Karen Ketchum uses bioinformatics to better understand cancer

Molecular genome biologist and data scientist Karen Ketchum is bringing understanding to the story of cancer by leading our efforts with the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC).

CPTAC is a national effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteogenomic analysis. Or, in other words, how changes in the genome (the genetic material in a cell) and proteome (the proteins expressed in a cell) behave in a cancer tumor.

Karen says, “I love bioinformatics because it’s similar to a painting. At one level there are very detailed pieces identified. Then when the pieces are put together through data management and computational pipelines, they provide a picture of the disease that you didn't see before.”

For 10+ years, Karen and her team of scientists, software engineers, project managers, graphic artists, writers, and more have provided bioinformatics and data management support to CPTAC in two key areas: data collection and analysis, and data dissemination.

“We pride ourselves on quality of data and attention to biological details because it informs real outcomes." — Karen Ketchum

First, we collect and analyze tumor data from research teams as mass spectrometry files. Organize these files based on cancer type. Count and categorize peptides and proteins to describe the specific tumor. Then use bioinformatics to assemble data from the cancer proteome into a story about the disease.

Then, we provide this information about the cancer proteome to other researchers and the public through the Proteomic Data Commons to advance data-driven scientific discovery about cancer. And so researchers and scientists can devise ways of personalizing treatment for patients using precision medicine.

Karen explains, “When you start comparing different markers on different types of cancers, you’re heading toward more personalized medicine. This means patients won’t have to go through unnecessary treatments because treatments will be more targeted to their specific cancer.”

Our work with CPTAC has grown quite a bit over the years. When we started, we were studying breast, ovarian, and colon cancer. We’re now up to 12 different types including lung, pediatric, and adult brain cancer.

For those looking toward a career in bioinformatics, Karen advises: “Be willing to start at the beginning level.” She started as a dishwasher in a laboratory to help fund her classes! One of her coworkers then taught her to run some experiments. And she went on from there, even helping with the sequencing of the human genome at one point in her career.

“To be successful in this field requires attention to detail, quality of data, independent work and teamwork, understanding that there are biological principles that can be structured in a software program, and the ability to adapt and evolve,” she says. There are always exceptions to the rule, which can be frustrating, but those exceptions can often open a completely new field of study. Or a new discovery.

There’s also the opportunity to keep learning new methodologies. For example, in Karen’s field there are many new “-omics.” What started with genomics, then proteomics, now has lipidomics, metabolomics, and more—each integrated with the other -omics.

Working in the field also means the opportunity to make a big impact. “Knowing that some of the patients whose tumors we’ve studied have passed is heartbreaking,” says Karen. “But also knowing that the tumor data they’ve provided and we’re analyzing is contributing to saving future lives is very rewarding.”