Tag Archives: Genomics
Melanie Swan of DIY Genomics describes the results of sequencing her own genome in the hopes of developing her own personalized preventive medicine strategies. She developed a mobile app that permits exporting of personalized sequencing data more easily. A series of small nucleotide polymorphisms (SNPs) were identified by Melanie in her own genome relating to cancer, immunity and aging. Importantly, she has made available the results of her own deep sequencing results to be combined and compared with those of other individuals. (Filmed at the Bay Area Quantified Self meetup at Singularity University.)
At the most recent New York City Quantified Self Show&Tell meetup, Esther Dyson took the microphone to talk about her recent experience at the GET (Genes, Environment, and Traits) Conference. She then answered questions from fellow QS’ers about the direct-to-consumer genome market, public perception (“why on earth would you want to sequence your genome?”), DNA art, and other fun topics.
The QS blog, as is obvious to anybody who glances at it, is hosted on kk.org, the web site of my friend and QS Show&Tell co-host Kevin Kelly. Here is a link to Kevin’s recent post on the inevitable public status of all individual human genomes. It is a counterintuitive idea, persuasively argued.
Kevin focuses on the health benefits that will stem from a new understanding of individual DNA as a public aspect of the self. It is interesting to think about some of the unintended consequences of having complete genomes easily accessible. Kevin mentions paternity cases; by extension you can start speculating about any civil case that involves a question of whether two people met at a certain place, or travelled together in a certain vehicle, or tapped on a certain computer where they may have dropped a hair or left a soiled cup. Criminal cases, ditto. But we can also think further afield. I’m impressed by Eliezer Yudkowsky’s invitation to explore possibility space of new developments by means of the concept of weirdtopia – not utopian or dystopian visions, where these are conditioned by our current values, but visions that strike us as utterly abnormal because they involve new inventions coupled with new values. What are the weirdtopian implications of public DNA?
Now that there are multiple companies selling genome scans, and urging their use as a guide in making decisions about health, the sociologists are following close behind. Marcie Lambrix, at Case Western University, contacted me recently to seek research help in putting together a report on consumer attitudes and experiences with personal genomics. The research is for an academic study whose results will be publicly available. It is not marketing research. I offered to post Marcie’s contact information on QS – if you have used 23andMe, Navigenics, deCODEME, or Knome, she would like to hear from you.
Case Western University, School of Medicine
(And if you are a user of Knome, please let me know, too. I would love to hear a description of how you are using this information at the next QS Show&Tell.)
(From MIT’s Technology Review: “A customer who pays $350,000 for Knome’s
service receives a silver box containing an eight-gigabyte USB drive
housing his or her genome sequence…”)
Last Tuesday 23andMe, the genome sequencing service, hosted the first meeting between its customers. Like Navigenics and deCode, 23andMe will sequence half a million “snips” from your own DNA to give you glimpse of your personal genetics. What you get for your $1,000 payment is lots of numbers and strings of letters, and a little bit of information of how these correspond to health studies and ancestry research. So far this is a very nerdy hobby, requiring a love of data and great patience with crude tools, bugs, and beta everything.
The idea behind gathering early enthusiasts face to face was to increase the exchange of information, methods, motivations in a way that Web 2.0 can’t do. There are ethical issues, social uncertainty, incredible technical complexity, and rapid advancement in this field; having a person in front of you who might know more than you is a great way to learn. 23andMe cleverly calls this initiative to harness customer-generated value 23andWe.
As a paying customer I attended this informal gen-con. I think of this event as the first Personal Genome User Group. We gathered at 23andMe world headquarters in Mountain View, CA, but I think we were outnumbered by the ever helpful staff on hand to answer questions. I was extremely curious about the other customers’ experience, and what they have learned by sequencing their DNA. I don’t want to speak for them, but here is what I have learned by messing around in personal quantified genomics in the last six months:
1) There is far less known about proven genetic diseases that I thought. The list of illness with established origins in genetic mutations is very short, and even then the genetic factors operate statistically. The presence of a particular gene will raise or lower the percentage risk for a health issue, at the most. So one thing I learned from having my DNA sequenced is that very few diseases have a single point genetic basis, which means that gene sequences will be just one factor in a very complex brew of influences. Personal genetic knowledge is sort of like knowing your blood type: Important to know but far from sufficient.
2) Sequencing is not just about health (and one of the reasons it should not be hijacked by the doctor squad). Your DNA can reveal much about your deep genetic past. Combined with research around the world into ethnic locations and migrations, your sequence can map out the movements of your distant ancestors in pre-history. I was surprised by how interested I became in these movements, both on my maternal as well as paternal side. I had zero interest in genealogy, and could not care less about my great-great-grandparents and their cousins. But I did find myself surprised by the ethnic pathways of my ancestors, because the identity I normally cling to is obviously (duh!) just the most recent one in a very long line. Naming myself after only one data point and ignoring all the others seems arbitrary. Many of other users at this meeting also expressed to me this pleasant surprise of discovering their interest in their deep ancestry via their sequences.
3) 23andWe is the perfect turn of phrase for another thing I learned. I have been surprised at how fast and how eager users have been to share their genetic data. We’ve been conditioned by anxious media reports to believe that people want to hoard their very personal genetic profile, in fear of what would happen if governments, corporations, insurance companies and the neighbors were to see it. But in fact like a lot of other things that have made it online, genetic information only increases in value when shared. Experts thought only a fringe minority would dare share their genes, but swapping genetic info will mostly likely be the norm for a generation that shares everything else. Sharing your genetic info with family members, relatives, and even apparent strangers (who must be related somehow) is exciting, and certainly educational.
Gary Wolf and I have discussed starting a Bay Area Quantified Self User Group with a similar mission: to mutually assist those folks interested in inventing and mastering the tools of self-knowledge, including genetic sequencing. Write me if you are interested.
I’ve had my DNA sequenced by 2 of the 3 companies now offering this service to the paying public. I purchased the tests for 23andMe and Iceland-based deCode. I am still plodding my way through the results — it’s sort of an education. One question I had was how well do the two results matched? I give the same DNA to both companies; the results ideally should be identical. DeCode claimed to test for 1,000,000 SNPs and 23andMe for 500,000, so the problem of lining all these results up to see what differs is not trivial. Luckily another user has just done this.
Antonio Oliveira also used both 23andme and deCode. He writes in his new blog:
In order to determine the accuracy of the genome profile provided by 23andMe and deCODEme I arranged to be genotyped by both companies and wrote a computer program to compare the results. The downloaded files contains 576,105 snips in the case of 23andMe and 1,013,349 snips for deCODE. After removing the no-calls and matching the two files by SNP identification, 560,299 snips were present in both files. The comparisson revealed 23 cases in which the results do not agree.
Oliveira made a chart of his results, categorized by chromosome.
The 23 errors makes the agreement between the two sets of data about 99.995% accurate, or an error rate of .005%, which is pretty good for medicine. A better test might be to repeat the test on the same DNA, but I assume the manufactures of the chip have done that. The 23 “unequal” SNPs caught here in disagreement are not SNPs currently associated with any diseases, so these particular errors are inconsequential. I don’t know if there are location biases in the errors, but presumably errors can appear in significant locations — at that very low rate. However if your computer had the same error rate, you’d notice.
In April, 2005, the National Institutes of Health and Department of Energy launched a [task force](http://www.genome.gov/10001808) on genetic testing. The task force, which had broad academic and industry representation, tried to outline the issues, and recommend possible guidelines, for the coming age of consumer genetics. It was already obvious that cheap and ubiquitous genetic testing was on its way. The result will be a revolution in medicine comparable to the explosion of pharmacological knowledge in the twentieth century. But of course the complexity of pharmaceutical therapeutics has been mediated by the medical monopoly on prescription drugs. Some drug treatments are simple: have backache, take aspirin. Some are more complicated: have terrible backache, take [Demerol](http://en.wikipedia.org/wiki/Meperidine) ; no, take [Percocet](http://en.wikipedia.org/wiki/Oxycodone); or no, try good old fashioned [morphine](http://en.wikipedia.org/wiki/Morphine).
When the NIH-DOE task force looked at genetic testing, it envisioned an analogous system of mediated access; perhaps not as strictly regulated as the drug system, but still with trained professionals in a central role. “Consumers should discuss testing options with a health care provider competent in genetics prior to having specimens collected for analysis,” wrote the task force in its [final report](http://www.genome.gov/10002401).
“The Task Force discourages advertising or marketing of predictive genetic tests to the public.”
But medical professionals can only ethically recommend tests and treatments that have been proven to be effective, except under explicitly experimental conditions, when patients consent to take a risk and participate in research. Thus [23andMe](https://www.23andme.com), the consumer genetic testing company, does not offer “diagnostic” or “predictive” tests. Instead, the company offers a light dusting of information about the association of traits and diseases with particular genetic variations, along with a tremendously large amount of raw genetic information, in the form of hundreds of thousands of SNPs, or [single nucleotide polymorphisms](http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml).
Between these two features — a very slim and ambiguous set of potentially significant interpretations; and a big collection of raw SNPs — there is nothing.
The answer is not that 23andMe is being stingy, exactly. Rather, the power of genetic testing cannot be realized until genotype is linked to phenotype. The genetic variation in human beings has to be connected with its effects on our bodies and our behavior. This is the purpose of genetic research. Today, the territory between the genotype and the phenotype remains largely unmapped. Where there is ignorance, there is silence. The fakey quality of the 23andMe GeneJournal is, in fact, a side effect of this clinical silence.
Right now, the important thing about popular genomics is not the diagnostics but the data. 23andMe, along with the other consumer genetics companies, and academic research organizations around the world, are collecting raw genetic information. There are clear indications, from the 23andMe Web site, which I have been exploring carefully, examining the results of my own test, that the company intends to sell the genetic data its customers provide to commercial firms for research purposes. This has attracted some [critical comment](http://www.palidwor.com/blog/?p=63).
It seems to me that there ought to be a different basis altogether for this research. The future of genomic medicine hinges on a model that is neither the “closed” model of highly regulated drug research nor the “closed” model of opaque data-gathering by private firms. Instead, in my utopia, there is a culture of genetic openness. It should be easy to “donate” one’s genomic information to a common pool, and also easy to attach additional information about one’s phenotype. The only thing that needs to be masked from public view is personally identifiable information, the kind of information that would allow particular individuals to be tracked without permission.
This does not necessarily undermine the business model of companies like 23andMe. There is plenty of business to be done in the context of an open culture. But the actual data should be widely and conveniently accessible.
I recently emailed 23andMe to see if there was any easy way to export the hundreds of thousands of SNPs in my “Gene Journal” to a raw data file. This is not because I am a geneticist. Instead, I simply want to know how accessible the 23andMe data is. One of the themes of our exploration here on the Quantified Self is that tracking leads to data leads to experiment leads to self-knowledge. It remains to be seen whether one’s personal genome be an element of this process. The genome is a lot more complicated than many of the behavioral techniques we’ve discussed here. It can only become meaningful through massive collaboration.
At the basis of this collaboration will be a culture of genomic openness.
The New York Times published [several letters](http://www.nytimes.com/2007/11/23/opinion/l23dna.html?_r=1&n=Top/Opinion/Editorials%20and%20Op-Ed/Letters&oref=slogin) today about Amy Harmon’s [story](http://www.nytimes.com/2007/11/17/us/17dna.html?ex=1353042000&en=4e47cebf58fa5d93&ei=5088&partner=rssnyt&emc=rss) of having her DNA sequenced by [23andme](https://www.23andme.com/). One of them was by Hugh Young Rienhoff, Jr., whose blog, [MyDaughtersDNA.org](http://MyDaughtersDNA.org), is an example of exactly the mix of altruism, curiosity, and desire for medical progress that should power this movement in the first stages. Rienhoff, whose quest was the subject of a detailed, well-written story in Nature ([PDF](http://www.kk.org/quantifiedself/Nature%20on%20Hugh%20Rienhoff.pdf)) has been trying to understand the cause of a rare condition that interferes with normal muscular development. His daughter suffers from this syndrome, which appears to have a genetic cause. It is rare, and may even be new. Rienhoff had an advantage in his research – he is a doctor and a geneticist. The Nature story has the full account of how Rienhoff set about to sequence a portion of his daughters genome, and gain any relevant knowledge of how she can be helped. Rienhoff’s site does more than document his effort. It offers a template and repository for individual case reports, and ultimately for genetic information as well. It is an early, small, but important pointer toward realizing the potential of personal genomics.
Rienhoff’s site: [mydaughtersDNA.org](http://mydaughtersDNA.org)
Here is an excerpt from the Nature piece:
> With help from [George Church](http://arep.med.harvard.edu/gmc/), a Harvard Medical School professor with an extensive track record in new technologies for sequencing and synthesizing DNA, Rienhoff developed a sort of ‘phenotype spreadsheet’ on which to record his daughter’s clinical history. The idea is that such data representations might someday allow a computer to search through his daughter’s symptoms along with those of others with unidentified genetic disorders looking for clinical commonalities. Church plays down his contribution as just a seed of an idea that he thought worth testing, but says he is intrigued by Rienhoff’s gumption: “I’m interested in cases of altruists who, rather than hiding from genetics, are using the opportunity to be sort of social activists, working to raise consciousness and maybe raise money for diseases affecting their family and friends.”
> Such activism is not new. Parents quite frequently become advocates for research on behalf of their children — when they are rich, famous, persistent, lucky or very well placed, they can make a difference. But with a sequencer and a website, Rienhoff has stepped over the threshold of personal genomics in a way set to catch the imagination. As sequencing gets ever easier and knowledge bases ever larger, it may not be fanciful to imagine more and more people following him, developing theories about abnormalities and testing them through sequencing. Such attempts will often fail, and in some cases lead to frustration and heartache. But some may make significant contributions to our understanding of the function of various human genes.
And here is an excerpt from [a longer post](http://mydaughtersdna.org/Members/hyrjr/why) by Dr. Riehhoff in which he gives very clear description of why he has made the details of his daughter’s case public:
> **The reasons for making public a mysterious case.**
> Why am I making public my daughter’s medical findings and her history?
> I am in search of a diagnosis. It may be that my daughter has a new condition, it may be that she has a very rare condition that only a very few people know of and I have not met them, or perhaps she has an unusual form of a more common genetic condition. She is a mystery at present. If I broadcast her findings to other — doctors, patients and parents who may have seen a similar condition — I am more likely to pin down precisely what she has.
> Why does a diagnosis matter?
> A definitive diagnosis is very valuable because along with the right diagnosis comes some expectation of what will become, what to expect. Do problems disappear; do they get better? Are there some aspects of the condition that require special vigilance? A diagnosis can also bring along a treatment. In short, if I know what it is, I know what to expect and I know how to treat. Without that diagnosis, we are all in the dark.
Finally, here is Dr. Rienhoff’s letter to the Times, in which he raises the possibility that personal genomics, if neglected by the medical establishment, could end up being dominated by vanity procedures.
> To the Editor:
> The real news is that the genetic genie is out of the bottle. The consumer’s embrace of genetic analysis is now unstoppable. And though the medical community warns how little we can actually learn from most of our genes, these caveats do not diminish our curiosity.
> The truth is that the medical establishment has not co-opted the genetic paradigm because doctors are busy and see little value right now for themselves or their patients. As such, genetics may go the way of cosmetic dermatology and surgery.
> Hugh Young Rienhoff Jr., M.D.
> San Francisco, Nov. 18, 2007
Kevin [posted earlier](http://www.kk.org/quantifiedself/2007/11/access-to-personal-genomics.php) on self-knowledge through consumer genetics and linked to Amy Harmon’s [story](http://www.nytimes.com/2007/11/17/us/17dna.html?ex=1353042000&en=4e47cebf58fa5d93&ei=5088&partner=rssnyt&emc=rss) in the New York Times. I spent the weekend catching up on the very successful wave of publicity orchestrated by [23andMe](https://www.23andme.com/ourservice/labs/), with major stories by Harmon in the Times, Thomas Goetz in [Wired](http://www.wired.com/medtech/genetics/magazine/15-12/ff_genomics), David Ewing Duncan in this month’s [Portfolio ](http://www.portfolio.com/news-markets/national-news/portfolio/2007/10/15/23andMe-Web-Site), Kara Swisher at the [allthingsd.com ](http://kara.allthingsd.com/20071119/kara-visits-23andme/)site, and onward and outward through the Web.
The stories are interesting. As Kevin says: *Personal DNA sequencing is here*. I want my genome, too.
Still, within all of these stories I caught the first hint of a backlash. This backlash has little to do with the main objection all of these writers presented, which was: do I really want to have this important knowledge about my genes? I don’t think this objection is serious. I don’t even get a sense the writers seriously entertain it. I suspect it is a rhetorical effect, an exaggerated worry that lends interest to the promise at hand. ([Gray goo](http://en.wikipedia.org/wiki/Grey_goo) serves this function for nanotech.) Perhaps it is the nerd in me, but I have difficulty imagining that accurate medical self-knowledge would be rejected by consumers because they are afraid to know.
Anyway, there’s a bigger problem. The companies offering these tests carefully insist that they are not be taken diagnostically, and acknowledge that that are not currently accurate indicators of clinical risks. They give these caveats, while of course also trying to satisfy our desire to get accurate clues to our genetic predispositions to scary diseases.
Here’s how Kara Swisher walks 23andMe co-founder Anne Wojcicki through this dance during their [video interview](http://kara.allthingsd.com/20071119/23andmes-anne-wojcicki-and-linda-avey-speak-part-1/). In this portion of their conversation, Wojcicki has been talking about the possibility that a 23andMe customer might discover from the study of their genome that they do not easily metabolize caffeine. Swisher asks Wojcicki to explain why this information is useful. Does it tell you not to drink so much coffee?
> Wojcicki: 23andMe service is definitely not, you should not be taking action from the information.
> Swisher: Right, you’re no doctors…
> Wojcicki: We’re not doctors..
> Swisher: Consult your own physician
> Wojcicki (grinning): Yes you should consult your own physician. That said, our goal, not necessarily now, but in the future, that this information will be actionable…
But of course the reporters who get a chance to use the 23andMe service, including Goetz and Harmon, develop a fascination with the predictive power of their results, as would anybody with a normal level of curiosity and fear. They repeat the caveats, but then disregard them.
Here’s Harmon at the New York Times:
> My risk of breast cancer was no higher than average, as was my chance of developing Alzheimer’s. I was 23 percent less likely to get Type 2 diabetes than most people. And my chance of being paralyzed by multiple sclerosis, almost nil…I was in remarkably good genetic health, and I hadn’t even been to the gym in months!
Here’s Goetz at Wired:
> Variations of three SNPs double my risk for prostate cancer, leaving me with a 30 percent chance of developing it in my lifetime… And my risk for exfoliating glaucoma, a type of eye disease, is a whopping three times the average American’s. While the average person has just a 4 percent risk, my risk factor of 12 percent means it’s something to mind.
Here’s David Ewing Duncan in Portfolio, describing another personal genome company, Navigenics:
> Navigenics is positioned to go after the millions of Americans who are spending money outside of the traditional health-care system to stay healthy, buying vitamins and dietary supplements, gym memberships, and diet and self-help books.
Just as the dietary supplements sold in row after row of shelves at the pharmacy are “[not for the treatment of any disease](http://www.purehealthsystems.com/cetyl-myristoleate.html),” and state lotteries are “[for entertainment purposes only](http://www.calottery.com/Games/SuperLottoPlus/WinningNumbers/WinningnumberSearch.htm),” so the results given to customers by 23andMe are **not** supposed to be clinical predictions.
So here is the voice of the future backlash, the voice of the angry doctor whose patients are looking to these tests to guide their medical decisions. This self-described MD with the silly pseudonym published the following comment on the Wall Street Journal health blog, in response to a [story](http://blogs.wsj.com/health/2007/11/16/decode-me-personal-dna-sleuthing-on-a-q-tip/) by Ron Winslow about another personal genome company, [deCode Genetics](http://www.decode.com/News/2007_11_16.php):
> I watched the video that accompanies their announcement. Please people, this is (to quote the CEO on their video) “NOT genetic testing!” And “Do not use this to make medical decisions!” What this is “empowerment” and “networking” and a way to suck $1000 from gullible consumers. I hope some liability lawyers out there save that video and replay in in court as the CEO explains how, exactly, this is not genetic testing.
> I.P. Nightly, MD – November 18, 2007 at 8:13 pm
PS: Interesting, even harsher criticism of personal genomics companies comes from the [Gene Sherpa](http://thegenesherpa.blogspot.com/), who claims these companies are using their customers as [non-consenting research subjects](http://thegenesherpa.blogspot.com/2007/11/from-wired-magazine-quote-from-anne.html). I say “interestingly” not because the Gene Sherpa’s tone weirdly resembles that of Dr. I.P. Nightly, but because the aspect of 23andMe that most bothers the Gene Sherpa is exactly the part that I like best: the collection of a large database of SNPs from an active community of users creates new research opportunities that might benefit everybody, even those who never delve particularly deeply into their genome and don’t expect it to guide their health decisions in the immediate future. The personal genome is part of the extension of medical research into more naturalistic settings. It offers a new context for [population studies](http://www.cancer.gov/Templates/db_alpha.aspx?print=1&cdrid=561718). It’s clear that the founders of 23andMe recognize this possibility, and have thought deeply about it. This promise getting lost in the excitement – false for the moment – of being able to accurately predict the risk of a single individual dying in some specific and horrifying way. This larger, more complex effect of the advance in personal genomics is harder to narrate, but it may be the one that changes our life.
Personal DNA sequencing is here. The New York Times has an excellent story by Amy Harmon on what happens when you get your own DNA sequenced. She had about half a million SNPs sequenced by 23andMe, a personal genome start up. In the article she explores both her hesitancies and exhilaration in discovering her genetic self. She writes:
Logging onto my account at 23andMe, the start-up company that is now my genetic custodian, I typed my search into the “Genome Explorer” and hit return. I was, in essence, Googling my own DNA.
I had spent hours every day doing just that as new studies linking bits of DNA to diseases and aspects of appearance, temperament and behavior came out on an almost daily basis. At times, surfing my genome induced the same shock of recognition that comes when accidentally catching a glimpse of oneself in the mirror.
She annotates the process of how each gene she discovers in her self is measured, contrasted and reckoned with — a very irrational process in fact.
For instance, I tragically lack the predisposition to eat fatty foods and not gain weight. But people who, like me, are GG at the SNP known to geneticists as rs3751812 are 6.3 pounds lighter, on average, than the AA’s. Thanks, rs3751812!
There will be a huge appetite for understanding what these little numbers mean, and an entire industry trying to explain sequence results is already quickly rising. My friend Ryan Phelan is involved in one of these, DNA Direct, which will counsel patients on interpreting their DNA tests. None of the test makers offer counseling.
For now there are two companies that offer substantial (by 2007 metrics) sequencing to anyone willing to pony up the $1,000. Both are using technology from Illumina, based in San Diego.
$985 (PayPal only!)
One million SNPs
If you feel that you’d just like to wait until the price drops, I think you’ll wait a long time. My hunch is that the $1,000 cost will remain flat for a long time. What will change will be the numbers of SNPs you get done for that one grand. Right now, one million SNPs is just a tiny fraction of your total DNA, and only 10% of the 10 million SNPs in your body, but even this small amount spread widely over your chromosome can tell you something. More SNPs would be better. The curve of improvement will be a lot like computers, which still cost $1,000 twenty years later, but now they are a million times better. In 20 years you’ll get a million times as many base pairs (not just SNPs) sequenced for the same price.
I’ve singed up for both tests and will report my experiences as quickly as they are delivered.
I am fully aware that much of this genetic data is not useful to a layman like me at this point. As one VC says in a very good article in Portfolio,
“I tend to be more on the skeptical side for a genomics consumer play because, by and large, the information is not useful to the individual,” says Doug Fambrough of Oxford Bioscience Partners, a biotech venture capital firm headquartered in Boston. “First of all, the information is hard to understand for anyone who is not a trained molecular biologist. It has to be boiled down. Also, the science has not yet arrived. We can tell a single trait here and there, but what people really want to know is how this affects their life. We can’t yet make accurate predictions about this.”
But I am eager to get my genes sequenced primarily as a type of school, to increase my genetic literacy. It’s a new language, syntax, and world view, and I want to be conversant in it. Your own genome is the best teacher. Whatever medical knowledge comes about is a bonus. But even without life-altering news, this is another step in self-knowledge.