Piecing Together the Puzzle of Cancer Genomics

Livestrong Foundation
4 min readApr 14, 2022


A patient-centered care team can include professionals ranging from physicians to nurses to social workers. But what if technology was brought to the table and viewed as a member of the team?

Jeanne Kowalski-Muegge, Ph.D., professor in Dell Medical School’s Department of Oncology and associate director of cancer clinical genomics at the Livestrong Cancer Institutes, is creating tools to empower care teams in using precision medicine, ensuring that every patient has every treatment option possible at their disposal.

Jeanne Kowalski-Muegge, Ph.D.

What’s the problem you’re hoping to solve, and how did you come to recognize it?

I am hoping to solve the molecular cancer “puzzle,” one patient and one piece at a time. Every tumor is a puzzle with many pieces. Only when the puzzle is assembled can it reveal insights necessary for informed therapies and approaches to treatment. No one patient has within themselves all the pieces to their puzzle — that’s where care teams come in.

However, there’s an even more pressing challenge with cancer: How do you assemble a puzzle that does not have a reference photo? In the field of cancer clinical genomics, where we study molecular changes in a tumor to inform on their treatment, we are operating without a picture of what the puzzle should look like with each and every patient.

I came to recognize this problem through my 30-plus years in cancer research. I recall studying the HIV viral genome, sequenced then for the first time, while I was a postdoctoral fellow at Harvard. I designed a first-time trial for using the virus’s molecular pieces to inform on HIV therapy, meaning I had to learn in real time all about the HIV viral genome and then assign treatment based on brand new discoveries. At the time, HIV was a viral crisis.

Decades later, we find ourselves in another viral crisis with COVID-19; now we have more sequencing technologies and previous sequencing discoveries at our disposal. Yet, we find ourselves starting over — genomics in medicine is an unknown puzzle that keeps repeating, with more pieces to use, discard or keep for another’s puzzle!

What’s your approach to solving the puzzle?

I lead the Livestrong Cancer Institutes’ research molecular tumor board, in which we discuss patient case tumor reports for informed treatment. The approach differs from a typical review board in that each patient case is treated as a single research study, with the intent of understanding lack of tumor response to current treatment to inform treatment moving forward. We present results combined with real-world evidence that, in turn, builds our knowledge base. This way, each case ends up being a mini-analysis that furthers cancer knowledge bases.

To help facilitate these analyses, my lab developed an award-winning computational workflow titled W3: Whole Data, Whole Profile for Whole Patient Care. This workflow, supported by Texas Health Catalyst, connects all the data from tumor molecular profiling reports to uncover hidden insights that help us put together a total molecular “puzzle,” enabling us to evaluate and inform on targeted therapies. This model is in alignment with the Cancer Life reiMagined (CaLM) model of the Livestrong Cancer Institutes by reimagining the cancer genome, harnessing the power of patient influence on treatment choice.

What needs to happen to make strides in cancer genomics, or precision medicine broadly?

We need changes in perception. Patients participating in clinical trials should not just be viewed as participants — they should be viewed as partners in cancer research who share in the decision-making process of disease management.

Equally important is widening perceptions of what care looks like. The field needs to transition from single oncologist-enabled care to digitally enabled care. In digitally enabled care, technology is viewed as an engaged member of a patient’s care team.

The future of precision medicine is in understanding the kind of trials and treatment options that are in better alignment with patient values and preferences. In order for patient-valued precision medicine to take flight, technology must help teams fight disease from data-centric vantage points over time. Care teams are not a “pop-up shop,” and should grow and evolve with technology as partners, just as our understanding of disease evolves.

The New York Times asks readers to tell their “Tiny Love Stories” in just 100 words. What’s yours?

Just a Puzzle in a Bag. No Box. No Reference.

I often come across them at garage sales: just a puzzle in clear plastic bag. No box or reference picture. I once purchased one, thinking it might be a good challenge. If I could complete it, I would take a picture for future puzzlers so they know what they should be aiming for.

Less than halfway through the puzzle, I was disappointed to find that it was missing pieces. I go back and buy another puzzle in a bag, hoping to use pieces from it to one day complete my puzzle.

This blog was originally featured as part of Dell Med’s Voices, a series of profiles that highlight the people of Dell Med as they work to improve health with a unique focus on our community.