genomeboy.com

Stephen Quake discusses what he learned from his genome:

FWIW, Quake, co-founder of Helicos, interpreted his sequence using Trait-o-matic, an open-source app developed in the Church lab that I and the rest of the PGP-10 are using to interrogate our genomes and about which I expect to have more to say in the near future.

As Jason notes, filmmaker Marilyn Ness has taken on the unenviable task of making a documentary about the Personal Genome Project. I reckon the only thing crazier would be writing a book about it.  Anyway, I happen to think this webisode in particular captures George Church’s ch’i and his whole family’s remarkable ability to live in the moment. And I think this clip hints at—and I say this with nothing but affection—what unrepentant dorks the ten of us are.

I was fortunate enough to attend the Big Think forum a couple of weeks ago that included a stimulating session on personal genomics. The panel featured population geneticist and grad school pal Tara Matise as well as PGP-10er Esther Dyson, whose 58th birthday was that very day. Check out this cake.

Deoxyribolicious!

As usual, I am pathetically late on this (just throw me the odd crumb, once in a while, dude). A couple of months ago the attorneys at Charlotte-based Robinson, Bradshaw & Hinson, P.A. launched the Genomics Law Report:

The Genomics Law Report focuses on the legal implications of important developments in the fields of genomics and personalized medicine — including key litigation, legislative, regulatory and policymaking activities — in order to facilitate understanding of the complicated and shifting legal landscape governing genomic and personalized medicine commerce and research.

RBH has provided legal services to the Personal Genome Project and one of its attorneys, Dan Vorhaus, helped articulate the PGP’s initial vision for open consent.

Genetic Future has everything you need to know about 23andMe’s foray into genetic research on ten common diseases. Here are what I consider to be the nut grafs:

It’s easy to be cynical about 23andMe’s motives in launching this initiative - this is, after all, a profit-making exercise rather than a research charity - but I suspect that many academics will be watching 23andMe’s progress in this venture with considerable interest. Modern genomics studies require mind-bogglingly large numbers of samples to achieve the power required to find subtle genetic associations, and recruiting those numbers of patients is far from easy. If 23andMe’s model proves successful in recruiting and maintaining large communities of patients, I suspect large academic consortia will at least begin to consider the possibility of pursuing similar approaches.

That actually puts 23andMe in a potentially lucrative position. In order for academic consortia to pursue the 23andMe model, they need to be in a position to return comprehensive results from genome scans to their patients and controls. However, providing such complex information to a lay audience is extremely difficult, and probably beyond the means of most academic groups. That means (as I noted back in March) there’s a potentially massive possible market for 23andMe here in providing a mediation service for returning research data to patients, and for providing the resources required to keep participants engaged actively in the research community.

Ever since 23andMe began shouting from the rooftops that it wanted to do research, there has been more than a little suspicion about what the company was “really” up to. I think Daniel is absolutely right: in the simplest terms, the company believes that there is an unmet need in genetic research (subject ascertainment, data collection, return of results to subjects) that it can begin to help satisfy and in doing so it will generate revenue. Some might argue that there are already perfectly fine mechanisms for informed consent and human subjects research in genetics. GWAS are great! The status quo rocks!

Others, ahem, have a different view.

For those of you in the Raleigh-Durham-Chapel Hill environs, I will be at Tir Na Nog Irish pub tonight in Raleigh for a science cafe sponsored by the North Carolina Museum of Natural Sciences. Here’s some blurb:

Science Cafe: Letting it All Hang Out, The Personal Genome Project
Date: May. 19 - May. 19; 6:30-8:30 pm with discussion beginning at 7 pm followed by Q & A
Location: Other - Tir Na Nog, 218 South Blount Street, Raleigh, 919.833.7795
Fee: Free

Two years ago no one knew what personal genomics was; now it’s everywhere. For a few hundred dollars, you can have a peak at part of your own genome. You can theoretically learn your genetic risks for various diseases. And some companies say you can find romance based on your DNA. But what is all this stuff really? What does it actually mean? What will genomic privacy look like in the digital age? The Harvard-based Personal Genome Project is exploring large-scale DNA sequencing and seeing what happens when genomic data are made public; its organizers hope to help answer some of these questions.

So come on out, have a pint and/or some Irish coffee, and we can talk about 23andMe, exomes ($25,000–yeah baby), privacy and of course, Penguins Hurricanes hockey.

The Personal Genome Project, which recently began the process of expanding its ranks, is founded on the idea of open consent: if you become a participant, there will be no serious attempt made to keep your DNA sequence or phenotypic data confidential. Participants take an exam and must score 100%; they learn the risks before they sign up. Given the almost-daily revelations about performance-enhancing drugs in baseball, might something akin to the PGP’s libertarian/caveat-emptor approach to genomic information be taken with athletes and PEDs? Jere Longman seems to think it might:

If there is anything to be gained from this latest suspension, hopefully it will be a serious debate about whether punishing athletes is justified or selective persecution. Baseball must ask itself whether it is better to continue harsh punitive measures -– which have had unintended consequences in other sports — or to educate athletes about doping and let them proceed at their own informed risk.

I’m not sure what to make of this, but someone emailed last night and said, “…I’m guessing that I’m probably the first person to ever tweet your DNA.”

You are correct, sir!

And since you’ve obviously read my profile, maybe you could send me a business card just in case.

From the unedited Wikipedia discussion page on Harvard psychologist, bestselling author and most importantly, member of the PGP10, Steven Pinker:

• The man was born and raised in Canada and spent a large sum of his life within the nation of Canada (Pinker himself points this within his books). Make mention of it in the article with due respect and be done with it.

“just like we don’t call Henry Kissinger a German statesman or Tolkien a South African author (at most, German-born American statesman or South African-born author), we shouldn’t call Pinker a Canadian… Mikkerpikker.”

• I am at a loss as to this elusive WE!! Wikipedia belongs to the world not one Ameri-centric view point. The foly of the above stated logic is that infact famous people do often get recognised with multiple nationalities, it just depends on what text you refrence (and where the text was published). Alexander Graham Bell is credited as a Scotish, Canadian, and American, inventor of the telephone, regardless of where he was working at the time he created his invention. Sir James Naismith, the inventor of basketball, is credited as both a Canadian, and an American inventor. Following this line of logic, Pinker has invented many theories and can be credited in this method.

• Further, Pinker spent his university days studying experimental psychology at McGill University in Canada this information can be found within any of his recent publications, such as: How the Mind Works, About the author, penguin books, 1999.

• I would appeal to peoples commonsense that it is clearly accepted that a man born, raised, and schooled within a nation is clearly of that nationality in our commonsense use of the word, despite whatever documents he may posses of citizenship at the time. (How else would people be capable of conceptualizing such terms as 2nd or 3rd generation Italian-Canadian.)

• The encyclopedia britannica has decided to call Steven Pinker Canadian-born American.

“At the forefront of cognitive science in 1999 was Canadian-born American experimental psychologist Steven Pinker, who in October published an eagerly anticipated book, Words and Rules: The Ingredients of Language. In a highly praised earlier book, How the Mind Works (1997), Pinker discussed the development of the human brain in terms of natural selection, applying a Darwinian…”[3].

• At the very least it seems fitting to follow in suit with this title. It does not follow that this is to deny Steven Pinkers Canadian-ness, but to recognise it. And as is fitting, he can be cited as both a Canadian and American Professor (as in the above examples of famous people).

• In closing (jestfuly) I must point out that Steven Pinker enjoys the game of Hockey, unofficially that makes anyone 90% Canadian, by default.–Scottmcmaster 10:17, 17 February 2007 (UTC)

Clearly the genotype-phenotype problem continues to dog us. (Who is this elusive “US?!” — ed.)

I’m a bit late on this (anyone who has visited this site knows punctuality is not my forte), but the Personal Genome Project is among the early adopters of the new Creative Commons vehicle for surrendering copyright:

CC0 (read “CC Zero”) is a universal waiver that may be used by anyone wishing to permanently surrender the copyright and database rights they may have in a work, thereby placing it as nearly as possible into the public domain. CC0 is not a license, but a legal tool that improves on the “dedication” function of our existing, U.S.-centric public domain dedication and certification. CC0 is universal in form and may be used throughout the world for any kind of content without adaptation to account for laws in different jurisdictions.

***

Another early adopter of CC0 is the Personal Genome Project, a pioneer in the emerging field of personal genomics technology. The Personal Genome Project is announcing today the release of a large data set containing genomic sequences for ten individuals using CC0, with future planned releases also under CC0. “PersonalGenomes.org is committed to making our research data freely available to the public because we think that is the best way to promote discovery and advance science, and CC0 helps us to state that commitment in a clear and legally accurate way,” said Jason Bobe, Director of Community.