23andMe
From Razib: "Creative destruction in the personal genomics industry?"
I’m hearing about rumblings at 23andMe, and not in a good way.
Last year: "23andMe co-founder Linda Avey leaves."
23andMe
Common traits and GWA
Worth reading: Daniel MacArthur comments on 23andMe's reporting of genome-wide associations coming from their customer surveys of traits. The skinny:
23andMe has also nailed down a handful of genuinely novel genetic associations: a massively significant association between an olfactory receptor region and "asparagus anosmia" (the inability to smell asparagus in one's own urine), and two regions associated with hair curl.
On the topic of how genomics will go in the future, I think this section of MacArthur's post is revealing:
23andMe faces an unusual challenge that standard academic GWAS consortia don't: the possibility that a subject will give a biased trait report after seeing their own genetic data.
This was powerfully illustrated by results from the "athlete gene" ACTN3 (a gene close to my own heart). There was no association between the athletic performance-associated variant in this gene and self-reported sprinter/endurance preference in individuals who hadn't seen their genetic data - but in individuals who had already seen their genotype there was a marked shift towards carriers of the "sprint" or "endurance" allele self-identifying with those respective categories. In other words, people were altering their self-reported athletic affiliation on the basis of their genotype; Eriksson estimated that around 25% of individuals must be shifting their self-identification to explain the effect, a staggeringly large number.
This is such a common cognitive bias that it shouldn't surprise anyone, but it sure wrecks the statistics. Once people "know the right answer", they start aiming for it. That's why placebo-controlled blind trials are so necessary for medical treatments, it's also why so much genetic work applied to anthropological questions is bunk (because the mere knowledge of which dates are important, combined with many free parameters, will always allow one to generate the "right" answer).
Suppose I genotyped a bunch of people for OCA2/HERC2-linked SNPs and compared with eye color. There'd be a lot of people who, knowing the "right" answer, would push their eye color. You know, "I mean, maybe they're not really brown, maybe they're a little bit hazel..."
Last night on Mad Men, the Sterling Cooper crew were watching a dog food focus group. The owners start describing their dogs' personalities, and one of the guys from creative exclaims, "They're not describing their dogs, they're describing themselves!".
To which Don replied, "Is this your first focus group?"
Pretty much the same story. We project onto our genes what we want ourselves to be -- and what we want most is to fit the expected value.
Migraine at 23andMe
23andMe continues its strategy to look for genetic associations of traits that escape most funding for genetic reserach. Latest: migraine:
Two prominent migraine researchers have suggested that the blame for the slow progress in understanding migraine lies with a systemic lack of public funding for migraine research. They argue that the relatively recent, and incomplete, acceptance of migraine by the medical and research communities as a genuine medical problem, as opposed to mere melodrama, has led migraine’s funding to lag well behind that for diseases of similar impact. For example, they estimate that while $13.80 is spent for each sufferer of asthma, just 36 cents of federal research funds are spent per migraine sufferer.
The genetics of migraine are also only partially understood. That’s where our new survey comes in. Our community-based research program 23andWe seeks to empower the public to engage in genetic research from the ground up. We know our efforts cannot substitute for proper federal support of migraine research, but evidence of great public interest, plus a new finding or two, would add to our understanding of the disease and potentially send a message to Washington.
It's possible that they won't find anything; or that even finding something won't help with treatments (although both negative results would be good science). But participating in research like this is potentially a lot more helpful and empowering in the long run than many other things people try, like taking odd OTC supplements.
I wonder which neglected industrial disease will be next...
Is your genome worth guarding?
Katrina Voss wrote in New Scientist a couple of weeks ago: "Your genome isn't that precious -- give it away". After discussing legislative efforts to provide remedies for genetic data security breaches, she writes:
Yet much of our concern about the abuse of personal genetic data seems overblown. It betrays a fundamental delusion of self-importance: we assume that someone will find our individual genome interesting enough to hack into it and exploit it. In most cases, this would be a waste of time: our genetic secrets are rarely worth the cost of obtaining them clandestinely.
The article touches on the Personal Genome Project's aim to release data unconditionally. In that context, complete openness can be cast as a selfless sacrifice:
The PGP's open approach is pragmatic: society has much to gain from unrestricted access to genome sequences, medical histories and phenotypic data. For example, only by knowing how traits, experience and genes interact can we discover how both environmental factors and DNA affect disease. The prospect of such progress was a major factor in my family's decision to get involved. Whatever our fears about privacy, we have chosen to cast them aside for the greater cause. But no one who chooses to have their DNA tested should expect perfect anonymity - especially since DNA is the ultimate identifier.
Hmmm....the ultimate identifier.
I don't have anything against people choosing to make their data totally open -- I could imagine choosing to do so myself. I do think we should consider the rights of siblings, children, and parents, who after all share half each others' genomes.
But I read another article that I think makes an interesting juxtaposition: "How much are you worth on the black market?"
Ever wondered how much your online identity is worth to a cybercriminal? A new tool from Symantec Corp. will perform the calculation for you.
The Norton Online Risk Calculator, unveiled within a microsite to coincide with the launch of Norton 2010, calculates your net worth on the black market by asking a few questions about your personal Internet use.
It's a catchy intro for a story about data security -- later the miserable facts:
Mistakes Internet users continue to make include forgetting to renew their security software subscriptions, not keeping operating system patches up to date and failing to use the latest version of their Internet browser, Merritt pointed out.
Sure, a genome today is worth less than a credit card number on the black market. But suppose you knew somebody's DNA fingerprint, mtDNA sequence or other data used routinely in forensics. It would be trivial to synthesize fragments with the right lengths and primer sequences, use PCR to make a bunch of copies of them, and scatter them at a real crime scene.
Well, that's the paranoid scenario, anyway!
"Every four and a half minutes, a crime is committed on the streets of Los Angeles. Every three minutes, a crime is committed on the streets of Washington, D.C. In New York, a crime is committed every two minutes ... every three seconds, a crime is committed on the net," she said.
For genetics, the question hinges on whether there will ever be a practical use for the data. I mean, when we talk about "identity theft", we think there's something worse going on than thieves walking into your house and taking down the genealogy chart.
Blackmail is a use, but not very practical on a large scale. Now, if somebody could corrupt your data, say change a nucleotide or two, then they could spoof drug interaction risks and thereby damage your medical treatment courses. Still, that's not going to drive a huge underground of omecrackers.
Of more relevance: What could somebody do if they knew the average genetic makeup of an organization, say by cracking a representative sample?
Sending a cheek swab?
A reader wrote me today:
I am wondering if you could suggest a general article for me to give to people who tell me how exited they are about sending a cheek swab to National Geographic for analysis. I imagine you have written something like this, but don't remember where it is. Any thoughts?
I wrote back, and thought I should share. I have an article in Slate from a couple of years ago that covers that topic:
http://www.slate.com/id/2138059/
Also, there was a NY Times article in late 2007 that basically covers the same difficulties:
http://www.nytimes.com/2007/11/25/business/25dna.html
I blogged about that article at the time. I also have a post from the time of the Slate article.
And my "testing" tag leads to a bunch of posts on the topic of genetic testing. I've never really sat down to write an FAQ on the topic, but I think it would be worth doing. Genetic Future does a very good job of covering current commercial offerings in genetic testing, a beat also covered at Eye on DNA.
If someone was thinking of sending $100 to Genographic, I have nothing against it as a form of entertainment. I think the information you get that way is, for most people, very superficial and unsurprising. Basically, they're giving you your paternal Y chromosome lineage if you're a man, and your mtDNA if you're a woman. That fee pays for your test, the information they give out to you as a participant, and an extra amount that they will use to subsidize testing of various populations around the world.
But if you're looking for the entertainment value, you will be much better off saving up $400 to send to 23andMe. That pays for a whole-genome SNP survey, including various phenotype predictions. They have all the genealogical information from the Y and mtDNA that you would get from Genographic, and it's better-presented. Overall, it's a much better deal, and more likely to generate something interesting to share with your friends. Of course, it costs more, but it's a better value.
Now, for serious medical purposes, or for trying to do phenotype predictions of your children, I don't recommend 23andMe. I honestly think that gene testing now is best treated as expensive entertainment. You might get a laugh, or learn something about your ancestry that you didn't know. But you won't likely learn anything that would be worthwhile to your children. Not yet, anyway. This is not an investment.
In other words, don't spend your food money. Think of it as eight months of cable TV.
Pages
Neandertals
For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.
Denisova
From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.
Acceleration
The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.
Malapa
Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.