genomeboy.com

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.

My older brother, with whom I share 50% of my DNA*, gets his book pimped in today’s New York Times:

I’ve been reading a truly excellent book by Joshua Angrist and Jorn-Steffen Pischke called Mostly Harmless Econometrics: An Empiricist’s Companion. It’s not written for a general audience, but if you pulled an A- or better on a college-level econometrics course (and if you love Freakonomics), then this is the book for you.

It makes a swell gift, too.

*as far as I know anyway…oh Mom, you little minx

For those of you in the Raleigh-Durham-Chapel Hill environs, I will be at Tir Na Nog Irish pub tonight in Raleigh for a science cafe sponsored by the North Carolina Museum of Natural Sciences. Here’s some blurb:

Science Cafe: Letting it All Hang Out, The Personal Genome Project
Date: May. 19 - May. 19; 6:30-8:30 pm with discussion beginning at 7 pm followed by Q & A
Location: Other - Tir Na Nog, 218 South Blount Street, Raleigh, 919.833.7795
Fee: Free

Two years ago no one knew what personal genomics was; now it’s everywhere. For a few hundred dollars, you can have a peak at part of your own genome. You can theoretically learn your genetic risks for various diseases. And some companies say you can find romance based on your DNA. But what is all this stuff really? What does it actually mean? What will genomic privacy look like in the digital age? The Harvard-based Personal Genome Project is exploring large-scale DNA sequencing and seeing what happens when genomic data are made public; its organizers hope to help answer some of these questions.

So come on out, have a pint and/or some Irish coffee, and we can talk about 23andMe, exomes ($25,000–yeah baby), privacy and of course, Penguins Hurricanes hockey.

Misha Angrist, an assistant professor at the Institute for Genome Sciences and Policy at Duke University, completed his graduate studies with Chakravarti working on the genetic basis of Hirschsprung’s disease. Angrist remembers his mentor as an idea man above all else. “In the 1990s, I used to walk into Aravinda’s office and he’d be sitting there chain smoking and he’d have a yellow pad of paper in front of him and a pencil and he would sit there and…using only his own gray matter, solve a problem [in] population genetics, with no computer and no massive datasets,” Angrist says. “So he comes from this very pure intellectual tradition in genetics.”

I was extremely fortunate to have seven years in the Chakravarti lab, even if I didn’t always appreciate the experience at the time. Read the rest of the tribute to Aravinda here.

Peter Dizikes has a wonderfully nuanced article about genomic privacy in Salon (which I remember reading back when it was run by three people in their basement with an Apple II). The piece features quotes from Linda Avey, Amy DuRoss, Blaine Bettinger (a law student! who knew?), and yours truly, among others. My favorite is from the always pithy and thoughtful Hank Greely:

This is the seeming paradox of DNA: The better we understand our genes, the less important we might find them. “People believe in the magic of genes, and buy into the idea that they are the deepest secrets of our being,” Greely says. “Whereas maybe my credit card records come closer to being a deep secret of my being.”

James P. Evans, a genetics professor at UNC-Chapel Hill, cautions against making too much of genetic information.

Even if Angrist or one of his fellow participants learns he has the gene for a horrible disease. that is far from a guarantee that the disease will ever occur, Evans said. Even in a larger group of donors, Evans said, it would be difficult to make solid medical decisions based on what DNA shows. A woman whose DNA suggests future breast cancer, for example, shouldn’t necessarily run out and get a mastectomy.

“The information one gets is virtually all probabilistic; it’s not actionable information, medically,” he said. “To me, the biggest danger is that its utility will be exaggerated because people put this mystical value on DNA.”

As usual, Dr. Evans is absolutely right.

I appreciate the reporter’s hard work and I like the story, but I would offer a few corrections/clarifications:

• “Americans are notoriously hung up on privacy, and I get that,” he said. “[But] I don’t think that information is toxic.” That is an accurate quote, but that doesn’t mean I think we should all walk around naked or read each other’s mail.
• “When you make everyone anonymous, you impoverish the data,” he said. “You may have that person’s DNA, but you don’t have a name or a lot of the details that you may want someday.” Again, accurate, but I shouldn’t have emphasized names. I should have said that re-contacting research participants is important and you can’t do that when you sever the link.
• Since then, two pioneers in the field, James Watson and J. Craig Venter, allowed their DNA to be totally decoded and made public.  At the risk of nitpicking, Watson wanted his genotype at the Alzheimer’s risk gene APOE redacted. Alas, it couldn’t be done.
• In Angrist’s case, DNA was taken from a graft of his skin and mechanically sheared into smaller pieces; it will be put through a complicated, multistep process until the sequence is determined. Angrist’s DNA sample was taken in late October, and he hopes to have his genome sequence information within weeks. Actually, my genome sequence will be determined from white blood cells I donated in 2007. My skin cells will be used to create a cell line that is stem-cell-like.
• A native of Pittsburgh, he came to Duke in 2003 and works primarily in the areas of intellectual property and gene patenting. While it certainly feels that way at the moment, I’d like to think my work encompasses a lot of other stuff too: personal genomics, teaching, science writing, etc.
• [”Alzheimer’s is] in your 70s,” Angrist said. “Something that’s going to happen to me 30 years from now is not going to keep me up at night.” Of course I realize that many people develop AD much earlier. I did not mean for this to sound as blase and callous as it might. My point was, I have plenty of other stuff to worry about for the next couple of decades.

Jason has a comprehensive roundup of press coverage of Monday’s festivities. Closer to home, the Duke Today website attempts to cure insomnia by linking to this blog. If you go there and scroll down, you can take a poll on whether making one’s genome public is a good idea.

Remember cycle sequencing? No? Remember grunge?

Jeez Louise, you’ve got to wake up pretty early to beat these folks to the punch. Anyway, as they point out, the September/October issue of Technology Review features an opinion piece by yours truly:

As a participant in the Personal Genome Project, I’ve been asked more than once, “So…what will you do with your genome?” I have two boring stock answers, at least for now: not much, and I don’t know. But I do want to learn about my genome. I see personal genomics as akin to the first personal computers. What could we actually do with the Commodore 64 or the Apple II? Word-process? Occasionally. A bit of Lotus 1-2-3? I guess. Mostly, I remember software crashes and hardware freezes. In my house we managed to play a lot of solitaire and Minesweeper.

Obviously there’s not much to see here (other than the above photo of Django in repose). I am traveling around New England, trying to write and trying to prepare for the fall semester. Back soon, I hope…God knows I miss the spam…

“The author and his daughter, Lena, who has half his DNA.”

People often assume that because of what I’m doing and because I write a blog called GenomeBoy, that I must be a starry-eyed genome worshipper. But if anything, getting genotyped has reminded me how much more we are than our DNA. All of those common-sense behavior changes actually matter. We are the products, finally, of our genes and our environments. And there is nothing mystical about either.