Genetic sequencing has received a great deal of coverage lately, primarily due to an effort on the part of Roche AG to takeover Illumina (considered by many to be the leader in genetic sequencing). Last month, Roche submitted a $5.7 billion dollar offer, which was rejected by Illumina’s Board of Directors as “grossly inadequate”. Despite the rejection, many believe that Roche will increase its bid. Roche’s CEO Severin Schwan recently stated on CNBC that “this transaction creates a lot of value for both Illumina and for Roche. By combining the two organizations, we can leverage the Roche global footprint, our global customer base, and more importantly, we have the know how and expertise to bring sequencing primarily in the research lab into the clinical setting.”
Illumina however is not the only company with a genetic sequencer; Life Technologies has the Ion Proton Sequencer, which competes with Illumina’s machine. Both Roche and Life Technologies want to move this technology into routine medical diagnosis where the information can be used to diagnose difficult diseases, make treatment decisions and select appropriate medication all based on the patient’s genetic make-up. Experts believe that moving the use of genetic sequencing from the research lab to regular clinical use will increase the global market from about $1.5 billion to $10 billion and Life Technologies CEO, Greg Lucier believes this increase will happen over the “next few years.”
The move from the lab to the clinic is only possible because both Illumina and Life Technologies have introduced genome sequencing machines that make sense in a clinical setting. Previous machines were the size of a large copier and new machines are the size of a desktop printer. These new machines are relatively affordable at a cost of around $150,000 with sequence costs around $1,000 per genome. In addition instead of taking a week to run, it can be run in a day and perhaps in as little as two hours. These changes have made the idea of using this as a fast diagnostic tool a reality. One company is even taking it a step further, Oxford Nanopore recently introduced a handheld device about the size of a USB stick that is less than $1,000 and will run up to 5,000 pairs for $900. While some believe that this machine will allow doctors to carry these around and to run immediate testing on biopsies or look for pathogens such as viruses, many worry about the machine’s 4% error rate, which is too high to be used in diagnostics. At any rate, the technology exists and certainly the 4% error rate can be improved upon for diagnostic use.
The spotlight on this industry and the potential that genetic sequencing has to significantly change the course of medicine, as we know it, raises numerous possibilities for applications of this scientific breakthrough. One area where genetic sequencing could have a huge impact is in the area of diagnosis. A team headed by Michael Hammer from the University of Arizona used Genome Sequencing to determine the genetic reason behind a patient dying suddenly from unexplained epilepsy. They found that the cause was a previously unknown mutation in a gene coding for a sodium channel protein. These findings, published in the March 2012 issue of the American Journal of Human Genetics, were not able to help this patient, but the idea is that if this genetic mutation had been caught earlier it might have allowed the patient to receive treatment and for their life to be saved. “We are looking at the level of the entire genome,” Hammer stated, “something that was not possible until very recently.” “The Hammer lab plans to establish a diagnostics facility to make whole genome sequencing available to the clinical community in hopes to help children with early onset epilepsy and other rare undiagnosed disorders.”
Genetic sequencing isn’t limited to DNA, Robert Lanciotti, Chief, Diagnostic and Reference Laboratory, Arbovirus Diseases Branch, Centers for Disease Control and Prevention purchased an Ion Torrent Personal Genome Machine from Life Technologies to sequence RNA viruses. He said “The machine is faster and generates more data than the traditional sequencing methods so we can complete our projects faster.”
There are many of these examples in diagnostic applications and also in drug discovery. This is particularly true in the development of therapies against cancer. By using genetic sequencing, researchers are able to learn more about patients’ tumors – what makes them grow uncontrollably and what is the most effective way to turn those genes off? In an interview with Bloomberg, Harold Varmus, Director of the U.S. National Cancer Institute stated “With an exact understanding of the genetic alterations causing individual tumors to grow uncontrollably, doctors can target therapies for better effectiveness.”
In addition to direct diagnosis and treatment of patients, genetic sequencing is changing genetics in other areas. Genetic sequencing can help to characterize plant genetics and understand how changes in plant DNA might impact plant health, disease resistance and productivity. Ning Huang, Ph.D., Vice President of Research and Development at Ventria Bioscience states “If we can cost effectively determine changes in plant DNA from one variety to another, we can develop new varieties with improved genetic characteristics. In our case, we can use plants as the biopharmaceutical factory for cost effective and large scale manufacturing of recombinant proteins and peptides.” Ventria Bioscience is the first company to commercialize recombinant proteins derived from a plant-based manufacturing system.
In other areas of biomanufacturing, such as the use of Chinese Hamster Ovary (CHO) cells which are used to produce many biotech medicines today, a cost effective method to characterize the genetics of each CHO clone could lead to improved process consistency. Recently the first genome-wide CHO sequences have been published with great interest from the scientific community (Reference Xu et al. Nature Biotechnology). Genetic changes in a CHO clone can lead to variability, so identifying these changes more quickly could lead to more precise cell line development and better control over cell banking and seed train expansion prior to the use of these cells in biomanufacturing. “Better control and a better genetic information set for CHO cell lines will likely result in improvements in consistency and productivity, which is something we all want to see”, according to Dr. Steve Pettit, Director of Cell Culture R&D, InVitria.
There are so many ways to use genetic sequencing to improve medicine and now that machines are affordable and results are available quickly it is certain that genetic sequencing applications will continue to expand.