Meet the Informatics team that enables cancer immunotherapy research
At the Parker Institute, we believe there can be a world without cancer. We created a unique model that brings scientists together to collaborate on bold ideas. And, we provided an infrastructure where the most advanced technologies and computational resources are infused into our network to accelerate discoveries and bring therapeutics to patients faster.
A key differentiator of the institute’s model is our in-house informatics team. The group is dedicated to harnessing data collected from Parker Institute studies and drawing conclusions to improve patient responses to immunotherapy.
They are a diverse group of individuals, cherry-picked for their expertise and brought together to make sense of data generated by the institute’s 300+ researchers, to run our first sponsored clinical trial and to bring new technologies to our network of investigators.
The energy that emanates from the team is tangible. Their voices carry from the glass-encased meeting rooms where they test ideas over animated discussion. Endless clacking from keyboards and mouse clicks emit from where the team sits in the back room. Sounds of snapping fingers accompany their teammate Danny wherever he walks, as if the percussion powers his thoughts.
The team is led by the talented systems immunologist Nikesh Kotecha, PhD. A serene leader with a laid-back, open-to-discussion style, he has aligned his team to one overarching vision: use data to inform better treatments for patients and do it faster than ever.
To accelerate discovery, the team concentrates their efforts on getting the most out of all the data collected by the Parker Institute.
They are involved in every step of the research process – from clinical trial design, to data collection to interpretation, to informing the precision and robustness of the data. They create systems to collect and extract insights from the clinical trial data.
The right patient samples are precious, so each one is used to its fullest. By taking many measurements on patient tumor and blood samples – what they call “deep immune profiling” – the team hopes to identify factors that correlate with better responses to immunotherapy. They’ve worked with every data-type imaginable in immunology.
To study the immune system in new ways, the team is always on the lookout for new technologies that can deliver greater insights. They partner with companies to evaluate cutting-edge, sometimes pre-market, technologies and test them out in the labs of the institute’s cancer center partners. They work on defining standards and computational approaches that allow for a quicker uptake of these powerful new tools.
At the same time, they don’t want to reinvent the wheel. The team recognizes the wealth of information that already exists from public datasets like the Human Genome Project and the growing body of scientific literature. They make the most of existing data by absorbing the information in an automated way to easily query the data.
A perfect demonstration of the team’s efforts at work is the recent multi-center pancreatic clinical trial the Parker Institute launched in collaboration with the Cancer Research Institute this past August. The phase 1b/2 trial, which combats the nation’s third deadliest cancer, explores a novel combination of two immunotherapies and two traditional chemotherapies to activate the immune system to attack cancer.
Lead investigators at the University of Pennsylvania and Parker Institute leaders charged the informatics team to secure the technology that would be used to conduct the trial.
Despite researching a variety of options, the team realized there was a lack of “out-of-the-box” functionality for storing and analyzing clinical and molecular data in an integrated fashion. They set out to assemble the systems needed to run the trial, developing new pieces as required to fill the gaps.
The team imagined one umbrella system to collect patient’s clinical information, track and manage clinical trial tumor and blood samples, gather measurements from tests performed on these samples and pull in data from already-existing public literature. As if that wasn’t daunting, there was an urgency to get the trial running quickly to give pancreatic cancer patients, often with short prognoses, access to immunotherapy treatment options. By August, in fact. And by then it was already February. Time was ticking on a six-month countdown.
The team quickly architected a clinical data entry and management system, which clinical staff at University of Pennsylvania, Memorial Sloan Kettering Cancer Center, The University of Texas MD Anderson Cancer Center and University of California, Los Angeles, would use to document information about patient health and any samples collected from the patient.
Despite the short timeframe, the team saw starting from a blank slate as an opportunity and made room to innovate. One example was a system for tracking clinical samples that would replace a great deal of manual input, making it easier for clinic staff and eliminating potential data input errors common to other systems. The design effort was led largely by scientist Pier Federico Gherardini.
Once implemented, the system showed benefits immediately. “Because of the way we designed the system, we were able to quickly determine that a mix-up happened with some samples that might not have been caught for couple months,” said Gherardini.
An added benefit to designing the system fresh and in-house was that it could be improved to better serve the needs of the trial sites. The informatics team works in step-sync with the clinical operations team running the trial who are in close contact with the staff at the treatment sites. They collaborate regularly to refine the technology.
“It’s rare to see this kind of real-time collaboration in academia or industry. At PICI, all functions of a trial management team are able to get into one room, allowing us to be nimble and have the conversations we need to move quickly,” noted the trial’s program manager Jaclyn Lyman.
She added that “it demonstrates a remarkable paradigm shift in how we are collaborating, innovating and ultimately streamlining our ability to deliver trials to patients faster. It highlights the spirit PICI was founded on.”
To determine what kinds of data will be gathered on the patient samples, the informatics team has been closely collaborating with the study’s lead investigator Robert Vonderheide, MD, DPhil, director of the Abramson Cancer Center of the University of Pennsylvania, his team and experts across the Parker Institute network.
“They not only understand the biology but possess the technological know-how to answer the scientific questions and further the conversation,” said Vonderheide. “The technology they engineered has helped the clinical trial run smoothly, but more importantly ensures that the data we collect from the trial will be useful in progressing our understanding of how we can crack pancreatic cancer, a highly deadly disease.”
He finished by stating he was “impressed by the knowledge and ingenuity” of the informatics team.
The team is prepared, too. In the year leading up to the trial, they’ve been working with PICI researchers to develop tools to analyze all forms of immunological assay data to not only help them with their discoveries, but also to assemble the knowledge base needed for this trial. The team now has the experience and tools for every type of measurement they hope to use in the trial.
While the team has accomplished a lot, there is always more to do. Ongoing efforts include building pipelines to quickly analyze the rich data gathered from deep profiling of patient samples and linking them to meticulously noted patient medical records.
“We are working to smooth the process to correlate the data from, say, a gene expression assay to what medication a patient was taking, allowing our team to ask intelligent questions of the data and be able to draw conclusions faster,” notes Gherardini.
On the horizon for the informatics team
The Informatics team plans to use what they learn from this trial to inform the next trial design. But beyond that, they have a grander vision in mind – to be the centralized source of data on cancer immunotherapy to truly affect change in treatments for patients.
Data will get bigger and deeper, and they aim to make the most out of what they‘re collecting, says Kotecha. They’re preparing by putting together processes, pipelines and frameworks to automate and scale as needed. There will be newer methods and approaches and they will keep adapting.
Why? Because the stakes are high and they believe data and collaboration are the keys to answering cancer’s unsolved questions.
Meet the Team
Pier Federico Gherardini
Associate Director, Technology Development
2009: PhD, Cell Molecular Biology
2006: MS, Bioinformatics, University of Rome Tor Vergata
Trained as postdoctoral fellow with Garry Nolan, PhD, at Stanford studying experimental and computational approaches to single-cell analysis.
In his words
“I strongly believe that we can get greater insights by having multiple brains approach the problem from different angles.”
“Many of my friends and family are affected by cancer.”
2017: MPH, Behavioral Sciences & Health Education, Emory University
2015: BA, Spanish and Biology, University of Redlands
Interned in Garry Nolan’s lab at Stanford and at cytometry analysis company Cytobank.
In her words
“I’m annotating datasets of patients with cancer that have undergone immunotherapy. Afterwards, I draw comparisons between variables that could help inform further research for effectively treating patients with immunotherapy.”
“Health and happiness are two rights that I believe everyone should have.”
IT Support / Executive Assistant
2004: BS, Computer Science, Business Administration, Monterrey Institute of Technology
10 years of experience at nonprofits related to HIV, older adult health and cancer, namely On Lok Lifeways and the Flowers Heritage Foundation.
In his words
“From a young age I was involved in the community. In my hometown in Mexico, my father partnered with organizations to bring pediatric vitamins and food to families with underweight children. I’ve carried on that legacy serving nonprofit organizations for over a decade.”
“With the current technological advances, I think we have a shot at fighting it.”