Hacking Rare Disease

As a teenager, Bill Paseman worked with his father in the refineries around the Houston area. He remembers remarking to him at the time that a lot of people working in those jobs seemed to die young from kidney cancer.

Paseman won acceptance to MIT, which carried him far away from life in the oil fields and refineries in Texas and became a successful tech entrepreneur. But when he was diagnosed with kidney cancer forty years after working in the oil industry, he says he felt stupid and angry with himself. “I had made a perfect prediction 40 years out and still I was blindsided.”

Paseman’s kidney cancer was a rare form known as papillary kidney cancer. While doctors have an established treatment regimen for most cases of kidney cancer, there’s no standard of care for papillary kidney cancer. One of Paseman’s kidneys with the cancer was removed and he was told he was clear of cancer but faced a high chance of recurrence. An adjacent lymph node was clear, but he has spots on his lungs that haven’t grown. He also has a brain hemangioma that hasn’t grown. His remaining kidney is functioning, but he is regularly scanned to look for signs of the cancer’s return.

Without available treatments and with a good bet his cancer will be back, Paseman last month made his medical condition the topic of a hackathon in San Francisco organized by RareKidneyCancer.org, a group he founded, and the nonprofit Silicon Valley Artificial Intelligence. It was the second rare disease hackathon SVAI hosted, part of its effort to advance the convergence of computer sciences and the life sciences.

“If you want people with rare disease to have a shot at getting research done, one way to do that is to do pan cancer research—look at their condition in the context of other more common conditions and look at those in parallel,” he said. “By doing pan cancer analysis, looking at all of these rare diseases next to each other with other diseases that are out there, we have a shot of holding hands and trying to solve all these problems at once.”

Paseman had attended the first hackathon that SVAI had done, which focused on a patient with a rare disease known as neurofibromatosis type 2 tumor. At the end of that event, when the discussion turned to a next case to pursue, Paseman volunteered himself as the subject for the second one.

“It’s inevitable as more and more data are being built biologically it needs more and more in depth and complicated analysis. On the computer science side, there’s a huge interest in biological data, but there’s not necessarily a lot of exposure to it,” said Peter Kane, founder of SVAI. “We are principally working on bringing these two groups together to help the industry form in that vein.”

The hackathon brought together 19 teams of about 150 researchers from several top academic institutions across the country and internationally. A few groups worked remotely during the weekend-long event. The event also had support from Salesforce, Google, the National Institutes of Health and the National Center for Biotechnology Information. The hope was to understand Paseman’s tumor in relation to other cases of papillary kidney cancer, as well as all other cancers through use of the National Institutes of Health’s Cancer Genome Atlas.

“Hackathon’s not the correct term to describe what we did. It’s what we’ve been using because we haven’t come up with a better term yet,” said SVAI’s Kane. “The general sense of what’s going on is that there’s a bunch of people coming together for a weekend to quickly iterate on a problem. It’s a very good opportunity to pull together in a weekend format and see what insights could be generated.”

The researchers in the room were not only seeking potential targets to treat papillary kidney cancer, but also understand how Paseman’s cancer might return in a mutated form, how such mutations might progress, and potential targets for which existing treatments might be effective against those anticipated mutations.

The weekend generated plenty of ideas, but the hackathon was really just a starting point. At least five of the research groups that participated in the event are continuing work on issues that emerged from the weekend. Among those efforts are such things as pursuing the question of clonal mutations in this type of cancer, working on identifying biomarkers for the condition, and an effort to clean up the data from Paseman’s tumor and DNA to make it more usable for other researchers.

There are several lessons here on how to engage researchers in doing work on rare diseases, but one of the most important ones is the need for having available data for researchers to use and the role that can play in attracting their attention.

“I’m rare. I’m terminal. I’m incurable. And I’m 63. For me, HIPAA isn’t that big a deal. I’m taking my DNA, my blood, and my tumor and publishing them,” said Paseman. “If other rare cancer patients can make their tumor data and their blood data public, we’d have all of this out there that researchers can concentrate on that’s no longer sitting behind a fire wall or a paywall. Everybody would be paying attention to the rare diseases because they could get at the public data.”

June 11, 2018
Photo Bill Paseman, founder Rarekidneycancer.org