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.

What’s the story behind your blog’s name?

When I told a friend I was getting my genome sequenced, she said, “Why you? What makes you so special, Genome Boy?” I thought that was funny.

What do you think the greatest challenges will be for individuals in the future, as the technology makes accessing personal genomes more affordable?

There will be many. One will be logistical: How do we manage all of this data about ourselves? Another will be learning to think probabilistically: What does it mean to have a 35 percent lifetime risk of Type 2 diabetes? This gets at a larger question: How do we retrain ourselves not to view genes as destiny? They’re clearly not - we are incredibly complex creatures affected by thousands of genes and an infinite number of environmental stimuli. But that’s a hard sell, and as a consequence, genes have been marketed as destiny. We have to get beyond that.

The GET Conference 2010 marks the last chance in history to collect everyone with a personal genome sequence on the same stage to share their experiences and discuss the important ways in which personal genomes will affect all of our lives in the coming years.

Tickets are pricey. This is a (long overdue, IMHO) fundraiser for PersonalGenomes.org:

We foresee a day when many individuals will want to get their own genome sequenced so that they may use this information to understand such things as their individual risk profiles for disease, their physical and biological characteristics, and their personal ancestries. To get to this point will require a critical mass of interested users, tools for obtaining and interpreting genome information, and supportive policy, research, and service communities.

Four indigenous Namibian hunter-gatherers !Gubi, G/aq’o, D#kgao and !A?ˆ (referred to here as KB1, NB1, TK1 and MD8, respectively), each the eldest member of his community, were chosen for genome sequencing based on their linguistic group, geographical location and Y chromosome haplogroup representation (Fig. 1 and Supplementary Table 1). The Bantu individual is Archbishop Desmond Tutu (ABT), who represents Sotho-Tswana and Nguni speakers (from the broad Niger–Congo languages), the two largest southern African Bantu groups.

The importance of this paper, IMHO, is that these are the genomes of five identifiable Africans. Their photos appear in the manuscript.  If only everyone who’d been sequenced actually knew about it…

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)

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

For those few of you who are not regular readers of the European Journal of Clinical Investigation, I call your attention to the current issue. It features a debate between those who believe genetic risk information ought to be available to anyone with $985 who wants it, and paternalistic men in white coats defending the status quo those who believe it ought to be vetted by randomized clinical trials.

Gulcher and Stefansson:

The man who knows the nature of his disease is more likely to seek appropriate help to treat it and by the same logic, a man who knows the risk he has of developing a disease is more likely to seek help to mitigate the risk. It is also important to recognize that by learning about the genetic risk you have of diseases, you are simply learning certain aspects about who you are.

Ransohoff and Khoury:

If [randomized clinical trial] data are considered necessary to understand benefits vs. harms for a particular application, then so be it…RCTs may be needed indeed, unless we can be satisfied that the new test detects the same spectrum and subtype of disease as the old test and that intervention response is similar across the spectrum of disease [27]. These principles need to be applied, on a case-by-case basis, to personal genomic tests.

Okay then. We’ll see y’all in about eight years.

(Hat tip: Dana Waring)

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.

deCODEme is offering 23andMe customers free uploads to its site. Daniel has details and analysis:

So, why the free offer? I’m guessing deCODEme is gambling (quite reasonably) that offering free uploads will attract a non-trivial number of 23andMe customers over to deCODEme’s interface. That then provides the Icelanders with an opportunity to give people a fair trial of their own interface, and hopefully to impress them with the quality and accessibility of the data provided.

What then? Well, bear in mind that the entire chip-based personal genomics industry is really just a transient place-holder for the real deal: interpretation of complete genome sequences. All of the personal genomics companies currently out there are simply positioning themselves for a share of the potentially enormous sequencing interpretation market that will emerge within the next couple of years as the cost of DNA sequencing plummets.

It’s therefore crucial for deCODEme to place itself in the minds of likely early adopters of sequencing products as a serious and reliable player in the interpretation field. Right now it’s failing to do that, due to the extraordinary market dominance of 23andMe - but pulling over customers with this free offer will help.

I’m ready for the “potentially enormous sequencing interpretation market” to emerge anytime now…