genomeboy.com

In an effort to stop DNA testing on state campuses, a bill was introduced in the California legislature last week that would prevent the University of California system from:

“making an unsolicited request to an enrolled or prospective student of that segment for a DNA sample for the purpose of genetic testing.” It would also require that the universities report how much they are spending on such tests; the schools would then have their funding reduced by that amount.

Keep moving those goalposts, boys and girls. We may not be able to legislate morality, but ignorance is clearly within our grasp.

(hat tip: Dan Vorhaus)

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) 

If you’re like me and you go to way too many scientific and professional meetings, it’s easy to get jaded. I am trying to limit my travel to stuff that 1) I can afford; and 2) actually interests me. One meeting I am totally geeked up for is the Open Science Summit in Berkeley, California from July 29-31, and organized by Joseph Jackson and his merry band of paradigm-shifting partners in crime:

The well known “10/90” gap references the fact that only 10% of biomedical spending goes toward conditions that affect 90% of the world’s population.  Under this regime, “diseases of the poor,” such as malaria, are neglected, while companies focus on “blockbuster” drugs for conditions that affect citizens of the wealthiest nations.  This situation, appalling though it is, actually grossly understates the systemic flaws of the prevailing biomedical innovation paradigm.  Framing this as a tradeoff between Market vs Social Values or the need for balancing commercial interests with public health, implies that the bio-pharma industrial complex works for what it purports to do.  If only we could find some way to engage or tweak existing mechanisms, we’ll make it through.  Wrong! 

There will be sessions on synthetic biology, gene patents, open data/open access, biodefense, microfinance, entrepreneurship, drug discovery, tech transfer, and more. There will be smart, talented and good-looking presenters (and, uh, me). And it’s cheap!

Why am I pimping this so hard? I am supportive of the cause. These are ideas and approaches that are less likely to be embraced by funding agencies and academia (as you will learn in my forthcoming book). I like and respect the organizers and want to see them succeed.

See you in Berzerkeley!

On April 24th and 25th in Cambridge, MA, the Boston Open Source Science Lab will be amplifying and sequencing genes for anyone with 40 bucks.

Together, we’ll use the polymerase chain reaction (PCR) to amplify a fragment of one of your genes and have the DNA sequenced. The event will be part of the Cambridge Science Festival and will run from 12 - 4 pm on April 24th and 25th.

We’re doing it at the bosslab, located at 339R Summer St, Somerville, MA 02144, at Sprout. The cost of materials is $40 / person.

I will provide primers that will enable us to amplify sections of several popular genes. If you have a particular gene of interest, please get in touch…

That sound you hear is hundreds of clinical geneticists’ panties getting in a wad. And maybe a few IP lawyers, too…

See you there, you DIY rascals you!

CAP Today:

Last fall, Beth Israel Deaconess’ pathology residency program became what could be the first in the country to offer training in personalized genomics. The training includes lectures on current genotyping platforms, next-generation sequencing, genetic counseling, and the like, as well as the chance for residents to undergo genetic testing themselves. Dr. Saffitz hopes the training will not only introduce Beth Israel Deaconess’ pathology residents to the world of personal genomics, but also spur pathology residency programs at other institutions to include similar material. “Our goal is within two years to have every pathology residency program in the country incorporating something similar to what we’re doing—and having pathology as a discipline make a very bold and clear statement that we will do this in the future,” he says.

Beth Israel Deaconess’ effort was inspired at least in part by Dr. Boguski’s decision some time ago to have genetic testing performed on himself by three direct-to-consumer companies. “I’m the type of person who learns by doing,” he says. “I decided that rather than criticize this [direct-to-consumer testing] from the point of view of not having done it, I really did owe it to myself to see what was being offered to patients and how they might interpret this data, react to it, et cetera.”

Me, I’d rather criticize things I don’t know about.

Rare genetic variants that cause disease may be masked by common ones that don’t:

Sarah Tishkoff, a geneticist at the University of Pennsylvania in Philadelphia, says “this may make it challenging to identify the functional variant within an association”. Teri Manolio, a population geneticist at the National Human Genome Research Institute in Bethesda, Maryland, writes via email that “if their simulations are correct, and I suspect they are,” they suggest researchers will have to sequence a lot of DNA, up to 10 million bases, surrounding common variants.

Goldstein says that the work suggests more whole-genome sequencing will be needed in more targeted populations of affected individuals and families. In a sense, he says the issues being raised signal the need for shift from the powerful statistics of GWA studies to work more focused on specific genes in affected families and how they function biologically. As Goldstein puts it, “the importance of the family has really come back again.”

 To do:

1) Read it and weep

2) Buy stock in sequencing companies

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.

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.

If they had wi-fi, I’d be on the first spaceship out of town:

If it sounds unrealistic to suggest that astronauts would be willing to leave home never to return alive, then consider the results of several informal surveys I and several colleagues have conducted recently. One of my peers in Arizona recently accompanied a group of scientists and engineers from the Jet Propulsion Laboratory on a geological field trip. During the day, he asked how many would be willing to go on a one-way mission into space. Every member of the group raised his hand. The lure of space travel remains intoxicating for a generation brought up on “Star Trek” and “Star Wars.”

The standard treatment for infection with the hepatitis C virus is a grueling 48-week course of the antiviral drugs interferon and ribavirin that gives some patients flulike symptoms and severe depression. The treatment varies in its effectiveness, being much more successful in Americans of European descent than in African-Americans.A Duke University team has now uncovered the principal reason for the disparity between the races. It lies not in differing compliance to the treatment or access to health care, as some have assumed, but in genetics.Using a genetic test called a genome-wide association study, the Duke team, led by David B. Goldstein and John McHutchison, found that the coding at a single site on the DNA, out of the three billion sites in the human genome, made all the difference in people’s response to the treatment.

I suppose it’s all about what questions one chooses to ask.

[Hat tip: Linda]