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Nevada University students bring big data to cancer screening in start-up launch

Posted October 16, 2015

Prostate cancer survivor Tom Neville knows first-hand how scary a cancer diagnosis can be, especially in the face of conflicting advice about risks and treatment.

A controversial blood test, the prostate-specific antigen, or PSA, test, is often used to screen for prostate cancer, despite studies that have found unclear benefits from PSA testing as well as unnecessary treatment of non-life threatening tumors detected by PSA tests.

Now, a start-up company founded by Neville and staffed by computer science and engineering students from the University of Nevada, Reno is bringing big data to bear on the question, hoping to provide clearer answers for men who want to better understand how to interpret PSA test results.

“Over the past year and a half, I’ve examined the PSA test records of at least 10,000 individual guys,” said Marty Boren, a senior at the University who has been working with Soar Biodynamics since 2014. “Every sequence of PSA tests tells a story, and, in far too many of the cases that I’ve seen, it doesn’t have a happy ending. A significant fraction of these men either had unnecessary surgery or didn’t have surgery fast enough.”

Boren and seven other students have been working with Neville as part of a co-op program established with the Department of Computer Science and Engineering and Neville’s company, Soar Biodynamics, Inc. They are building a web application where men can input their PSA test results and receive back a personalized report that can guide their decision making about screening and treatment options, in consultation with their doctor.

“I’ve learned more about software engineering from this experience than the entirety of my formal education thus far. Nothing compares to real-world doing,” junior Jeff Soriano said. “The most rewarding part is knowing that the technology I’m helping to develop may actually help people make the best, most informed decision regarding prostate cancer.”

Big data sheds light on screening test results

The technology is based on 33 million PSA test results from 14 million different men – an amount of data that Neville calls unprecedented. The data was provided by the Department of Veterans Affairs and in collaboration with the VA Sierra Nevada Health Care System.

“We’ve developed analytical techniques that can detect prostate cancer earlier than traditional methods and differentiate it from non-life-threatening conditions,” Boren said. “I was able to use these findings to help a family member safely avoid an unnecessary prostate biopsy.”

The team’s approach analyzes changes in a man’s PSA levels over time, which is a controversial metric in the medical community. While some previous research has indicated changes in PSA levels could be meaningful, other studies suggest that the rate of change of PSA levels provide only limited insight into the probability of finding cancer.

But now, backed up by big data, Neville believes his team has unlocked key insights based on how a PSA level increases. In particular, smooth, exponential growth in PSA levels seemed to be characteristic of fast-growing, deadly cancers, while variable or slower increases were less likely to be caused by cancer. With that knowledge, Neville suggests PSA screening results can be more precisely used by men and their physicians.

“The results suggest that some men can reduce the urge to get a biopsy prematurely while identifying PSA patterns that are scary and need to be looked at earlier,” said Neville. “We hope to change prostate cancer screening for the better.”

Neville has been working closely with physicians from the VA and major medical centers, including the Mayo Clinic, the Cleveland Clinic, Yale School of Medicine and the University of California, to conduct the medical research underpinning the web application. University students conducted about a quarter of the medical research, according to Neville.

“I worked on analyzing trends related to prostate cancer death,” said Evan West, a senior majoring in computer science and engineering. “I developed trends to determine how deadly prostate cancer is, given factors such as age and tumor volume.”

Students’ work makes medical knowledge accessible online

While Neville’s collaborators are driving the medical research, and publishing findings in medical journals, Neville, remembering his own frustration with uncertain treatment options, wanted to find a way to make that academic knowledge accessible, enabling individual men to get actionable insight about their PSA results.

That personalized custom report has been the primary development focus of the students, and they have built the system from the ground up, managing the software development, website interface and data analysis. Because federal regulations strictly outline how medical advice can be delivered online, the students needed to find an algorithmic way to turn user-submitted data into a personalized report.

David Vaughn, a junior, worked on writing C++ code that powers that report.

“The co-op experience allowed me to practice and exercise skills from both my computer science and math classes,” said Vaughn. “It also allowed me to learn new engineering and mathematical techniques, particularly in the area of probability. The most rewarding part was getting to work with an actual team of programmers for the first time, collaborating on a large project.”

The system they built analyzes around 150 variables, using hundreds of logic statements, to create that report.

“In class, the professor gives an assignment with clear directions and limitations on what you can and can’t do,” said junior Tim Kwist. “At Soar, we did essentially the exact opposite. We were given a rather broad goal, with no limitations on what we could or couldn’t do and very limited on instructions. The goal was to get the task done, and get it done the best way we can within a certain time.”

That kind of experience is a valuable part of an engineering degree, said Computer Science and Engineering Professor and department Chair George Bebis. The department encourages students to pursue internship and active learning opportunities, both outside the classroom and through project-based courses such as the senior capstone course, so they gain experience tackling engineering challenges in a real-world setting.

“This opportunity has allowed our students to get hands-on experience by leveraging their programming and math skills,” Bebis said. “We look forward to continue supporting the mission of Soar Biodynamics in this and other exciting projects.”

The team is currently working on integrating the various components they’ve built, and Neville projects that the web application will launch at in January.

Source: University of Nevada, Reno

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