genomeboy.com

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) 

Some days it still feels like September 12, 2001:

Millions of Americans arrested for but not convicted of crimes will likely have their DNA forcibly extracted and added to a national database, according to a bill approved by the U.S. House of Representatives on Tuesday.

By a 357 to 32 vote, the House approved legislation that will pay state governments to require DNA samples, which could mean drawing blood with a needle, from adults “arrested for” certain serious crimes. Not one Democrat voted against the database measure, which would hand out about $75 million to states that agree to make such testing mandatory.

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House Speaker Nancy Pelosi and the Democratic leadership scheduled Tuesday’s debate on the bill–called the Katie Sepich Enhanced DNA Collection Act of 2010–using a procedure known as the “suspension calendar” intended to be reserved for non-controversial legislation.

“Suspension of the rules is supposed to be for praising the winner of the NCAA championship or renaming Post Offices,” Harper says. “Things like collecting Americans’ DNA are supposed to be fully debated in Congress.”

(hat tip: Jenny Reardon)

“So, Mr. Public Genome, why aren’t you on Facebook already?”

“Oh, I don’t know. Just because.”

Dan Vorhaus has written his usual cogent and insightful review of the issues raised by Amy Harmon’s piece on the Havasupai tribe and its settlement with Arizona State University. In my view, the core of the matter is fairly simple:

“I’m not against scientific research,” said Carletta Tilousi, 39, a member of the Havasupai tribal council. “I just want it to be done right. They used our blood for all these studies, people got degrees and grants, and they never asked our permission.” [emphasis added]

If, as researchers, we can’t be bothered to 1) tell research participants what they’re getting into insofar as we know; 2) respect their cultural beliefs; 3) go back to them if our plans change and ask for their consent again; and 4) share with them what we find and what we think it means in a timely and ongoing fashion, then we will find human subjects increasingly hard to come by…and increasingly litigious.

CNN:

Many parents don’t realize their baby’s DNA is being stored in a government lab, but sometimes when they find out, as the Browns did, they take action. Parents in Texas, and Minnesota have filed lawsuits, and these parents’ concerns are sparking a new debate about whether it’s appropriate for a baby’s genetic blueprint to be in the government’s possession.

“We were appalled when we found out,” says Brown, who’s a registered nurse. “Why do they need to store my baby’s DNA indefinitely? Something on there could affect her ability to get a job later on, or get health insurance.”

Just wait until they get hold of baby’s email.

(Hat tip)

At Nature News, there is something of a eulogy/finger-pointing festival for deCODE and indeed, for personal genomics in general:

…Some other researchers, however, say that deCODE’s scientific approach is to blame. The company worked to mine genetic data for common variations linked to disease through genome-wide association studies (GWAS), and some experts note that these studies have turned up only a small fraction of the variation that causes disease. “The translation to commercial value is just not very direct,” says [Duke’s David] Goldstein, “in part because it is now clear that GWAS is not the tool of choice for unlocking the genetics of most common diseases.”

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…companies that focus exclusively on personal genomics services, such as the one sold by deCODE as deCODEme, might find themselves in more trouble, [Leerink Swann’s Isaac] Ro says. The services are not seen as a medical necessity, diminishing their appeal, particularly in difficult economic times. This year the personal-genomics company 23andMe, based in Mountain View, California, announced two rounds of lay-offs, lost one of its two co-founders and announced a series of product and price restructurings.

“There’s no clinical trial supporting the value of these results, so it’s really recreational genomics,” Ro says. Large academic centres, not consumers, will find value in the rich genetic databases; 23andMe has tried to move into the research market, but because its data come from a self-selected customer population their value is limited, he says.

Here we go, still trotting out the same tired tropes. I agree: GWAS is of limited value and this probably contributed to deCODE’s demise. But whatever deCODE’s fate, if whole human genomes can be sequenced for < $2000, isn’t it about time we stopped kicking GWAS’s ever-stiffening corpse?  Second, just because something is not a medical necessity, does it follow that it is worthless? Ask the participants in the REVEAL study or anyone else who’s received an APOE genotype because she WANTED to know. Ask the people who learned something about their hereditary breast cancer risk from 23andMe. Is that recreation? What about abacavir hypersensitivity? And finally:  yes, DTC genomics customers are self-selected. So are the 50,000 PatientsLikeMe participants. So are the 10,000 in the Coriell Personalized Medicine Collaborative. So are the 15,000 on the Personal Genome Project waiting list. So are the 400,000 in the UK Biobank. Maybe we should just toss out all of that data, too.

From a compelling story in the New York Times Magazine:

In an age of DNA, when biological relationships can be identified with certainty, it can seem absurd to hew so closely to a centuries-old idea of paternity. And yet basing paternity decisions solely on genetics places the nonbiological father’s welfare above the child’s. Phil Reilly, a lawyer who is also a clinical geneticist, has been wrestling with the policy implications of DNA testing for years, and even he is stumped about how society should manage the problem that men like Mike face. “We’re at a point in our society where the DNA molecule is ascendant, and it’s very much in the public’s consciousness that this is a powerful way to identify relationships,” Reilly says. “Yet at the same time, more people than ever are adopting children, showing that parents can very much love a child who is not their own. The difference here for many men is the combination of hurt and rage over the deceit, the fact that they’re twice beaten. I can see both sides of this argument. As a nation, we’re still in search of what the most ethical policy should be. Every solution is imperfect.”

The Personal Genome Project includes disclosure of nonpaternity as one of the explicit risks of participation. That said, having been warned is probably not much consolation to people who discover certain surprising things about their families.

Given the Halloween season, this story seems appropriate somehow:

A report in 2007 by the lobbying group Privacy International placed Britain in the bottom five countries for its record on privacy and surveillance, on a par with Singapore.

But the intrusions visited on Jenny Paton, a 40-year-old mother of three, were startling just the same. Suspecting Ms. Paton of falsifying her address to get her daughter into the neighborhood school, local officials here began a covert surveillance operation. They obtained her telephone billing records. And for more than three weeks in 2008, an officer from the Poole education department secretly followed her, noting on a log the movements of the “female and three children” and the “target vehicle” (that would be Ms. Paton, her daughters and their car).

From the HIPAA, SHMIPAA files:

A new survey of medical-school deans finds that unprofessional conduct on blogs and social-networking sites is common among medical students. Although med students fully understand patient-confidentiality laws and are indoctrinated in the high ethical standards to which their white-coated profession is held, many of them still use Facebook, YouTube, Twitter, Flickr and other sites to depict and discuss lewd behavior and sexual misconduct, make discriminatory statements and discuss patient cases in violation of confidentiality laws, according to the survey, which was published this week in the Journal of the American Medical Association.

From “ESPN’S ADDITIONAL GUIDELINES FOR SOCIAL NETWORKING”:

• Personal websites and blogs that contain sports content are not permitted
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