genomeboy.com

Pretty soon I’m gonna get indoor plumbing…

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…

ScienceDaily (Feb. 12, 2010) — Just because you don’t swallow the worm at the bottom of a bottle of mescal doesn’t mean you have avoided the essential worminess of the potent Mexican liquor, according to scientists from the Biodiversity Institute of Ontario (BIO) at the University of Guelph.

They have discovered that the liquid itself contains the DNA of the agave butterfly caterpillar — the famously tasty mescal “worm.”

***

“Showing that the DNA of a preserved specimen can be extracted from the preservative liquid introduces a range of important possibilities,” said Dr. Mehrdad Hajibaebi, a member of the research team. “We can develop inexpensive, high-throughput and non-invasive genetic analysis protocols for situations where the original tissue cannot be touched or when there is simply no sample left for analysis.”

The awesome Susan Orlean on mules (subscription):

The mule’s commitment to survival is interesting in a Darwinian context, because mules–the hybrid result of mating a male donkey with a female horse–have an uneven number of chromosomes and are therefore sterile. Every mule, then, is sui generis; it leaves no legacy beyond itself, no radiating gene pool to mark its visit to this world…Even the sheer persistence of the breed seems a stroke of genius. Since a horse and a donkey rarely mate on their own, mules are essentially man-made. It has been a successful invention–in fact, mules are probably the most successful and enduring animal hybrid, with beefalo coming in a distant second.

Jerome Groopman offers a withering assessment of comparative effectiveness research:

There is a growing awareness among researchers, including advocates of quality measures, that past efforts to standardize and broadly mandate “best practices” were scientifically misconceived. Dr. Carolyn Clancy of the Agency for Healthcare Research and Quality, the federal body that establishes quality measures, acknowledged that clinical trials yield averages that often do not reflect the “real world” of individual patients, particularly those with multiple medical conditions. Nor do current findings on best practices take into account changes in an illness as it evolves over time. Tight control of blood sugar may help some diabetics, but not others. Such control may be prudent at one stage of the malady and not at a later stage. For years, the standards for treatment of the disease were blind to this clinical reality.^[7]

Orszag’s mandates not only ignore such conceptual concerns but also raise ethical dilemmas. Should physicians and hospitals receive refunds after they have suffered financial penalties for deviating from mistaken quality measures? Should public apologies be made for incorrect reports from government sources informing the public that certain doctors or hospitals were not providing “quality care” when they actually were? Should a physician who is skeptical about a mandated “best practice” inform the patient of his opinion? To aggressively implement a presumed but still unproven “best practice” is essentially a clinical experiment. Should the patient sign an informed consent document before he receives the treatment? Should every patient who is treated by a questionable “best practice” be told that there are credible experts who disagree with the guideline?

Amen, Jerry. CER may be well on its way to becoming the “No Child Left Behind” of health care. “Let’s create some immutable standards, wield them like a sledgehammer, and then declare victory!”

Doctors are pooh-poohing personal genomics. Yet they would put their faith in behavioral economics? Talk about going “off label”…

Words fail:

The authorities do not know exactly how many people have been killed warbling “My Way” in karaoke bars over the years in the Philippines, or how many fatal fights it has fueled. But the news media have recorded at least half a dozen victims in the past decade and includes them in a subcategory of crime dubbed the “My Way Killings.”

The killings have produced urban legends about the song and left Filipinos groping for answers. Are the killings the natural byproduct of the country’s culture of violence, drinking and machismo? Or is there something inherently sinister in the song?

The Lancet has retracted a 1998 paper linking the Mumps-Measles-Rubella vaccine to autism. The journal’s editor spoke to On the Media this week.