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Metastatic Breast Cancer Project Releases First Genomic, Clinical Data From 100 Patients


NEW YORK (GenomeWeb) – The patient-driven Metastatic Breast Cancer Project has publicly released its first genomic and phenotypic data set that researchers can query for their own investigations.

Within the Metastatic Breast Cancer (MBC) Project, experts at the Broad Institute and Dana-Farber Cancer Institute have been using social media to connect with patients and their online networks, and enlist the participation of "outliers," those with an extraordinary response to treatments and those traditionally underrepresented in research. 

In the US this year, more than 250,000 women will be diagnosed with invasive breast cancer, 5 percent of whom will be diagnosed with metastatic disease. When the cancer is located in the breast, the five-year survival rate is 99 percent. But once the cancer has spread to other parts of the body, the five-year survival rate drops to 26 percent. There is no cure for metastatic breast cancer.

The goal of the MBC Project, according to Nikhil Wagle, assistant professor of medicine at Dana-Farber Cancer Institute, is to partner with patients and allow them to contribute whatever information they're willing to, from answering surveys and providing patient-reported data, to giving access to medical records and donating biological samples.

Ultimately, the project aims to generate a large database of molecular and clinical information that is publicly available to researchers. Specifically, Wagle's team is releasing information on patients who have had whole-exome analysis done on tumor and germline samples, and those samples have been annotated with demographic, diagnostic, pathology, treatment (including all drugs received in the metastatic setting), and patient-reported data.

Last week, Wagle's team released this data for around 100 metastatic breast cancer patients. The exome sequencing data are available on cBioPortal, a web-based platform that enables users to explore genomic data. However, the raw exome data from sequencing these patients' tumor and saliva (germline) samples will soon be available on the National Cancer Institute's Genomic Data Commons. Anyone can access the cBioPortal somatic data, but the raw data within GDC requires credentialed access.

As of October, 4,100 patients have signed up for the project. Of these participants, 95 percent have so far completed the survey to provide patient-reported information, which is a much higher engagement than is typical with surveys of this kind.

Even before the project got started, researchers worked with patients to figure out what data to collect and how to collect it, getting their feedback on even the wording of survey questions. "We worked with patients to understand what [they] would be able to answer and what would make this not intimidating," Wagle said. "We didn't want people to open this up, see a long list of questions, and shut the window. We wanted them to feel like this was doable."

Given their success in collecting patient-reported data, Wagle's team is developing additional surveys to probe different aspects of patients' experience. "With patients' help we're going to come up with a whole bunch of other modules and really turn this into a registry," he said, which he hopes will inform epidemiological studies of metastatic breast cancer and allow researchers to compare the data in the medial record against what patients are reporting. To date, comparisons between information patients are reporting and what's in the medical record matches well, but when there are differences, Wagle said that the patient is often right.

Around 2,400 have so far agreed to allow Wagel's team to access their medical records, while 1,400 patients have donated saliva samples. "The dropoff is around 60 percent, from sign up to consent," Wagle said.

Some participants initially interested in joining the project may have second thoughts after reading the consent form, he said. Others may not want to donate their tumor sample to research because they are worried they might need it to inform their treatment later. (Although Wagle noted that the project safeguards against this by offering concerned patients the chance to donate blood instead of tumor tissue.)

Wagle suspects, however, that the dropoff is more a reflection of the fact that these are often very sick patients, who are at different points in their cancer journey, and many patients just haven't gotten around to submitting all the things the study is requesting. As such, it has taken Wagel's team some time to gather all the pieces of information, including locating and obtaining all the samples, performing the exome sequencing on tumor and normal samples, and abstracting the relevant medical records and putting it into a structured format.

The last bit has proven the most time consuming, he said, so the number of patients included in this first data release is much smaller than the total number of participants.  

"With 103 samples, it's probably not enough to see broad patterns in the data," Wagle acknowledged. "We need to get up to the several hundreds, if not thousands, before we can start to see those patterns."

Nonetheless, the data that's currently available has generated lots of interest and is already yielding some interesting insights about metastatic breast cancer patients' resistance and response to treatments. At a recent medical meeting, a researcher shared with Wagle the case of a cancer patient who had an extraordinary response to a specific therapy. The MBC Project cohort also includes patients who have had outlier responses to treatments.

They looked in the MBC Project data, and one of the patient's experiences matched the question this other researcher was asking, Wagle said, suggesting that the data collected so far is already helping investigators explore their hypothesis. "We'd said all along that as we generate data we just want to get it out into the real world," Wagle said. "This hopefully will serve as a repository for lots of researchers to tap into, and shave years off of any individual research project that needs this kind of data."

The project has also garnered the interest of researchers studying specific therapies, who want to evaluate genomic and phenotypic data from patients that got that particular drug. Other researchers want to dive into the raw data because they are exploring different analytical techniques for metastatic breast cancer. Still others want to look at how breast tumors have evolved from the primary setting to the metastatic phase.

"There's another group of folks that are interested in cancers that are at low risk of metastasis initially, like stage I or ductal carcinoma in situ, but nevertheless have become metastatic," said Wagle. The project also contains data from patients with rare metastatic breast cancer subtypes and at least one man with the disease.

"As we increase the diversity of the patients participating, we and many others are interested in understanding if there are genomic differences either in the germline or in the tumor from different racial or ethnic groups that get metastatic breast cancer," Wagle added. "That's been really understudied to date."