genomeboy.com

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.”

In the New York Times Magazine (11 January 2009), Steven Pinker writes eloquently and thoughtfully about his own genome and everyone else’s. A couple of my favorite passages:

Today, as the lessons of history have become clearer, the taboo is fading. Though the 20th century saw horrific genocides inspired by Nazi pseudoscience about genetics and race, it also saw horrific genocides inspired by Marxist pseudoscience about the malleability of human nature. The real threat to humanity comes from totalizing ideologies and the denial of human rights, rather than a curiosity about nature and nurture.

…

Assessing risks from genomic data is not like using a pregnancy-test kit with its bright blue line. It’s more like writing a term paper on a topic with a huge and chaotic research literature. You are whipsawed by contradictory studies with different sample sizes, ages, sexes, ethnicities, selection criteria and levels of statistical significance. Geneticists working for 23andMe sift through the journals and make their best judgments of which associations are solid. But these judgments are necessarily subjective, and they can quickly become obsolete now that cheap genotyping techniques have opened the floodgates to new studies.

Highly recommended.

If you want to know where biotech is headed, you could assemble an army of consultants, or convince [George] Church to talk to you for five minutes.

- Matthew Herper, Forbes.com

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.

Thanks to all who emailed me about the New York Times article. Amy Harmon did her usual stellar job. And in case you’re wondering: yes, skin biopsies hurt.

I have to say, this whole extravaganza felt more like a walk-through or a dress rehearsal. Several of us did not get our sequence data yesterday and those who did got very rough, low-coverage data. So besides the fact that assembling the ten of us is like herding cats, what was the point? I think there were two: First, to demonstrate that the PGP is indeed a community. While personal genomics is finally about the individual, if we are ever to to destigmatize this information, then I think it’s critical that we start to move away from the Venter and Watson “me me me” models. There are now 5000 people in the queue to be PGP participants. Which brings me to the second point: even though we are hardly the first to make our SNP data public, my hope is that our collective example might nudge still more folks in that direction.

A note on my still-to-come sequence data: As loudly as I’ve agitated for public release of genomic data on this blog, I have reserved the right to redact any or all of my sequence data and my Coriell EBV-transformed cell line. I am alone among the PGP-10 in doing this and I feel a little sheepish about it, but I am unapologetic. I have two young daughters. Yes, genomic information is probabilistic information and my genome is not theirs. But I have what I imagine every other loving father has: a fierce instinct to protect his children. If I carry a known mutation in a highly penetrant mendelian disorder, I want them to find that out from me and my wife, not from the internet or from some precocious classmate.

My public profile is here. I am bracing myself for the SSRI spam.

My SNP and sequence data will eventually be there as well. My SNP data will appear are on SNPedia very soon now.

This video was posted a few months ago, but typically for me, I am just seeing it now. It is as concise and cogent a description of the PGP as I’ve seen.

Mackenzie Cowell (left) and Jason Bobe are trying to create simple, at-home methods for doing sophisticated biology. (Dina Rudick/Globe Staff) 

The clash between the potential benefits and dangers of doing home science were highlighted by the case of Victor Deeb. The retired 71-year-old chemist in Marlborough saw his basement lab dismantled by authorities this summer after it was noticed by fire officials putting out a second-floor air conditioner fire.

The state DEP said officials intervened in Deeb’s workspace because it did not meet lab standards. Chemical companies shipping Deeb their materials were unaware that they were shipping to a residence, authorities said.

Deeb, who said he was trying to make safer surface coatings for food containers, insists that the chemicals he was using were less hazardous than common cleaners and household chemicals. He questions why his hobby was seen as more dangerous than, for example, a hunter with a gun collection, or a person using a propane grill.

“The more I tried to explain, the more they thought I was a lunatic,” Deeb said, questioning why he should need permits to tinker in his basement.

One wonders if maybe we couldn’t use a few more lunatics.

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.

…on George Church stories. I forced myself not to read this until I got my hard copy of Wired. I am sorry to report that it’s really, really good. Please don’t write a book in the next year, Thomas.