Michael Cariaso, developer of the human genetics wiki SNPedia and the online gene analysis tool Promethease, has helped thousands of people unlock the secrets of their own genetic code. But when it comes to making his own gene screening tests publicly available for all the world to see, Cariaso prefers to hold the key close to his vest, worrying that such transparency might lead to personal embarrassment or discrimination by insurance companies or future employers. “Someone later might discover,” he says, “that I have genes for a short penis and low intelligence.”
Cariaso is certainly a smart guy, and he is hardly alone in his general concerns. (With regard to his genitalia, as the philosopher Wittgenstein said, “Whereof one cannot speak, thereof one must be silent.”) But he’s wrong. Fears about the loss of genetic privacy are greatly exaggerated. We are fast approaching an era in which genetic information is no longer exclusive or medicalized. Instead, as screening costs plummet and our knowledge about genetics expands, virtually everyone will soon be able to have their genotypes at their fingertips. Knowing and sharing that information will enhance, not jeopardize, our sense of ourselves, change the way we consume medicine and plan for the future, and influence how we relate to each other.
That’s why I’ve decided to post my genotype screening information online. You can read all about me at snpedia.com/index.php/User:Ronald_Bailey. As a service to future consumers and as a guide to the world we will all soon be living in, here are my answers to the most common questions about and objections to genetic testing.
How does genetic screening work?
Right now the cheapest, simplest way for a consumer to get some preliminary insight into his or her genetic makeup is to pay a few hundred bucks for the services of a gene screening company, such as 23andMe, deCODEme, Navigenics, or Pathway Genomics. Unlike colonoscopies or even ordinary blood tests, a gene screen isn’t gross, scary, or inconvenient. Simply spit into a test tube, send it off, and a few weeks later you get a read-out of up to 1 million single-nucleotide polymorphisms (SNPs) from your genome. SNPs are variations in an individual’s genetic code that are useful in understanding differences among people and for identifying some disease risks.
In May 2010 one company, Pathway Genomics, even arranged to offer its screening test over the counter at Walgreens drugstores. Unfortunately, a hyper-cautious Food and Drug Administration (FDA) sent a letter to Pathway Genomics asserting that the test was a regulated medical device, prompting Walgreens to postpone selling the service for now. In June the FDA sent a letter to other gene screening companies, to test-chip maker Illumina, and to the whole-genome sequencing company Knome, ordering them all to show why their tests should be exempt from the agency’s premarket clearance regime for regulated medical devices. In his letter, the FDA’s Alberto Gutierrez expressed worry that “consumers may make medical decisions in reliance on this information.” Well, yes; that’s the whole point.
People already are making those same decisions, but with much less information. Vague stories about Aunt Sally’s breast cancer prompt a mammogram; an uncle’s heart attack leads to some half-hearted jogging. People make health decisions all the time. The FDA’s aggressive regulation of direct-to-consumer gene testing does little more than keep information away from decision makers.
Despite these regulatory travails, there are at least nine companies in the U.S. that will go beyond checking for gene variants and will soon offer to decode all 3 billion DNA base-pairs in a person’s whole genome. This is astonishingly rapid progress from very expensive pure science to relatively cheap commercialization. The first complete human genome was sequenced back in 2000, a government project that cost around $3 billion. In November 2009, the privately held Complete Genomics sequenced a whole human genome for just $1,700. One company, Pacific Biosciences, claims that by 2013 it will be able to map a consumer’s genome in 15 minutes for less than $1,000. Many of these companies are competing for the $10 million Archon Genomics X Prize funded by the Canadian geologist and diamond mine entrepreneur Stewart Blusson and his wife Marilyn Blusson, which will be awarded to the first group to build a device that accurately sequences 100 human genomes in 10 days for less than $10,000 per genome.
I doubled up on genetic testing, receiving reports from two different companies, 23andMe and Pathway Genomics. I signed up for an early 23andMe test at $1,000 and a later Pathway Genomics test for $399. In both cases, about six weeks after I sent off my spit, I received an email message telling me my test results were available. I got 23andMe’s results first, and I logged onto its website with the kind of happy anticipation one feels opening birthday presents.
What do results look like?
The good news: I have low odds of suffering from male pattern baldness, and my chance of getting rheumatoid arthritis is less than 1 in 100, compared to the average risk of 2.4 per 100 people.
Unfortunately, I carry two gene variants that increase my risk of age-related macular degeneration and one variant that reduces the risk, which means that combined my risk of going blind is 9.5 out 100, compared to the typical risk of 7 out of 100. It is just as well that I have no plans to become a competitive short-distance runner, since I do not have the gene variants for fast twitch muscles often found in world-class sprinters. I also have gene variants suggesting that being breastfed likely would have raised my IQ by six or seven points.
The tests revealed there’s no truth to the family legend that we’re related to a Cherokee princess. 23andMe’s ancestor screening tests suggest that it would be hard for someone to be more genetically European than I am. According to my mitochondrial DNA, my maternal line descends from Haplogroup U5, which arose among early Homo sapiens sapiens colonizers of Europe around 40,000 years ago. According to my Y chromosome, my paternal line appears to hail from Ireland. The results from Pathway Genomics later confirmed this genealogy.
In the course of making information understandable to users, both 23andMe and Pathway Genomics generally cite research that has been strongly confirmed by the peer-reviewed literature. But if you’re hankering for more detailed and speculative insights into your genetic information, you can run the raw data through Promethease, a trait analysis tool that links test results to research reports compiled at the wiki-style SNPedia. As is often the case with crowd-sourced information, SNPedia is comprehensive but messy. When I compare the reports from 23andMe and Pathway Genomics with the results I got at Promethease, however, all three pretty much agree.
Promethease tells me I have the complement of alleles strongly suggesting that I am male. Very reassuring. It also agrees with 23andMe that I have some alleles indicating a low probability of being bald. Check. An allele for light skin color. Check. A set of alleles showing I can digest milk as an adult. Check again. I was also happy to learn that my risk of ovarian cancer is likely one-third lower than average.