There appears to be a full-scale race underway to bring affordable next-gen DNA sequencing into diagnostics and clinical medicine, as demonstrated over the past week or so by Roche’s hostile $5.7 billion-dollar bid for Illumina. Roche’s move should come as no shock. The multi-national healthcare giant has been a leader in diagnostics by virtue of several earlier acquisitions. But this action signifies a formal acknowledgment that next-gen sequencing will be part of the diagnostic and clinical toolbox—perhaps sooner than we thought.
Roche’s aggressive move may be motivated by an optimism that arose from whole genome-sequencing on the individual level. We noted this rising tide of optimism early last year, and many advances have been reported since then. We’re certainly seeing many examples of the application of next-gen sequencing to diagnose disease and to help match the right drugs to the right patients. Examples of companies that are staking claims over the early application of targeted sequencing of specific panels of genes for diagnostics include our client Multiplicom, which develops CE-marked, multiplexed PCR kits to generate templates for next-gen sequencing, and Foundation Medicine, which is using targeted sequencing to help diagnose certain cancers and to guide the treatment of cancer patients.
But when viewing the widespread adoption of DNA sequencing, there’s a vast difference between the targeted sequencing of selected panels of genes, exome sequencing, and whole genome sequencing. As noted in our coverage of the 2011 Molecular Med Tri-Con, the challenge of interpreting the large reams of data gathered from scanning the full genome remains the elephant in the room. We will be attending this year’s Tri-Con later this month and look forward to hearing about progress in this regard.
In addition to the challenge of data analysis, we still face some persistent technical issues. Although the cost of DNA sequencing is declining rapidly, there are significant improvements to the technology that are yet to be realized. Speed, cost, and accuracy will be key drivers of clinical and diagnostic DNA sequencing. Although costs are declining rapidly, most next-gen sequencing platforms are somewhat error prone and they have relatively slow cycle times. The accuracy problem is overcome by re-sequencing samples to a high level of coverage or redundancy to help eliminate stochastic errors. High sequence coverage is also needed to identify cancer causing mutations that are present at low frequency and in samples that often contain a mixture of both healthy and cancerous cells.
In clinical applications where patients’ lives are at stake, an accurate diagnosis is crucial. So improved accuracy will not only generate more reliable data, but will also reduce the computational burden, and lower the overall cost and the time required for analysis. Achieving the 1000x sequencing coverage that is required for cancer-related applications is a weighty burden. Sequencing platforms with higher levels of accuracy, lower cost and higher speed will provide a significant advantage. LaserGen is a forward-thinking company (and Popper and Co client) that has developed advanced sequencing chemistry with greatly improved accuracy, reduced cycle times, and lower cost relative to existing next-gen chemistries. This combination of improved speed, cost, and accuracy could help to drive more widespread adoption of next-gen sequencing for clinical and diagnostic applications.
Also, as noted in a recent Bloomberg News article about young twins whose illness was clearly identified via genome sequencing, many obstacles, including lack of health insurance coverage for sequencing, will likely impede progress. Until payers wrestle with a future that includes a populace that is well-informed about their genetic predispositions, even affordable gene-sequencing may find itself relegated to a pile of non-insurable “preventative” claims. And as mentioned earlier—we still do not fully understand the function of every part of the genome.
Ultimately, I believe Roche’s acquisition of Illumina—if it goes through—will be good for the gene sequencing industry, good for Roche’s competitors and good for healthcare consumers. The buyout of Illumina helps validate the idea that sequencing will become part of the diagnostic and clinical toolbox in the near future. Whether companies realize this and plan accordingly, or whether the wave simply carries everyone along, remains to be seen.
Do you agree that this is a good move for the diagnostics and sequencing industry as a whole? What might it mean for your company or your spot in the life science industry? Please share your thoughts with us here.
Tags: diagnostics industry, DNA sequencing, illumina, next-gen DNA sequencing, Roche, sequencing industry, universal DNA sequencing
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Now that the Molecular Med Tri-Con 2011 has ended and attendees are back at their offices, labs, practices, and/or hospitals – or perhaps have landed at their next business meeting or conference destination – it’s a good time to reflect on some of my general observations from the event.
The conference covered so much information that it would be impossible to review every topic. Following are a few areas that captured my attention and remain in my thoughts:
- STEM CELLS – There was a lot of focus on induced pluripotent stem cells (iPSC), in particular how to better characterize and understand those cells. Pluripotent stem cells can differentiate, or change, to become any one of the many types of cells that make up an organism. These cells are already being used for applications such as drug testing and drug screening. Once they are induced to re-differentiate, iPSC can provide good models for disease: what some conference speakers referred to as a “disease in a dish.” Some discussion among presenters focused on the idea of isolating cells from patients, producing iPSC, and then reintroducing the produced cells into the patient to replace cells that have been damaged or lost as a result of disease – an elegant form of cell-based therapy. Although widespread use of this approach is likely a ways off, I’m both optimistic of the therapeutic potential and somewhat cautious because of regulatory hurdles and potential safety issues (including some data showing tumor production in animals).
- CIRCULATING TUMOR CELLS (CTC) – This field of study is moving very, very rapidly. There’s immense scientific and medical interest in the clinical utility of these cells – as diagnostic biomarkers or as prognostic markers of disease recurrence. Also, as we’ve written before, there’s an emerging trend not just to count, but also to characterize CTC (which could increase their diagnostic utility, according to many conference presenters). Further characterization will provide information that will enable physicians to guide the treatment of patients in an increasingly personalized way, which is a very attractive idea. Also on CTCs: Discussion occurred on the need to isolate and characterize more types of cells (beyond those from epithelial tumors; “epithelial” = outside layer of cells that covers open surfaces, including skin) and to broaden the definition of CTC to include other types of rare, circulating cells.
- DNA SEQUENCING – One of my favorite topics, DNA sequencing, was a focus area at the conference. Jonathan M. Rothberg, Ph.D., Founder, Chairman & CEO of Ion Torrent (recently acquired by Life Technologies) described the most recent version of his company’s sequencing instrument. He shared an anecdote of how their instrument was used to sequence the genome of Gordon E. Moore, founder of Intel, who developed Moore’s Law (which states that the number of transistors on a chip will double about every two years). Rothberg explained that he and his company have been inspired by Moore’s Law and by Moore himself, noting that the Ion Torrent sequencer is based on semiconductor technology that uses electrons rather than light as the readout – so the sequencing of Moore’s genome takes science in a full circle. As for the next step in DNA sequencing, the big issue appears not to lie in generating the sequence data itself, but rather in the analysis and interpretation of the data. We have now realized the $10,000 genome (and the $1,000 genome is very close), but there was a lot of talk about the need to interpret all of that data, and much tongue-in-cheek reference to the “$1M analysis,” which reflects widespread concern about the magnitude of the challenge associated with making full use of the data.
- INFORMATICS: As a result of sequencing and other data-delivering trends, there’s now a great deal of effort underway to manage extremely large volumes of data and information. One trend discussed at the conference is the application of cloud-based computing to provide horsepower to analyze these complex data sets, to query large databases, and more. Virtual computing clusters may allow for widespread analysis by researchers who might not otherwise have sufficient computing infrastructure at their fingertips.
I could go on and on here, but I think you get the idea. Technology is advancing so rapidly that the landscape looks a lot different than it did even six or eight months ago. As a result, people are thinking of applications in health care differently, which is a great thing.
We would love to hear your thoughts on both the potential for and challenges of new technologies to affect the delivery of health care. Please use the comments link below.
Tags: circulating tumor cells (CTC), DNA sequencing, gordon e. moore, informatics, intel, ion torrent, life technologies, molecular med tri-con 2011, moore's law, personal genomics, stem cells
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