genomeboy.com

GenomeBoy has moved. I have joined a fantastic new network of science bloggers. This blog will now lie fallow. Please come visit me here and check out my amazing colleagues in the PLoS Blogosphere.

This month, PLoS Genetics is publishing an article from the company 23andMe reporting the first genome-wide association studies (GWAS) on multiple traits ascertained by self-reported information provided through the Internet from over 10,000 participants who pay the company for providing whole genome genotypes [1]. The paper passed through scientific review by a panel of three experts relatively quickly and is sure to attract the attention of anyone with freckles, curly hair, or an aversion to asparagus. Novel associations are described for four intrinsically interesting traits (out of 22 considered), while known associations with hair and eye color are replicated in a dynamic data-gathering context. Additionally, intriguing observations on the interaction between genetic self-knowledge and self-report of phenotypes are described. The implications of the successful application of this Internet-enabled approach to GWAS research were considered to be more than sufficient to warrant publication in the journal.

 

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The editors of PLoS Genetics recognize that the decision to publish this study, without IRB review as human subjects research and with some concerns over the consent document, and the fact that there is limited access to the raw data, will not sit well with some, perhaps many, readers. As outlined above, though, a prima facie valid IRB exemption was obtained, and, while there are ambiguities in the consent form, there was no evidence that these amount to an inadequate document. After considering all of the evidence, we decided that publication, accompanied by an editorial providing transparent documentation of the process of consideration, was the most appropriate course.

Seems like this Interwebs thing might be starting to catch on.

(Hat tip: the indefatigable Bora Z) 

 UPDATE: full episode is here.

Don’t miss Rebecca Skloot tonight on the Colbert Report. Extra special guest: The BioBus!

I put down Rebecca Skloot’s first book, “The Immortal Life of Henrietta Lacks,” more than once. Ten times, probably. Once to poke the fire. Once to silence a pinging BlackBerry. And eight times to chase my wife and assorted visitors around the house, to tell them I was holding one of the most graceful and moving nonfiction books I’ve read in a very long time.

Hear hear! Listen to her on Fresh Air. Go see Rebecca. Buy the book. Give to the foundation. Get the action figure. Read the book!

As he strikes out on his own at Duke, Ge is interested in developing software packages to detect these genetic contributions to human diseases. When looking through sequencing data, he says there are a lot of questions to answer for each SNP: does it cause a premature stop? A frame shift? Does it disrupt the normal gene function? “Now, to answer that question may not be so difficult when you look at them individually, just browsing NCBI Genome Browser or [another] genome browser, but it is if you look at millions,” Ge says. He developed a package called the Sequence Variant Analyzer that allows users to annotate variations uncovered through whole genome sequencing and compare them to control genomes.

Dongliang is one of many who have helped me begin to navigate my own genome. People like him and the developers of Trait-o-matic are pushing enormous rocks up steep hills so our children won’t have to.

Jason Bobe, DIYBio co-founder and Personal Genome Project Director of Community, on NPR:

RAZ: And so, are most of the people who are sort of these citizen scientists, I mean, are they actual scientists, or are they amateurs?

Mr. BOBE: It’s actually a wide range of different types of people. There are quite a few graduate students and professional scientists who moonlight as a citizen scientist. And we’re actually starting to see groups in various cities setting up laboratory space that’s a shared laboratory. They sort of pull their resources like clay potters have done with kilns or woodworkers have done with expensive lathes.

Listen to all of it here.

Mazel tov to the chromosome-centric Nobelists:

Greider, 48, said she was telephoned by just before 5 a.m. her time with the news that she had won.

”It’s really very thrilling, it’s something you can’t expect,” she told The Associated Press by telephone.

People might make predictions of who might win, but one never expects it, she said, adding that ”It’s like the Monty Python sketch, ‘Nobody expects the Spanish Inquisition!”’

23andMe co-founder Linda Avey is leaving for the nonprofit world:

I’ve decided that I’d like to focus my efforts on an area that is personally significant and will continue to have a huge impact on our healthcare system–Alzheimer’s disease. Effective today, I’m leaving 23andMe and have begun making plans for the creation of a foundation dedicated to the study of this disorder. The foundation will leverage the research platform we’ve built at 23andMe–the goal is to drive the formation of the world’s largest community of individuals with a family history of Alzheimer’s, empower them with their genetic information and track their brain health using state-of-the-art tools. We’ve always planned to include Alzheimer’s in our 23andWe research mission…I’m just approaching it from a new angle.

Some of you might be aware that my father-in-law suffered from Alzheimer’s and passed away last year. For this reason, Randy and I are motivated to do what we can to improve the understanding of what leads to the debilitating symptoms and what might prevent them from starting in the first place. The ApoE4 association is barely understood but gives us a great starting point.

More details here. Speaking personally, even when we’ve disagreed, for as long as I’ve known her, Linda has been nothing but gracious to me and incredibly generous with her time. I wish her the best and have every expectation she will succeed at whatever she puts her mind to.

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.

My older brother, with whom I share 50% of my DNA*, gets his book pimped in today’s New York Times:

I’ve been reading a truly excellent book by Joshua Angrist and Jorn-Steffen Pischke called Mostly Harmless Econometrics: An Empiricist’s Companion. It’s not written for a general audience, but if you pulled an A- or better on a college-level econometrics course (and if you love Freakonomics), then this is the book for you.

It makes a swell gift, too.

*as far as I know anyway…oh Mom, you little minx