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Nonprofit Count Me In to Return Genomic Results to Patients With Rare Cancers


CHICAGO – With a $16 million National Cancer Institute grant in hand, the Broad Institute, the Dana-Farber Cancer Institute, and nonprofit cancer research organization Count Me In are developing workflows to involve patients with rare mutations more directly in studies about their diseases.

The centerpiece of this new initiative is a plan to return patient-specific results of germline and somatic sequencing in two rare cancers, osteosarcoma and leiomyosarcoma.

"This new effort that they're taking is incorporating returning results to patients, which is tackling a huge issue," said retired aerospace engineer Janet Freeman-Daily, a 10-year lung cancer survivor and patient advocate who has previously engaged with Count Me In. "There would be so many more patients willing to participate [in clinical trials] if they knew they could get the results of the genomic testing back."

The goal of Count Me In is essentially to elevate the patient experience in cancer care by including patients as partners in sharing biospecimens, clinical information, and experiences with the research community.

According to Count Me In Director Nikhil Wagle, the grant, from NCI's Cancer Moonshot program, allows the organization to engage adult and pediatric patients with the two forms of cancer, form a data network, collect and sequence biospecimens, and gather clinical and survey data to represent the patient experience as researchers try to understand genomic and phenotypic aspects of the diseases in search of new treatments.

The money also will support Count Me In in two areas it had not previously entered: returning individual genomic results to patients and to set up a study within each project to, in Wagle's words, "understand the act of patient engagement and to optimize how we engage and interact with patients, making sure that we are focused on inclusion" of historically underrepresented groups.

Wagle, a medical oncologist and cancer researcher at both Dana-Farber and the Broad, is principal investigator for the NCI grant.

Though Count Me In dates to 2014, The Broad incorporated it as a nonprofit in 2018 in partnership with the Biden Cancer Initiative, Dana-Farber, California-based social change group the Emerson Collective, and cancer patients. The Biden Cancer Initiative, started by current US President Joe Biden and first lady Jill Biden as an outgrowth of the Cancer Moonshot program, shut down in 2019.

Count Me In allows cancer patients in the US and Canada to share their medical information, personal experiences, and tumor samples for genetic analysis. Patient information is rapidly processed, deidentified, and made available to researchers worldwide through public databases such as the cBioPortal for Cancer Genomics and the NCI's Genomic Data Commons.

Each research project within Count Me In combines patient data with information from genetic analysis of tumor, blood, and saliva samples. These data will then be released at regular intervals to provide a continuously growing resource. 

Count Me In started with metastatic breast cancer and has since initiated projects in several other cancers, including angiosarcoma, metastatic prostate cancer, gastric and esophageal cancer, brain tumors, and now osteosarcoma and leiomyosarcoma. Count Me In Associate Director Corrie Painter, director of the Broad's Angiosarcoma Project, has angiosarcoma.

"Our [eventual] hope is to be able to open things up to anyone who's ever been diagnosed with cancer," Wagle said.

Until now, Count Me In has only shared information in the aggregate since the data was generated in research labs, not CLIA-certified facilities. The NCI funding will help the partners work within CLIA guidelines. Wagle said that the Count Me In partners will be developing a process for choosing "key clinically relevant pieces of information from both the tumor and the germline" to send to patients in a responsible manner.

As it has done with other projects, as a baseline for osteosarcoma and leiomyosarcoma, Count Me In will employ whole-exome sequencing of tumor samples, blood, and cell-free DNA, plus RNA sequencing of tumor samples. Wagle said that he is open to modifying these assays or adding other modalities if the research calls for it.

Germline sequencing will include genetic counseling. The somatic sequencing data will have to include annotations, according to Co-PI Katie Janeway, director of clinical genomics at Dana-Farber/Boston Children's Cancer and Blood Disorders Center.

Count Me In introduced its Osteosarcoma Project in February 2020, but has not previously involved patients as much as the new phase aims to. The disease mostly affects patients between the ages of 10 and 30, according to the Broad, and treatments have not really advanced in four decades.

The leiomyosarcoma program is new. This rare form of cancer often has already metastasized by the time it is diagnosed.

"They are very rare diseases where we have made very insufficient progress in terms of fundamental understanding and most importantly, in terms of new treatment approaches over the past several decades," Janeway said. She said that existing approaches such as immunotherapy and molecularly targeted therapy have not had much of an effect on either leiomyosarcoma or osteosarcoma, because they are so rare and involve complicated changes to the genome.

"We're bringing the power of that patient partnership [in the Count Me In framework] to these diseases, and I think it's going to have a tremendous impact," said Janeway, an expert in children's cancers in general and osteosarcoma in particular, who pushed hard to include children, adolescents, and young adults in the program.

As with other Count Me In research, the work in osteosarcoma and leiomyosarcoma will include outreach to patients and, for minors, their parents or guardians, through social media and advocacy groups in an effort to diversify the research pool across racial, ethnic, geographic, and socioeconomic boundaries.

"I think that this way of direct patient engagement through things like social media and the internet has the possibility of being transformative in terms of research in adolescent and young-adult cancer," Janeway said.

In some ways, the Count Me In plan to share results with patients is like OpenNotes, an initiative to make unedited progress reports and test results available to millions of patients. That program, which has become a nationwide movement, originated as a research study involving primary care physicians at Boston's Beth Israel Deaconess Medical Center, Geisinger Health System in Pennsylvania, and Harborview Medical Center in Seattle. Like the Broad and Dana-Farber, Beth Israel Deaconess is affiliated with Harvard Medical School.

An initial fear with OpenNotes was that patients would not be able to understand what was in their medical records, but that has largely proven unfounded, plus it has prompted many participating doctors to write progress notes in clearer language.

Freeman-Daily said that there are similar concerns in the complicated world of genomics, but that efforts like the Cancer Moonshot Biobank, a longitudinal study launched by the National Cancer Institute last year, are trying to bring patients in anyway by promising to return results to participants.

Freeman-Daily has a rare, nonheritable form of non-small cell lung cancer caused by a ROS1 mutation. She was diagnosed in May 2011, about a year before evidence of the biomarker was first published. Because so little was known about her form of cancer at the time, Freeman-Daily became an advocate for herself and other patients while trying to learn about her condition on social media.

Freeman-Daily said that she had some difficulty getting her medical records and other data through portals at her hospitals and medical practices.

After the biomarker was validated, she was accepted into a clinical trial at the University of Colorado. "I had to be my own advocate. I had to get my own records. I had to arrange for my own genomic testing," Freeman-Daily said. "It's a lot easier now, but we still have a problem."

She has since joined with other patient advocates to start a group called the ROS1ders. Freeman-Daily said that many physicians she encounters had never before seen a patient with her rare form of cancer, so they rely on patients to educate them.

Count Me In is trying to educate medical professionals by regularly and publicly sharing its aggregated data in all of its research projects, including the new NCI-funded ones. "We will definitely try and write academic papers, but the major goal is to try and accelerate research, so while we're working on the data and trying to analyze it and writing academic papers, the data will also be shared so that others can do the same," he said.