Big Data research includes sarcoma

By Suzie Siegel

Dr. Bill Dalton is betting on Big Data.

In 2006, when he was CEO of the Moffitt Cancer Center in Tampa, he led the development of the Total Cancer Care Protocol and M2Gen, a for-profit subsidiary.

As part of Total Cancer Care, more than 140,000 patients — including 3,392 with sarcoma — have given permission to have their blood and tissue samples stored and analyzed at Moffitt and to be followed throughout their lives. This produces huge amounts of data that researchers and M2Gen can analyze further.

“We have one of the oldest and largest databases of its kind, especially in molecular genomics,” said Dr. Dalton, MD, PhD, now executive chair of M2Gen, a health-informatics company. “We are continually updating patients’ data to try and learn from each patient’s experience.”

Researchers group patients' de-identified data by their similarities, and then break out the groups with more and more similarities. For example, they might start with patients whose cancers had NTRK gene mutations, and then create a subset that have Ras mutations, too. Because some patients may have the same genetic mutations, patients with different kinds of cancer might be able to take the same drug.

Sarcoma is rare, and doctors often struggle to enroll enough patients in the clinical trials needed to gain FDA approval of a new drug. We may benefit from trials that enroll patients with different cancers who have the same mutations. Targeting these mutations in a person’s cancer is called precision or personalized medicine.

In sarcoma, the first targeted treatment was imatinib (Gleevec) for gastrointestinal stromal tumor (GIST), which often shares the same mutation as chronic myeloid leukemia (CML). The FDA approved imatinib for CML in 2001 and GIST patients followed soon after.

In the past, GIST had often been classified as gastrointestinal leiomyosarcoma (GI LMS). Although my LMS was vaginal, I was checked for the mutation when I was diagnosed in 2002, just in case. My first sarcoma oncologist, Dr. Andy Burgess, now retired from MD Anderson Cancer Center in Houston, told me that imatinib for GIST was the best thing that had ever happened to him in his life.

One of Dr. Dalton’s sons was diagnosed with GIST last year and is doing well on imatinib. “I’m becoming a student again,” Dr. Dalton said, as he learns more about sarcoma. As a physician, he treated patients with multiple myeloma.

My tour to learn more about Total Cancer Care began at Moffitt, where I peered into the pathology lab near the operating rooms. If possible, a diagnosis is made while the patient is in surgery to help the surgeon know how to proceed. With sarcoma, for example, surgeons try to take some normal tissue around the tumor — just in case some microscopic cancer cells have spread that far. In ovarian cancer, surgeons often take much more.

Tissue donated for research is snap-frozen, usually with liquid nitrogen. When tissue is needed for patient care, hospitals store tissue in wax, technically called formalin-fixed paraffin-embedded (FFPE) tissue blocks, said Michelle Fournier, manager of Moffitt’s central biorepository (also known as a tissue bank).

“But that isn’t the best for genomic sequencing,” she said. Ten years ago, Moffitt couldn’t extract good quality genetic information from paraffin blocks, but it now has the technology, Dr. Dalton noted. This matters because Moffitt often receives FFPE samples from other hospitals when patients seek second opinions.

If a patient may benefit from genomic testing, most Moffitt doctors use FoundationOne, Fournier said, which is not always covered by insurance. She said Moffitt wants to create its own genomic-testing lab.

Samples of blood and other bodily fluids are also important parts of Total Cancer Care, she said. Like their colleagues elsewhere, Moffitt researchers hope to develop technology to allow the use of liquid biopsies. Drawing blood for a biopsy would be easier on patients than minor surgery to remove tissue.

Genesis Blanco, left, and Michelle Fournier, right

“I have a lot of patients who say they came to Moffitt because of the research,” said Genesis Blanco, a Total Cancer Care research coordinator.

Total Cancer Care draws from electronic medical records (EMR) created by clinic staff, as well as results of surveys from patients. This two-part system helps ensure accuracy, Dr. Dalton said. “I’d sometimes trust patient-reported outcomes for such things as patient’s pain over EMR.”

M2Gen, built on 30 acres near the main Moffitt campus, promotes research using the Total Cancer Care data. The data are de-identified so that researchers don’t know who the patients are. M2Gen partners with five pharmaceutical and biotech companies, which provide funding for further analysis of the data.

M2Gen also looks into the future. Researchers use statistical algorithms to predict how someone’s cancer might change if it spreads and what treatment options might be available.

In 2014, Moffitt and the Ohio State Comprehensive Cancer Center in Columbus, cofounded the nonprofit ORIEN (Oncology Research Information Exchange Network). M2Gen manages the network.  Seventeen cancer centers participate.

"We’ll be up in Canada next month, and then in Europe,” seeking more partners, Dr. Dalton said.

M2Gen is leading the Avatar Research project within ORIEN that does whole exome sequencing, which looks at the part of DNA that encodes protein, as well as RNA sequencing on tissues collected as part of TCC. Dr. Dalton would like to create a portal so that patients could learn how their donations of tissue and data are advancing research.

ORIEN is using resources on a focused group of Total Cancer Care tissues. “For Avatar we’re looking at a subset of high-risk patients who may be in need of clinical trials,” explained Erin Siegel, MPH, PhD, Scientific Director of TCC.

In this Avatar Research project, researchers in and outside of the ORIEN network can ask to use the data for specific projects. For example, Dr. Damon Reed is looking at teenagers and young adults up to age 40. Dr. Reed, MD, is director of the Adolescent and Young Adult Program at Moffitt and medical director of its Sarcoma Department. Working with Dr. Reed, Moffitt will include over 250 sarcoma tumors in the Avatar project.

"We need champions in this research, like Damon,” Dr. Dalton said.