CLIN I C AL
Open Source: How a Data Scientist Is Bringing Precision Medicine to the People By Matt Windsor, UAB Reporter
In
some ways Elizabeth Worthey, Ph.D., is a typical nerd. She likes having lots of computer screens and solving puzzles and nothing so much as coming up with novel ways to use software to solve complex problems. Unlike most geeks, though, Worthey is intimately familiar with her own source code. A chunk of her laptop hard drive is dedicated to a complete copy of her DNA, which she had sequenced nearly a decade ago.
‘I had them all’
When she hears about an interesting new deleterious variant at a genetics conference, “I go in and look at my genome and see if I have it or not,” said Worthey, who joined UAB in July as director of the Bioinformatics Section in the Division of Genomics Diagnostics and Bioinformatics in the Department of Pathology, director of the Center for Computational Genomics and Data Sciences in the Department of Pediatrics, and the associate director of the Hugh Kaul Precision Medicine Institute, all in the School of Medicine. Worthey hails from the Vale of Leven, in between Loch Lomond and the River Clyde on the west coast of Scotland, an area where heart problems run rampant. “Nobody in my family has cardiovascular disease, though,” she said. “I was at a conference and they put up a list of protective genetic variants. I looked and I had them all.”
The original genomic miracle
She knows from personal experience that many people aren’t so fortunate. In 2009, Worthey was part of a team at the Medical College of Wisconsin that was the first to solve a medical mystery with precision medicine. Worthey and her team created a unique software program, CarpeNovo — Latin for “seize the new” — that identified the ultra-rare genetic mutation responsible for 4-year-old Nicholas Volker’s devastating illness. With this crucial information, clinicians were able to identify a treatment (bone marrow transplant) that saved the boy’s life
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and resulted in a Pulitzer Prize-winning series and book about the case by reporters at the Milwaukee Journal Sentinel. The Volker case was the first in the world to demonstrate the power of genomic sequencing and analysis in patient care, but the costs and time involved in sequencing and analysis meant these methods could only be used in extraordinary cases.
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“That first clinical case took three months, and fortunately the child was healthy enough to wait that long. Many times they are not. We developed some of the first methods that allowed shortening of that timeframe down to where we are today, which is being able to do sequencing and analysis in less than a week or a couple of days in some cases.”
Later, at the HudsonAlpha Institute for Biotechnology in Huntsville, Worthey and her team developed new software tools that have dramatically reduced analysis time. “That first clinical case took three months, and fortunately the child was healthy enough to wait that long,” Worthey said. “Many times they are not. We developed some of the first methods that allowed shortening of that timeframe down to where we are today, which is being able to do sequencing and analysis in less than a week, or a couple of days in some cases.”
Making the miracles routine
Worthey’s mission is to help open up genetic insights as a routine part of clinical care at UAB. She is working with Alexander “Craig” Mackinnon, M.D., Ph.D., the inaugural director of the Genomic Diagnostics and Bioinformatics division in Pathology, to support the Precision Diagnostics Laboratory, which will combine and enhance efforts across the hospital. Genetics,
