genomeboy.com

With the help of the Personal Genetics Education Project’s Dana Waring Bateman, I have teamed up with Dr. Chris Korey at the College of Charleston. Both of us are teaching mavericky, genomicky classes this semester and Chris asked if his students could post on genomeboy in response to a series of questions he and Dana developed regarding the use of preimplantation genetic diagnosis to select for or against particular traits. “Anything to crowd out the spam,” I told him. I have modified the questions slightly to make them a bit bloggier.

• When we select for or against a trait, does it change how we as a society view that trait?
• How will the proliferation of sequenced personal genomes change our thoughts on what constitutes a disability? Or will it?
• How and whether genetic and genomic information ultimately leads to the expression of human traits remains unclear. How should that affect our use of this technology?
• Should the government restrict the use of this technology for positive and/or negative selection?  Why or why not?
• Is PGD a good idea? Make your case.

I confess I haven’t thought a whole lot about PGD, but I will say this: I see the emergence of this technology as inevitable and I think any attempts to ban it or drastically curtail it will fail. If parents want to select for or against a highly penetrant mendelian trait and they can’t do it in the US, they will go to China or Russia or the Cayman Islands or the UK. And it will only get cheaper. Thus, I think it would behoove regulatory agencies to get off their patooties and try to figure this out. The time for hand-wringing is long past.

Having said that, I worry about what we don’t know regarding the epigenetic effects of PGD and other assisted reproduction technologies. When we’re tiny balls of cells, we are extremely vulnerable. When we mess with a preimplantation embryo’s environment, we are likely to alter that embryo’s patterns of cell division, gene expression and/or morphology.

UPDATE: Will Saletan discusses the advent of increasingly sophisticated prenatal testing and its implications.

Please have at it in the comments.

I don’t always agree with Christopher Hitchens, but this paragraph made my heart flutter for its celebration of two things I love: genetics and Pittsburgh, PA.

It was in 1933 that Thomas Hunt Morgan won a Nobel Prize for showing that genes are passed on by way of chromosomes. The experimental creature that he employed in the making of this great discovery was the Drosophila melanogaster, or fruit fly. Scientists of various sorts continue to find it a very useful resource, since it can be easily and plentifully “cultured” in a laboratory, has a very short generation time, and displays a great variety of mutation. This makes it useful in studying disease, and since Gov. Palin was in Pittsburgh to talk about her signature “issue” of disability and special needs, she might even have had some researcher tell her that there is a Drosophila-based center for research into autism at the University of North Carolina. The fruit fly can also be a menace to American agriculture, so any financing of research into its habits and mutations is money well-spent. It’s especially ridiculous and unfortunate that the governor chose to make such a fool of herself in Pittsburgh, a great city that remade itself after the decline of coal and steel into a center of high-tech medical research.

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.

Some of my colleagues have had their genomes scanned as part of the Duke Personal Variome Project:

 Willard, though not a participant in the study, said he has had his genome analyzed several times, revealing that he is at a greater risk of developing cancer. Still, he knew of this risk before he ever submitted blood or spit to a laboratory-he was diagnosed with colon cancer and also has a family history of the disease.

“Getting colon cancer changed my lifestyle,” he said. “My genome testing hasn’t changed my lifestyle… but I’m already in this behavioral mindset of thinking about cancer risk and trying to modify behavior to reduce that risk in a very general way.”

Family history of a disease can be just as indicative of one’s chance of getting the disease as genomic testing, Willard said. But he added that for some people, the results of a genetic test might spur them to take care of their health in a way that family history does not.

“As people think about what DNA means and about what the genome means, there really is a sense that this is much more directive and impactful than the generic ‘Uncle Joe had heart disease,’” he said.

Ach, Ringo, we hardly knew ye…

Apparently “Peace and love” is the new “Get the hell off my lawn.”

Slate says to quit slagging your Mama’s uterus:

It’s easier—for parents, doctors, educators—to say an obese toddler has a slow metabolism than to teach the family better eating and exercise habits. Since 1970, childhood obesity rates have quadrupled. If fetal programming mattered a lot, adult obesity increases would lag years behind. But they don’t. According to intelligence researcher James Flynn, the average IQ of the first wave of professional Asian-American immigrants was almost 10 points lower than that of white professionals; within one generation, the gap closed, suggesting that genes don’t shackle the mind. As Malcolm Gladwell points out: “There should be no great mystery about Asian achievement. It has to do with hard work and dedication to higher education.”

I’m at the Personal Genomes meeting at Cold Spring Harbor. Maybe I’m jaded by now, but my expectations were low. I was wrong (admittedly it’s hard to know because they don’t give you an abstract book until you arrive). Watson gave his unique and pointed first-person history of the Human Genome Project, Francis Collins talked about finding rare and semi-rare variants (unemployment has been good for him), and Mary-Claire King gave an absolute tour de force on breast cancer as a paradigm for personal genomics. This morning Richard Gibbs reflected on Watson’s genome and Elaine Mardis talked about using Illumina sequencing to decode the first cancer genome. And it’s not even 10AM.

What would you do with $5000? Buy a used car? Fight a war for one second? Put it in the stock market? Bwahahahahahaha.

How about your own full diploid genome sequence at 40x coverage? The $5000 genome is here–or it will be in six months:

Mr. Reid said Complete Genomics hoped to perform 1,000 human genome sequences next year and 20,000 in 2010, with a goal of completing a million by 2013. That assumes the company can raise the money and find partners to build 10 sequencing centers at a cost of $50 million each. It also assumes there will be enough demand.

To put that in perspective, the number of human genomes sequenced to date by all parties combined is, at most, in the double digits. Knome, for instance, says it is on track to have 20 customers by the end of this year.

Volume, of course, could further drive down prices. “If we’ve got a million genomes sequenced by 2013,” Mr. Reid said, “it’s going to be very hard for anyone to compete with us.”

Not to get all hyperbolic, but this is quite simply, as my boss says, a game-changer.  It is Moore’s law run amok. “Church’s Law” anyone?