Sara Balch, BS, Project Manager, Count Me In and the Broad Institute of MIT and Harvard
Abstract: Count Me In is a research initiative whose aim is to engage patients living with all major cancer types, as well as those with rare cancers. Along with this goal, Count Me In hopes to bring about a cultural shift that empowers patients, researchers, and clinicians to work in partnership and accelerate medical progress by allowing researchers to work directly with patients and advocacy groups along with software engineers and computational scientists, to collect, analyze, and share de-identified data. The combined power of thousands of individual experiences will assist researchers in understanding, why patients respond differently to treatments, uncover new genetic targets for therapies, and help propel groundbreaking discoveries that transform cancer care.
The Scientific Need in Cancer Research
Count Me In’s ultimate goal is to understand what drives cancer in order to identify the optimal treatments as well as anticipate and preempt resistance before it arises in every patient. To accomplish this, Count Me In generates and shares de-identified genomic data annotated with comprehensive clinical and patient-reported data with research databases. These data releases are pre-publication and occur as the data is generated. Any research can use the data generated by Count Me In to accelerate discoveries. The team at Count Me In includes computational scientists, clinical research coordinators, oncologists, and molecular and cellular biologists.
Count Me In Direct-to-Patient Research
Patients have the power to advance cancer research in a way that no one else can. Each patient’s clinical history and tumor samples provide a unique viewpoint into how cancers differ between people. Currently, most patients’ experiences are not included in research because 85% of cancer patients are being treated in community settings where genomic research is not being done. Therefore, Count Me In’s approach is to engage directly with patients as partners in order to provide all patients, independent of where they live or where they are being treated, with the ability to participate in research.
Count Me In wants to answer research questions that could not be answered before with a handful of patients at one cancer center. Researchers and other staff want to engage more than 100,000 cancer patients and want to develop detailed molecular and genomic characterizations of thousands of tumor and germline samples. By pairing this with clinical data, they will be able to start to answer major research questions in cancer.
Count Me In has projects in specific types of cancer and hopes to develop projects in many more types of major and rare cancers. The first project Count Me In launched was the Metastatic Breast Cancer Project in 2015. The Count Me In team worked with metastatic breast cancer patients directly to develop every piece of the project, from the website to the design of the sample kits that are sent out. Since its launch, more than 5,600 patients in all U.S. states have registered for the Metastatic Breast Cancer Project. This first project served as a proof of concept that the model of patient-partnered research was feasible in a major cancer.
Next, Count Me In wanted to see if the concept worked in a rare cancer and launched the Angiosarcoma Project. Only 300 patients in the United States are diagnosed with angiosarcoma each year. More than 450 patients have enrolled in the Angiosarcoma Project, and three publications have already cited Count Me In data. Since then, Count Me In has launched the Metastatic Prostate Cancer Project, the Esophageal and Stomach Cancer Project, and the Brain Cancer Project, which was launched in early fall 2019.
The Count Me In Process
Count Me In is very transparent about its process and to what patients who participate are actually consenting. Before launching the first project, Count Me In staff did a listening tour with metastatic breast cancer patients to ensure that the process would be as easy as possible for patients.
In order to sign up, patients begin by visiting the website for the cancer that they have. Patients then click Count Me In where they can fill out a survey. The survey questions for each project are developed in collaboration with oncologists and researchers. Every question is optional. The patient survey provides valuable data that can be used to build cohorts.
Patients are then presented with a consent form. This form provides details about the project and asks for permission to obtain copies of their medical record and to ship a saliva collection kit to them. The patient can also opt in or out of allowing the team to collect leftover tissues from previous procedures as well as to send a collection kit for a blood sample. The enrollment process takes patients 12 to 17 minutes.
Count Me In’s internal software system then triggers saliva and/or blood sample kits to be mailed to the patient’s homes. Patients who choose to also send a blood sample can have a complimentary blood draw at the hospital where they are receiving their care or at Quest Diagnostics. Patients then send the saliva and/or blood sample back to Count Me In.
Behind the scenes at Count Me In, the study team is working. This starts with cleaning and standardizing patient-reported survey data, which are used to build cohorts of interest. From the consent form, the study team determines what kinds of biological samples the patient has consented to provide. The study team works directly with the medical records department at the patients’ hospitals to obtain medical records. This is one of the most difficult parts of the process.
If a patient consents to Count Me In obtaining a small piece of archived tissue, the study team will create detailed surgical histories and work with pathology departments to identify any available tissues that can be sequenced without interfering with the patient’s future clinical care. Once the study team has received either a blood sample, a saliva sample, or both, they will push the appropriate samples for sequencing.
Clinical data elements pulled from the medical records, patient-reported survey data, and sequenced data are aggregated. The data are linked, de-identified, and shared as they are generated for use by scientists to start making discoveries. Updates and insights are provided to patients on a regular basis.
Patient Response to Count Me In
The patient response to Count Me In has been amazing. Without prompting, Count Me In began receiving many patient selfies showing patients with their blood kits. The patients find it empowering to be asked to join a movement to participate in research. They wanted people to know that they were helping to make discoveries. Patients often decorate their blood kits before they send them back to Count Me In.
Patients who are visiting the Cambridge area can visit the Count Me In office to learn more about genomic sequencing and data collection. Transparency is crucial.
Count Me In Data
Data produced are based on medical records, saliva samples, blood samples, and archived tumor tissue. Whole exome sequencing is performed on archived tumor tissue, enabling the study team to understand some of the somatic mutations, and it is performed on copy number alterations that may drive one patient’s cancer but not another patient’s cancer. Count Me In data enable researchers to look at needles in the haystacks, exceptional responders, and rare cancers that could not be studied before.
Count Me In releases data through cBioPortal.org, a public database that hosts genomic and de-identified clinical data. Developed and hosted by Memorial Sloan Kettering Cancer Center, anyone can look at the de-identified data on this public cBioPortal site. As of September 2019, researchers have used Count Me In data in 17 publications:
- Metastatic Breast Cancer Project: 13 publications
- Angiosarcoma Project: 3 publications and 1 abstract.
The Future of Count Me In
Count Me In is always incorporating new processes and technologies in order to address the developing questions that scientists are working on. For example, when the Metastatic Breast Cancer project initially launched, it did not collect blood samples because staff thought that patients would not want to give blood samples to people who they had never met. Feedback from patients indicated otherwise, and soon the project began sending out blood kits and obtaining blood samples from those patients who were interested. Now the collection of blood samples is a core process in all of Count Me In’s projects.
Soon, Count Me In will be allowing patients to opt into providing serial blood samples. Tumor evolution and drug resistance is a massive issue in many cancers. Obtaining serial blood samples over time will enable scientists to start to understand how cancers are evolving over time. This genomic data paired with longitudinal clinical data may elucidate what changes in a tumor’s genetic makeup are causing differential responses to drugs
Over the next few years, Count Me In aims to launch projects in every major cancer type as well as pediatric and rare cancers. The combined power of thousands of patient experiences is the only way to accelerate discoveries that could impact as many patients as possible. Count Me In’s database would not be possible without the thousands of patients who are participating in this research and more than 60 advocacy partners with whom Count Me In partners.