genomeboy.com

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]

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.

I’m not always the biggest Gina Kolata fan, but her piece in this morning’s New York Times is a must-read:

Yet the fight against cancer is going slower than most had hoped, with only small changes in the death rate in the almost 40 years since it began.

One major impediment, scientists agree, is the grant system itself. It has become a sort of jobs program, a way to keep research laboratories going year after year with the understanding that the focus will be on small projects unlikely to take significant steps toward curing cancer.

“These grants are not silly, but they are only likely to produce incremental progress,” said Dr. Robert C. Young, chancellor at Fox Chase Cancer Center in Philadelphia and chairman of the Board of Scientific Advisors, an independent group that makes recommendations to the cancer institute.

“My concern is that [these tests] are being marketed to the public as if there is no question about it,” says Merikangas, speaking generally about direct-to-consumer genomic tests that purport to offer people any truly predictive health advice. “Some people might understand that it is not a death sentence to them, but to others who are struggling, it could lead them not to have children or get married.”

Oy vey. 

The editor-in-chief of a journal is to resign after claiming that the publisher, Bentham Science Publishing, accepted a hoax article for publication without his knowledge.The fake, computer-generated manuscript was submitted to The Open Information Science Journal by Philip Davis, a graduate student in communication sciences at Cornell University in Ithaca, New York, and Kent Anderson, executive director of international business and product development at The New England Journal of Medicine. They produced the paper using software that generates grammatically correct but nonsensical text, and submitted the manuscript under pseudonyms in late January.

Well, now I know what I want for my birthday.