Mike Cariaso discusses personal genomics for the rest of us.
November 16, 2010 | In case you missed its quiet entry, Personal Genomics is here. The list of early adopters begins with famous names like J. Craig Venter, James Watson and George Church’s Personal Genome Project (PGP). Approximately 100,000 names followed, buying SNP (single nucleotide polymorphism) kits from 23andMe, Navigenics and others, acquiring some level of information about their own DNA. There is a wide range in how much of each genome was read, but no technology today is able to tell you everything you might want to know at any price. Buying early was no bargain and in the past two years, direct-to-millionaire sequencing has fallen from $1 million to $20,000. Even in today’s $1,000 to $100 direct-to-consumer (DTC) market, paying more has little correlation to learning more. That’s good news, since many of the early adopters have paid even less, having instead been subsidized by investor speculation and the need for reference data.
Knowing your raw data is not the same as understanding its implications. Every day new studies are published, which expand our ability to interpret a personal genome. Last week’s high confidence result often fails to replicate in this week’s new population. Today’s accumulated genetic information still fails to explain much of the observed family inheritance of common diseases. What we do know with near certainty rarely causes more than a 20% increased risk in some disease, often while decreasing the risk of something else.
Since 2006, SNPedia.com has been tracking this progress. Of 20 million known genomic variations, we’ve cataloged 13,000 that have been published in the scientific literature as having some observed consequence. It is quite remarkable how rare and few are the ones which are directly causative of anything noteworthy. Instead, most have subtle effects on how the body responds to its environment. In an environment as diverse and dynamic as our planet, it’s hard to say that any one genotype is good or bad. The genome has many stories to tell, but so far it stubbornly refuses to share its biggest secrets.
You are probably not a member of this genomic secret society, but as a reader of Bio•IT World, someday you probably will be. Is it yet worth the price of admission? For the healthy but science minded, the most useful thing you can expect to learn today is not about disease. Environmental factors make most common diseases still too hard for us to predict, but pharmacogenomics is yielding early fruits. Users of Plavix, Warfarin, statins and many other medicines may find value in genetic testing today. James Watson exemplified this when he noted that he is homozygous for the ‘10’ variant of the cytochrome P450 drug metabolizing gene, CYP2D6. He has subsequently reduced his beta-blocker dosage from daily to weekly.
Genomics for Genealogy
Following in the footsteps of scientists, technophiles and their families, the next wave of personal genomics will come from family genealogists. Their numbers and their eagerness to share and compare genomes and family pedigrees will fuel companies and Facebook applications. Empowered by DNA’s precise audit trail, they will entirely ‘solve’ genealogy by mapping the full flow of human ancestry. Any anonymous DNA sample will immediately fit in exactly one place in this tree of humanity, and from it we will know all of your ancestors. Being adopted will never be the same again.
That same public network of genomes will be used for non-genealogical purposes. The hair and skin cells we continuously shed will incriminate the guilty, and free the innocent. Even if the perpetrator is not actually in such a database, relatives will be, and that will help focus the investigation. Prospective parents will consider genetic compatibility early in the dating process, and dating services will make that sort of screening a first step in suggesting matches for lonely hearts. Parents will not rely on dangerous trial and error to identify food allergies in their newborns. Indeed, the answers to many of today’s larger medical mysteries will be obvious in such a detailed network.
The majority of the first 100,000 DTC customers have been genotyped on an Illumina microarray. It was labeled ‘For Research Only’ but as the marketing of DTC companies has become bolder, so has the FDA’s opposition. Some sort of regulation is coming to the field, but what kind? Today the only thing certain is that the would-be regulators are as uncertain as the rest of us.
While there is considerable trepidation at the marketing of genomes, I’ve been pleasantly surprised by the nearly universal consensus that you have a fundamental right to your genome. The biggest reluctance comes from those who want you to have the data, but only after they tell you what it means for a reasonable fee. But the head of the NIH, Francis Collins, has said, “free and open access to genome data has had a profoundly positive effect on progress.” FDA regulations may curtail the marketing, but it seems increasingly unlikely to limit the fundamental availability of personal genomes for the masses. The learning curve is still steep and much uncertain remains, but the path seems safe with no fundamental barriers to continued progress in all directions. •
This article also appeared in the November-December 2010 issue of Bio-IT World Magazine. Subscriptions are free for qualifying individuals. Apply today.