January 31st, 2011
Posted by Shane Climie, Ph.D.
“We said that once we had finished sequencing the genome we would make it available to the scientific community for free. …And we will be doing that on Monday morning at 10am.” – J. Craig Venter, February, 2001
It’s been ten years since the famous unveiling of the first human genome sequence. Since then, we’ve developed the ability to sequence large numbers of individual human genomes thanks to rapidly changing technology that translates into ever lower costs per genome and higher throughput sequencing capabilities. The $10,000 genome has arrived – even sooner than anticipated – and now the challenge is to figure out what to do with all of the information that is starting to accumulate.
The past year has seen a number of key developments and there are no signs that things will slow down over the coming months:
- Several next-generation and third-generation DNA sequencing platforms have been launched and many genomes have now been sequenced.
- Last June, Illumina, Inc. announced that it would sequence whole genomes at 30-fold coverage for $19,500, and then promptly dropped the price to $9,500 for orders placed by physicians who would use the resulting information for genuine clinical relevance.
- Genome sequences can be delivered to your iPad. Take a look at Jim Watson’s personal genome sequence to get an idea of how all of this may start to take shape.
- The Personal Genome Project, which is spearheaded by George Church and coworkers is recruiting 100,000 volunteers to donate their DNA and medical histories to help create a critical mass of data that will enable the development of tools to assess various risk factors and to generally interpret the information encoded within ones genome.
All of these developments have been eclipsed, however, by several recent announcements that hold the promise of moving the DNA sequencing field into an even higher gear. At this month’s JPMorgan Healthcare Conference in San Francisco, for example, several companies announced hardware upgrades and new sequencing platforms.
- The just-announced $50,000 Ion Torrent Personal Genome Machine from Life Technologies has already been upgraded to deliver 100 megabases per run.
- Illumina announced its $125,000 MiSeq instrument, which will deliver up to 1.5 gigabases per run (current output is a more modest 120 megabases) at a cost of $750 per run.
- Both of these platforms compete with the $100.000 Roche 454 GS Junior, which produces 35 megabases per run.
- Pacific Biosciences also described its long-read technology; average 950 BP read length (vs. ~50-400 for most other platforms), with many reads exceeding 2500 BP.
- And lastly, Complete Genomics announced that its service offering has expanded significantly; the company expects to be able to deliver between 800 and 1200 genomes per month by the end of the year, and that has a current order backlog of 1000 genomes.
And, just last week, diagnostic testing company PerkinElmer entered the fray by announcing that the company would create a service business to allow researchers to get genetic data without owning their own DNA sequencers or high-powered supercomputers. PerkinElmer customers would be able to access and then analyze sequencing data in the “cloud” after entering a password-protected site.
So where will all of this lead? Basic science and molecular diagnostics seem poised to reap major benefits. However, diagnostic applications will not entirely come to fruition without significant growing pains. Although personalized medicine has arrived on the scene, regulatory and reimbursement issues remain a challenge for companies that plan to apply the most recent sequencing technologies for diagnostic applications. It’s also not yet clear how best to use the available information and to avoid the temptation to interpret the massive amounts of data given the relatively limited number of clinical studies that have been undertaken.
Nevertheless, we expect to see a lot of sequencing being done in diagnostics labs over the coming months. It’s just a matter of time before the business catches up with the science, and the clinicians catch up with the sequencers. Where do you think it will lead? What are the implications for your predictions? Please share your thoughts here.
Tags: diagnostic applications of genome sequencing, DNA, genetic data, Genome project, illumina, jim watson, molecular diagnostics, personal gemone project, personal genome sequence, Shane Climie
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