genomeboy.com

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

Not only can the past never really be erased; it co-exists, in cyberspace, with the present, and an important type of context is destroyed. This is one reason that intellectual inflexibility has become such a hallmark of modern political discourse, and why, so often, no distinction is recognized between hypocrisy and changing your mind.

- Jonathan Dee in the New York Times Magazine, 24 January 2010

As he strikes out on his own at Duke, Ge is interested in developing software packages to detect these genetic contributions to human diseases. When looking through sequencing data, he says there are a lot of questions to answer for each SNP: does it cause a premature stop? A frame shift? Does it disrupt the normal gene function? “Now, to answer that question may not be so difficult when you look at them individually, just browsing NCBI Genome Browser or [another] genome browser, but it is if you look at millions,” Ge says. He developed a package called the Sequence Variant Analyzer that allows users to annotate variations uncovered through whole genome sequencing and compare them to control genomes.

Dongliang is one of many who have helped me begin to navigate my own genome. People like him and the developers of Trait-o-matic are pushing enormous rocks up steep hills so our children won’t have to.

The New York Times talks to literary theorist Terry Castle:

What are the latest trends in academia? Is poststructuralist theory dead yet?
Well, it carries on in its zombielike, jargon-ridden way here and there. But it’s on the wane. The smartest literary scholars right now are interested in evolutionary psychology and brain science — how we may be hard-wired for fiction-making, aesthetic appreciation and the like.

Is that a good development? How do you feel about seeing the adventure of life reduced to a function of DNA?
I guess I’m down with it because I’ve always felt, for instance, that my own lesbianism was genetic. My cousin, whom I was just visiting in London, we have the same DNA, and we’re both big, old dykes.

Um…you go girl?

Watch for a quick shot of the Personal Genome Project’s Joe Thakuria at 0:04.

Sequencing the genome yields information that is fantastically important, but it does not tell you the exact location of the gene and most importantly what function is specified by the gene or by a mutated disease causing gene. I can understand why one should not be allowed to patent DNA without having any knowledge about its function, but an isolated DNA where the function of its products has been determined is a different story - here, an invention has been made. Moreover, if you figure out a direct link or an association between a gene sequence and a cause for or if you figure out the correlations or associations between a gene sequence and an increased risk for a specific disease, this discovery can be used to develop diagnostics and drugs that help people. I do not see any reason why a patent should not be awarded for such inventions.

- From the Declaration of Joseph Schlessinger, PhD, 21 December 2009

…without the promise of a period of market exclusivity provided by patents and the infusion of  venture and risk capital derived therefrom, companies that capitalize on innovation simply would not be created. Their products would not be brought to market, to the clinic, and most importantly, to patients. This of course, holds true for companies such as Myriad and its BRCA1/2 diagnostic tests.

- From the Declaration of Philip R. Reilly, MD, JD, 21 December 2009

Association For Molecular Pathology et al v. United States Patent and Trademark Office et al UNITED STATES DISTRICT COURT FOR THE SOUTHERN DISTRICT OF NEW YORK, Robert W. Sweet, presiding

Stephen Asma:

Feeling unworthy is still a large part of Western religious culture, but many people, especially in multicultural urban centers, are less religious. There are still those who believe that God is watching them and judging them, so their feelings of guilt and moral indignation are couched in the traditional theological furniture. But increasing numbers in the middle and upper classes identify themselves as being secular or perhaps “spiritual” rather than religious.

Now the secular world still has to make sense out of its own invisible, psychological drama—in particular, its feelings of guilt and indignation. Environmentalism, as a substitute for religion, has come to the rescue. Nietzsche’s argument about an ideal God and guilt can be replicated in a new form: We need a belief in a pristine environment because we need to be cruel to ourselves as inferior beings, and we need that because we have these aggressive instincts that cannot be let out.

You can’t make this stuff up.

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)