genomeboy.com

“If I’m to take a consumer genetic test, how do I know if I can trust the results, and should I be scared of what I might find out?”

Mary Carmichael of Newsweek asked me and a number of others to reflect on this question. And so I have.

• The short answer to the first part is, you may never be able to trust ALL of the results. Personal genomics companies type customers for several hundred thousand or a million variants (single-nucleotide polymorphisms or SNPs) and return results on a few hundred at most. My sense is that those few hundred are selected based on 1) the scientific validity of their association with particular traits; and 2) the presumptive interest of customers in those particular traits. But just because an association between a genotype and a trait is “real” doesn’t mean it’s predictive. Height, for example, is highly heritable, but it is probably mediated by thousands of genes. The other issue, as I’ve pointed out previously, is that the consumer genomics companies have thus far declined to issue standards. They use different SNPs in many cases. To assess multiple sclerosis risk at present, for example, 23andMe looks at two SNPs: one in a gene encoding a growth factor that sends signals to the immune system (IL7RA), and one that is tightly correlated with a SNP (HLA-DRB1) in the HLA complex, which is a region on chromosome six that harbors many genes involved in immune function. By contrast, Navigenics looks at those two plus another SNP in the IL2RA gene, which is important in T-cell activity and is a suspect in other autoimmune diseases. Both companies tell me that my lifetime MS risk is slightly lower than average, but the two numbers are not identical (23andMe: 0.24%; Navigenics: 0.17%). Meanwhile, a collaborative group of scientists has developed an algorithm incorporating 16 SNPs that is modestly predictive of MS risk. And SNPedia, the public wiki that collates SNP associations with human traits, lists more than 25 SNPs contributing to MS risk. Thus, the current level of confidence one can have in a SNP-based prediction of one’s chances of developing MS is weak at best.

• Should you be scared? Well, clearly in the case of MS, unless your neurologist tells you otherwise, you should not. But some consumer genomics companies return results on certain genetically mediated traits where the results are not so ambiguous. 23andMe, for example, returns results on three mutations that, if present, render women highly susceptible to breast and/or ovarian cancer. This is done on an opt-in basis: these data are not returned automatically with the rest of one’s 23andMe results. Some bioethicists believe that returning this information without explicit involvement of a doctor or genetic counselor is a bad idea. I do not share this view, but I understand it.

• Which brings me to my real take-home message: like most activities in life, personal genomics is not for everyone. I am not terribly interested in bungee jumping or climbing Mount Everest. Were I to let a friend talk me into doing either of those, assuming he wasn’t misleading me, then the onus would be on me for going along with it. But I’ve watched enough YouTube of bungee jumpers and I read Into Thin Air. Ergo, extreme sports and me: not happening. It is incumbent upon potential genome explorers to educate themselves before setting themselves up for possible disappointment and/or anxiety. I worry that critics of consumer genomics start from the assumption that would-be participants don’t know what they’re getting into and ultimately, cannot know, so, you know, let’s call the whole thing off. If you believe, as I do, that genetics education is in a sorry state and must be fixed, then advocating willful ignorance for everyone is both logically and morally indefensible.

• Okay, so who is personal genomics for? People who “opt in” should know upfront that:

• These are still very early days. The information attached to complex conditions controlled by many genes and the environment (like MS) is tentative and subject to radical changes in content and interpretation.
• Some information (e.g., possible high risk of breast cancer) may already be stuff you don’t want to know. “RTFM” as the kids say.
• The ideal personal genomics user is curious about the science, recognizes much of its tentativeness, and is an information seeker such that she won’t shy away from information that may not bode well for her future health.
• Sending a company $400 and spitting in a tube is not the only way to get involved. There are a bevy of research studies that involve personal genomic information. Take some time. See what’s out there, what’s involved, what your rights and responsibilities are, and what your expectations should be. This is your DNA and–unless you’re an identical twin–no one else’s. Do your own due diligence.

• Ask yourself what kind of person you are and why you would want to do this. Despite pressure from friends (and plenty of spam from Facebook), I’ve declined to join Facebook because I don’t like the way FB has handled its privacy policy and the contempt with which it has treated its customers. Plus, I find I already have enough trouble managing my online life; Twitter and email are about all I can handle, not to mention my book pages. Some social interactions make me anxious in a way that my genome does not. Your feelings may be the exact opposite of mine. And that’s perfectly fine: we shouldn’t need each other’s permission.

Personal genomics is, finally, personal. Look in the mirror and decide what’s right for you.

If you’re like me and you go to way too many scientific and professional meetings, it’s easy to get jaded. I am trying to limit my travel to stuff that 1) I can afford; and 2) actually interests me. One meeting I am totally geeked up for is the Open Science Summit in Berkeley, California from July 29-31, and organized by Joseph Jackson and his merry band of paradigm-shifting partners in crime:

The well known “10/90” gap references the fact that only 10% of biomedical spending goes toward conditions that affect 90% of the world’s population.  Under this regime, “diseases of the poor,” such as malaria, are neglected, while companies focus on “blockbuster” drugs for conditions that affect citizens of the wealthiest nations.  This situation, appalling though it is, actually grossly understates the systemic flaws of the prevailing biomedical innovation paradigm.  Framing this as a tradeoff between Market vs Social Values or the need for balancing commercial interests with public health, implies that the bio-pharma industrial complex works for what it purports to do.  If only we could find some way to engage or tweak existing mechanisms, we’ll make it through.  Wrong! 

There will be sessions on synthetic biology, gene patents, open data/open access, biodefense, microfinance, entrepreneurship, drug discovery, tech transfer, and more. There will be smart, talented and good-looking presenters (and, uh, me). And it’s cheap!

Why am I pimping this so hard? I am supportive of the cause. These are ideas and approaches that are less likely to be embraced by funding agencies and academia (as you will learn in my forthcoming book). I like and respect the organizers and want to see them succeed.

See you in Berzerkeley!

This is 17 kinds of awesome:

Scientists are to map Ozzy Osbourne’s genetic code in a bid to find out how he is still alive after decades of drug and alcohol abuse.

(hat tip)

UPDATE: “Throw some fag ash on his cornflakes.”

(hat tip #2)

But Dovekie’s test results were utterly baffling. The “Canine Heritage” swab test from MMI Genomics showed four breeds in the mix — in order of prevalence, golden retriever, wirehaired pointing griffon, bearded collie and miniature schnauzer. This means that Dovekie’s mom, Charlie, whom we met and felt confident was a purebred golden retriever, was anything but. It also meant that Romeo was no Chocolate Lab.

Typical. When you’re in heat, they always tell you what you want to hear. “Hey, Baby, I’m totally Chocolate Lab.”

I have to start watching more TV.

An Italian court has cut the sentence given to a convicted murderer by a year because he has genes linked to violent behaviour—the first time that behavioural genetics has affected a sentence passed by a European court. But researchers contacted by Nature have questioned whether the decision was based on sound science.

***

“90% of all murders are committed by people with a Y chromosome—males. Should we always give males a shorter sentence?” says Steve Jones, a geneticist at University College London. “I have low MAOA activity but I don’t go around attacking people.”

Farahany points out that prosecutors could use the same genetic evidence to argue for tougher sentences by suggesting people with such genes are inherently ‘bad’.

“The question is where do you stop,” Jones adds.

If they had wi-fi, I’d be on the first spaceship out of town:

If it sounds unrealistic to suggest that astronauts would be willing to leave home never to return alive, then consider the results of several informal surveys I and several colleagues have conducted recently. One of my peers in Arizona recently accompanied a group of scientists and engineers from the Jet Propulsion Laboratory on a geological field trip. During the day, he asked how many would be willing to go on a one-way mission into space. Every member of the group raised his hand. The lure of space travel remains intoxicating for a generation brought up on “Star Trek” and “Star Wars.”

Japanese researchers announce a major accomplishment in this issue of Nature: the creation of the first transgenic primates able to pass on a foreign gene to their offspring (see pages 492, 515 and 523). Because the primates in question are marmoset monkeys that are distant from humans in an evolutionary sense, this experiment has little immediate bearing on the modification of human germ lines — a prospect that many people find unacceptable in any case. But the advance will lead to more sophisticated models for human disease, physiological development and neurogenetics. And in so doing, it will inevitably draw more attention from animal-rights activists.

I love this [via Genomeweb]:

In a sign that genome-mapping is becoming increasingly common, a company called Knome plans to offer its personal gene-sequencing service to the highest bidder in an eBay auction set to begin on Friday and continue for 10 days. The company plans to opening the bidding at $68,000.

Daniel has his usual cogent breakdown, explaining why patience is a virtue.

Anyway, um, while you’re waiting for the genome bidding war to commence, perhaps I can interest you in something else that is considerably less expensive and easier to interpret?