Philips Research is developing a software platform intended to help oncologists analyze, interpret, and interactively present data from next-generation sequencing instruments in order to prioritize treatment for cancer patients.
The software, called PAPAyA, for Platform for Personalized Analytics Applications, is currently being developed as a prototype. The company is planning to begin a pilot study in the fourth quarter in partnership with an undisclosed cancer center in order to evaluate its effectiveness in the clinical setting.
Sitharthan Kamalakaran, a senior member of the research staff at Philips Research, told BioInform that the project is part of a broader effort to take advantage of genomic data to treat cancer patients.
Philips offers a large suite of products for oncology, with a solid presence in mammography, CT scanning, digital pathology, and picture archiving and communications systems. The company is also a major provider of healthcare IT solutions. Hans Hofstraat, vice president and a member of the Healthcare Program Board at Philips Research, said that the research division is looking to help the company stay ahead of the curve by developing clinical decision support tools for cancer genomics, though he noted that the project is still in R&D and the company has not yet developed a commercialization strategy for PAPAyA.
"Our goal now is to start collaborating with cancer centers and hospitals to get feedback on the platform and how to take it further," said Nevenka Dimitrova, who leads the PAPAyA team. The team is currently signing up evaluation sites, with a particular focus on comprehensive cancer centers and hospitals, to use the platform and generate feedback.
The software has been under development for several years. In a 2009 paper in BMC Bioinformatics, Kamalakaran and colleagues highlighted PAPAyA's ability to discover molecular signatures for the clinical stratification of breast cancer samples.
More recently, the group has focused on the system's reporting capabilities. At a presentation at Cambridge Healthtech Institute's Molecular Medicine Tri-Conference earlier this year, Kamalakaran noted that while software is needed to rapidly analyze genomic data for oncology patients, a more pressing need is delivering that data to the oncologist in a format that helps guide treatment.
"The analysis and interpretation is one thing, but the delivery of the information is a completely different thing," Kamalakaran said in his talk. "A software system that helps bioinformaticians [analyze] genome data in a very fast manner is not the best way of showing those results to an oncologist who has very limited time to look at the output of bioinformatics analysis and is more interested in clinical actions and to prescribe a treatment for a patient," he said.
Philips Research is developing PAPAyA to fulfill both needs. The software is designed to analyze, store, and manage genome data, as well as present this data in an interactive format that allows clinicians to query it in an intuitive manner. Intended users are pathologists or genome scientists who are analyzing the data, as well as oncologists, genetic counselors, and others who need to translate the results into patient care.
"We transform the NGS pipelines into a clinical question-based answer system," Kamalakaran said. "So instead of looking for fusions or mutations, we're looking to integrate multiple lines of evidence for what is the most relevant line of action for this patient."
The Philips developers recognize that "the way we think as bioinformaticians is different than how a clinical oncologist would look at the data when treating the patients," he said. "We're thinking, 'What is the predictive nature of this particular mutation in this cancer?' but an oncologist doesn’t care if it’s a mutation or a copy number variation or a fusion. All they care is, 'What is the diagnosis for my particular patient? What's the prognosis? What is the best therapy that I can give him or her?'"
PAPAyA separates the analytical component from the clinical decision support component, he said. Each patient's data is available in two separate views: one for genotype data, and another for clinical questions. The oncologist can drag specific variants into the clinical view to get information on the patient's likely response to different drugs.
Philips is not the only player looking to provide software-based solutions for the clinical interpretation of genomic data. For example, Life Technologies is partnering with CollabRx and Ingenuity Systems to develop a physician portal that will provide information about treatment options based on patients' molecular profiles. And a number of informatics startups, such as N-of-One, MolecularHealth, and Annai Systems, are targeting oncologists for their interpretation tools.
Kamalakaran told BioInform that PAPAyA's dual focus on interpretation and the presentation of results has the potential to set it apart in the marketplace. "We believe that the need to deliver sequencing information to directly and comprehensively assist clinical decisions is not currently addressed by others in this ecosystem," he said. "The integration of genomic data interpretation pipelines with a storage/computing infrastructure in the hospital is a key differentiating factor of PAPAyA."