patients with cancer,” said Dr. Piening. For example, in the past people with cancer were matched to clinical trials and treatments based on their type of cancer. Taking a more targeted approach – also referred to as precision medicine – recommends treatment or a clinical trial to patients based on specific genetic changes to their tumor, not only their type of cancer.
However, resistance to targeted therapies can be an obstacle in treating all types of cancer. The GENIE data set, which has samples from patients with late-stage, heavily treated cancer, can serve as an important resource to examine mechanisms of resistance to targeted therapies.
Providence Molecular Genomics Laboratory
Creating high quality data for GENIE requires not only the expertise of the bioinformatics team, but also the Molecular Genomics Laboratory, the largest molecular genomics sequencing facility on the West Coast. The lab uses next generation sequencing (NGS) technology to simultaneously test many genomic biomarkers from small tumor tissue samples in a matter of days.
“By sequencing the tumor DNA and RNA, scientists can map out genetic mutations that are caused by environmental factors, family history or both,” said Dr. Bifulco.
The information provides a molecular profile to help experts recommend a targeted therapy or immunotherapy, either as a standard of care treatment or clinical trial, for cancer patients.
“When we analyze our sequencing data in the context of sequencing data from the other cancer centers participating in GENIE, we see that our Molecular Genomics Lab is doing a great job. It’s important to hold ourselves to a high standard, which we’ve done,” said Dr. Bernard.
How GENIE might adapt and grow
One of GENIE’s goals was to prove that with a limited budget they could establish a workflow and an ecosystem for clinical genomic data sharing. So far, GENIE has been a success.
But that is only the tip of the iceberg. As Project GENIE expands to include new data types such as cell-free DNA sequencing, pathology and imaging, the population pool will expand as well to reflect the diverse global population.
In the Cancer Discovery article, the authors wrote that “underrepresentation of racial and ethnic groups more likely represents a paucity of such patients receiving care at tertiary referral centers as opposed to implicit bias.”
The consortium recognizes the need to improve the data pool and is expanding the next open call to include institutions and cancer centers in underrepresented communities and geographic areas.
The participation of Providence and Swedish in the GENIE consortium is important to the growth and recognition of our research arms and our contributions to pioneering cancer treatments and care. We are in the unique position to quickly translate this work from the lab to the clinic, greatly impacting Providence and Swedish patients throughout the Pacific Northwest.
“It’s great to see our Providence and Swedish cancer programs come together on Project GENIE. This effort is of local, regional and national importance,” said Dr. Urba.
Working together to provide precision medicine for our patients
In 2021, the virtual Providence Molecular Tumor Board (MTB) was launched to help match patients of Providence Cancer Institute, Swedish and other sites across the Providence health care system who had genomic testing via the Molecular Genomics Laboratory (or other commercial lab) to precision cancer therapies. Twice a month, experts in oncology, anatomic and molecular pathology, genomics, cancer genetics, pharmacology and clinical research come together in a virtual setting to discuss clinical questions and make therapeutic recommendations for variants – changes in the genetic code – identified in patients’ tumors, as well as clinical trial considerations. A patented cloud-based platform collects and organizes patient data for cases being discussed by experts. Within the first six months of forming the MTB, 30 patient cases were reviewed with 62% recommended for targeted therapy or immunotherapy.