Genomics 2.0: Ten Years After the Bubble, it’s Getting Really Interesting Again
What do 10,000 people with autism, 50,000 people in some remote islands in the North Atlantic, and 1,000 healthy old folks in southern California have in common? They are on the front edge of one of the most exciting stories in science today, and their contributions will have a huge impact on our long-term understanding of biology and medicine.
The headlines from just the last couple weeks in genomics are jaw-dropping. Experiments are being announced almost every week which would have been unimaginable even a year ago when sequencing a whole genome cost around $10,000. Suddenly an individual’s entire genome, the complete 6 billion letter signature of DNA units in each human, can be had for $4,000 or less, in a few weeks. And that has enabled scientists and business people to dream some pretty big dreams, like these:
—BGI, formerly known as Beijing Genomics Institute and the world’s largest genomic organization, said last week it will sequence the entire human genomes of 10,000 people from 2,000 families who have at least two children with autism. The project, in collaboration with the patient advocacy group Autism Speaks, will look to unravel the complex interplay between genetics and environment that is thought to contribute to this developmental brain disorder.
—The Faroe Islands are a remote speck in the North Atlantic Ocean, where about 50,000 people live under a self-governance agreement with Denmark. The local ministry of health has exercised some of that self-governing authority by teaming up with DNA sequencing leader Illumina (NASDAQ: ILMN) to capture the genomes of all 50,000 people in the Faroe Islands. Only 100 people will get their genomes sequenced in the pilot phase of the project, but this experiment has big promise. Like Iceland, home of the well-known scientists at deCODE Genetics, the Faroe Islands are a place with a relatively homogenous population, good genealogy records, and medical records. This is the kind of place that can help scientists connect the ever-elusive dots between genetic abnormalities and various diseases.
—Mountain View, CA-based Complete Genomics (NASDAQ: GNOM) said earlier this month it will work with Scripps Health in San Diego to sequence 1,000 genomes of healthy people in their 80s and up, to look for the secrets to long, healthy life. The trial, known as the “Wellderly Study,” will include 1,000 people who are “well” without any major diseases or long-term health complications, and “elderly,” from the ages of 80 through 108.
The size of these experiments does matter. While having individual genomes like those from Craig Venter or Jim Watson are nice to have, their main use is as a reference for all that work mentioned above. By sequencing many, many genomes and looking carefully for the subtle differences in them that make everyone different, suddenly there’s potential to generate all sorts of new ideas about what causes various diseases.
Many of these ideas will go nowhere. But the opportunity to gain fundamental knowledge is enormous. Biologists today don’t really know what causes lots of society’s common diseases—autism, Alzheimer’s, rheumatoid arthritis, to name a few—where the complex symphony of genes and environment gets out of kilter. Once those genomes are stashed in databases, then scientists can start looking more seriously for patterns that will offer clues to what’s going wrong.
“We’re still really at such an early stage of sequencing,” says Alex Dickinson, a senior vice president at Illumina. “We have maybe 10,000 genomes or so sequenced right now. It’s statistically unlikely that we would have gotten profound data out of that. But as the number of people goes up, we’ll have an avalanche of information coming out. It’s driving a huge amount of activity in the industry.”
I know what quite a few biotech readers are thinking about now—haven’t I seen this movie before? Scientists sequenced the first human genome a decade ago, a couple scientists had their photo op on the White House lawn, and some overhyped biotech companies cashed in on irrational Wall Street exuberance. Patients saw almost zero benefit.
A lot of the same dangers remain if people take a short-term view of what’s happening now. But over the past decade, companies like Illumina, Life Technologies, Complete Genomics, and PacBio have made progress on speed and output with sequencing instruments that moved faster than Moore’s Law. The $1,000 genome is only a couple years away, most industry observers agree, and it will probably even go as low as $100 per genome at some point. This trend is creating some very interesting challenges for computing, for medicine, and society—all things we’ll talk about at next Monday’s Xconomy conference in San Francisco.
What people need to remember is that just because scientists can crank out all this data, and wax eloquent in the press, miracle cures aren’t coming around the corner anytime soon. Yes, all their grant applications and media quotes will play up the impact for human health. But big hurdles remain. All this genomic data needs to be efficiently stored, analyzed, visualized, and placed in context. Putting the data in context means comparing genomes from one person to the next to see why one person is healthy, and why one is diseased. Even that kind of data might not provide very much insight without a good family medical history, or electronic medical records from a person’s whole life.
While this past decade was about generating DNA sequence data, the next will be about interpreting it. This is not going to be easy since there’s so much at work in the interplay between genes and environment in conditions like obesity. Like with any form of basic science, a lot of it will lead down dead ends. Even when the best discoveries are made, it will take decades for genomic data to bear fruit with new treatments. And there will be really thorny ethical debates that society will have to confront sooner or later.
Personally, I can’t imagine a better time to be following what’s going on in genomics. Tens of thousands of people are there right now on the tip of a genomic iceberg, and hundreds of thousands are sure to get there soon. Now is when it’s getting really interesting.