One girl, one exome

By Razib Khan | October 22, 2012 12:22 am

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.

CATEGORIZED UNDER: Personal Genomics
  • John Emerson

    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.

    I hope that this is true for all fields. The academic monopoly has had a number of harmful effects in many areas.

  • zach

    the problem I see with this and the DIY approach is that the scientist’s family isn’t going to be a big enough n for most association metrics and, for many applications, the covariation due to relatedness will possibly obscure learning, not enhance it.

    What are your thoughts on this: do DIY geneticists have the kind of data available to get the most of their statistics?

  • Razib Khan

    #2, in this case i obviously wasn’t talking about GWAS. i think one of the ‘low hanging’ near term fruit with mass adoption of 100x coverage may be a better understanding of individual mutational load. re: GWAS, etc., the sample sizes are way too small. see openSNP for testament to that. but they won’t be (and 23andMe is trying to really scale this up). platform matters, but so does cost so that the data pipeline gets fat. talk to me in 2-3 years. there are firms working on this sort of thing….


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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