Sequencing in polio, baseball pitching and cancer: sometimes the order of events matters

This piece originally appeared in the Timmerman Report.

What do the polio virus, baseball pitch choice and cancer have in common?

The answer, of course, is sequencing. But not in the “figure out the DNA” way (although that’s involved). Instead in the “what comes first” way. Confused? Read on!

A big perk of Seattle is proximity to great institutions of biomedical research like the University of Washington and the Fred Hutchinson Cancer Research Center. Ever since my graduate student days in genetics at UC-Berkeley I’ve enjoyed going to seminars–especially seminars that are outside my field of study. Very little beats a good seminar for giving you a quick, condensed view of the state of a field of research. A bad seminar…well…we all could use more sleep, right?

In early October, Raul Andino of UCSF came to the Hutch to talk about his work on viral evolution. His team has been examining a clever real-world system to track the evolution of viruses. The near-eradication of polio (one of the great public heath victories of the past century) has led to the curious problem that as of the middle of this year most new cases of polio arose as a result of vaccination efforts. The live, attenuated vaccine that’s used in the developing world can, in very rare cases, mutate in just the wrong ways in its host, leading to the creation of a virulent strain that can infect others. In the US we use an inactivated polio vaccine which requires several injections; in much of the developing world the oral polio virus is preferred due to its ease of administration, lower cost, and immunization profile. The Andino lab realized that by studying these isolated outbreaks, which all originated with the same, genetically identical progenitor, they could test a hypothesis about the adaptive landscape of virulence evolution. Continue reading


Baseball analytics, arthritis, and the search for better health forecasts

All opinions are my own and do not necessarily reflect those of Novo Nordisk.

It’s Fourth of July weekend in Seattle as I write this. Which means it’s overcast. This was predictable, just as it’s predictable that for the two months after July 4th the Pacific Northwest will be beautiful, sunny and warm. Mostly.

Too bad forecasting so many other things–baseball, earthquakes, health outcomes–isn’t nearly as easy. But that doesn’t mean people have given up. There’s a lot to be gained from better forecasting, even if the improvement is just by a little bit.

And so I was eager to see the results from a recent research competition in health forecasting. The challenge, which was organized as a crowdsourcing competition, was to find a classifier for whether and how rheumatoid arthritis (RA) patients will respond to a specific drug treatment. The winning methods are able to predict drug response to a degree significantly better than chance, which is a nice advance over previous research.

And imagine my surprise when I saw that the winning entries also have an algorithmic relationship to tools that have been used for forecasting baseball performance for years.

The best predictor was a first cousin of PECOTA. Continue reading

Gaming to help beat cancer

All opinions my own and do not necessarily reflect those of Novo Nordisk.

Plants versus Zombies 2: It’s About Time just came out.  My son spent a significant fraction of his weekend playing it on my iPad.  Okay, fine, I did too.  It’s a lot of fun, it challenges (but not too much) and it teaches you facts like, uh, like that Egyptian society in the past had a real fascination with pyramids.

So it’s not the most educational of games.

Which is why I was stoked to see the writeup of Re-Mission 2 in FierceBiotechIT.  This game takes elements of cancer treatment and places them in the context of a game that both educates patients undergoing cancer treatment as well as provides them a way to feel more in control of their situation.  Version 2 also builds on the impact of the first Re-Mission game, which showed success in improving adherence of patients to their treatment regimens.  Adherence is an important element of medical treatment and trying to make sure people take their medicines is an ongoing problem as we try to improve the efficiency of our healthcare systems.

In addition to behavioral metrics being changed by Re-Mission, functional Magnetic Resonance Imaging (fMRI) also showed that playing the game activated brain areas associated with motivation–again, tying gameplay to elements of adherence.  Some brain region activations also correlated with subject described positive and improved attitudes towards chemotherapy after gameplay. Continue reading