Fox Chase Researcher Develops New Analytical Methods for Large-Scale Genomic Studies to Help Distinguish Cancer Subtypes and Predict Outcomes

Karthik Devarajan, PhD, an associate professor of population science in the Biostatistics and Bioinformatics Facility at Fox Chase.
Karthik Devarajan, PhD, lead author on the study and an associate professor of population science in the Biostatistics and Bioinformatics Facility at Fox Chase.

PHILADELPHIA (October 5, 2021)—In a recently published study, a researcher at Fox Chase Cancer Center outlined new methods for handling heterogeneous data types from large-scale studies. These studies generate genomic profiles with the goal of identifying subgroups of patients who may have a better prognosis or benefit from a particular treatment.

Genomic profiling is a process used to understand the way genes interact with each other and the environment of a specific individual. It can be used to develop new methods of monitoring, diagnosing, and preventing diseases—including cancer—by identifying specific genomic features that are unique to a subgroup of individuals with the disease. The number of such genomic markers of interest typically far outnumbers the subjects that can be followed up clinically.

“Our approach provides a unified framework for handling various types of genomic feature measurements,” said Karthik Devarajan, PhD, the study’s lead author and associate professor of population science in the Biostatistics and Bioinformatics Facility at Fox Chase.

“We developed a generalized algorithm that facilitates the delineation of tumor samples into homogeneous subgroups with similar genomic profiles which can, in turn, be linked to clinical outcomes. For instance, it can ultimately aid in determining which patients are likely to respond favorably to a new therapy.”

In order to fully comprehend the genomic profile of a tumor sample, it is often necessary in practice to measure and quantify diverse aspects of it. This is made possible by an array of genomic technologies that are currently available for profiling tumor samples.

Methods such as the ones developed by Devarajan are critical in predicting cancer outcomes, particularly because there are several challenges researchers face when using standard statistical methods in analyzing and interpreting the effect of genomic profiles on patient survival, disease progression or recurrence, and response to a particular treatment. In addition, they are useful for discovering a completely unknown cancer subtype or distinguishing lesser-known subtypes.

“Our methods are designed to handle the large volume and disparate nature of genomic data, incorporate relevant clinical information, and account for confounding clinical factors,” said Devarajan.

He added that by accurately identifying specific genomic markers associated with clinical outcomes in subgroups of patients, their work could aid in the design of clinical studies that could ultimately lead to improved and personalized cancer treatments.

The study, “A Statistical Framework for Non-Negative Matrix Factorization Using Generalized Dual Divergence,” was published in Neural Networks.

Fox Chase Cancer Center (Fox Chase), which includes the Institute for Cancer Research and the American Oncologic Hospital and is a part of Temple Health, is one of the leading comprehensive cancer centers in the United States. Founded in 1904 in Philadelphia as one of the nation’s first cancer hospitals, Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. Fox Chase is also one of just 10 members of the Alliance of Dedicated Cancer Centers. Fox Chase researchers have won the highest awards in their fields, including two Nobel Prizes. Fox Chase physicians are also routinely recognized in national rankings, and the Center’s nursing program has received the Magnet recognition for excellence six consecutive times. Today, Fox Chase conducts a broad array of nationally competitive basic, translational, and clinical research, with special programs in cancer prevention, detection, survivorship, and community outreach. It is the policy of Fox Chase Cancer Center that there shall be no exclusion from, or participation in, and no one denied the benefits of, the delivery of quality medical care on the basis of race, ethnicity, religion, sexual orientation, gender, gender identity/expression, disability, age, ancestry, color, national origin, physical ability, level of education, or source of payment.

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