One girl, one exome

Interesting story in The San Jose Mercury News, Open-source science helps San Carlos father’s genetic quest:

“We used materials that are public, freely available,” said Rienhoff, a physician and scientist, as Beatrice frolicked nearby. “And everything we’ve learned we’ve put back out there, in the public domain. It’s for the patient’s good, and the public good.”

Born with small, weak muscles, long feet and curled fingers, Beatrice confounded all the experts.

No one else in her family had such a syndrome. In fact, apparently no one else in the world did either.

Rienhoff — a biotech consultant trained in math, medicine and genetics at Harvard, Johns Hopkins and the Fred Hutchinson Cancer Research Center in Seattle — launched a search.

He combed the publicly available medical literature, researching diseases, while jotting down each new clue or theory. Because her ailment is so rare, he knew no big labs or advocacy groups would be interested.

In the end, basically he compared his daughter’s exome to that of everyone else in the family. By comparing in such a fashion he managed to zero in on a possible causal mutation. This is awesome (the fact that now they know, not the mutation itself). In the near future (~2 years) I plan to have everyone in my daughter’s pedigree sequenced to a high degree of accuracy so that I can trace with precision the sequence of de novo mutations which make each individual distinctive. Not only that, but it may be useful in the future in assessing possible disease risks unique to a given individual.

Hugh Reinhoff told his story at the Open Science Summit. I don’t think open and DIY science is going to be the whole future, but it is going to be a substantial part of the future. There are just some things that you as an individual have strong incentives to do which you can’t get others interested in. Additionally, collaborative open source science is probably one major push on the margins to make those selling services be more professional and add genuine value. If any reader in the Valley is excited about this sort of project you might want to contact Joseph Jackson. He’s got a lot of ideas and enthusiasm, and is genuinely interested in making a difference in peoples’ lives with a new “bottom-up” paradigm. I’m normally skeptical of such populism, but I’m not entirely happy with the status quo, so a shake up might do science some good.

Source: Discover Magazine – Gene Expression