DNA Sequencing

To find out more about the world of DNA sequencing, NGP asked Christopher K McLeod, President and Chief Executive Officer, 454 Life Sciences Corporation and Robert Bondaryk, Ph.D, General Manager and Unit Head, Cogenics, for their thoughts on this increasingly important area.

NGP. How scalable are your solutions to manage workflow, maximize their research, and handle quantities of data with managing and analyzing DNA?
RB. Cogenics is constantly assessing the latest platform technologies applicable to our core sequencing business and the needs of our sophisticated customer base. In this way we continue to remain at the leading edge of technology, offering commercialized regulated and non-regulated sequencing services.

The infrastructure that revolves around sequencing is highly automated, interfaced with LIMS, and highly scalable with the ability to utilize capacity across four sites spread throughout the US and Europe.

Development of more seamless e-commerce solutions for order placement and data retrieval will continue to improve the service we provide our customers.

The depth of experience in the area of sequence data analysis, from single gene to full genome, is exemplary in the industry and has been gained over the last 17 years from working with many of the top pharmaceutical and biotech companies around the world.

CM. Our solutions are extremely scalable. By simplifying the sample preparation process and eliminating the need for any cloning, one person in one day can prepare any size genome, be it viral or mammalian. There is no need to invest in expensive robotics. The system enables ground-breaking applications in the fields of whole genome sequencing, amplicon analysis and transcriptome and gene regulation studies.

454 Life Sciences has invested significantly in developing data analysis tools to aid the scientist in their research. Our amplicon analysis software tool aligns individual reads of the same gene from thousands of different cells, permitting unparalleled sensitivity in mutation detection.

NGP. As the strategy for determining sequence of complete genomic DNA is so incremental, how tailored are your DNA sequencing solutions to meet your clients needs of their every day practices they can use to get their work done?
RB. With a wealth of experience in DNA sequencing, data assembly, and analysis, Cogenics provides fully tailored services to meet all of its customers’ needs.

The current development of whole genome sequencing technology platforms is being watched very closely and assessed to provide for all of our customers’ current and future needs. No system currently available has a major advantage over current platforms, and the utility of these next generation platforms for the traditional Cogenics business remains undetermined. We remain committed, however, to adjusting our service offerings/platforms to meet our customers’ needs for regulated and validated sequencing services.

CM. Our customers no longer need to wait for incremental progress in DNA sequencing. Our growing list of pioneering sequencing applications published in top-tier scientific publications clearly demonstrates our ability to meet every day needs today. By making whole genome sequencing rapid and economical, 454 Life Sciences is transforming the current de novo and re-sequencing paradigm. In less than one week, a typical bacteria can be prepared and sequenced, and the data assembled into a draft genome. 454 Sequencing technology lacks the bias often seen with Sanger sequencing, which also makes ‘finishing’ of genomes much easier and less expensive.

With the increased amount of sequencing data in the industry, what are your approaches to solving problem sequences and how do you change the style and pace of DNA sequencing? (ex. Sequencing data per day)

454 Sequencing technology is accelerating the pace of DNA sequencing. Today a single Genome Sequencer 20 has a throughput of over 80 million bases per day using 100 base pair reads. Our second generation GS FLX instrument, available in the first half of 2007, will have sequencing throughput in excess of 300 million bases per day with even longer reads (greater than 200 base pairs) to enable higher quality annotation and broader range of de novo and re-sequencing applications. Contrast the output of a single GS FLX instrument with the throughput of a typical large scale genome center using Sanger sequencing, that requires dozens of instruments and a capital investment totaling tens of millions of dollars to yield only 150 million bases per day.

RB. In the era of therapeutic diagnostics, the extensive experience and capabilities of Cogenics and its sister division PGxHealth provide tailored solutions for sequence data generation and analysis to support the delivery of genomic-based tests and the development of efficacy and safety biomarkers for appropriate drug utilization. Solutions for utilizing unique biomarkers to determine which individuals will experience optimal benefits from specific therapies and, in some cases, to identify genetic diseases, are now available to support the personalized use of specific drugs or provide diagnostics answers as to propensity for developing a particular disease.

Numerous solutions to resolve problems with difficult-to-sequence templates have also been evaluated/developed by Cogenics stemming from the 16 years of experience sequencing a wide range of template types, including those with structural issues and a variety of repetitive regions. These solutions involve a variety of different chemistries and cycling conditions, as well as utilizing our highly trained staff. As a result, the process does run at a slower pace despite the utilization of a number of automated systems.

Certain highly conserved, large repetitive sequences however continue to remain a challenge to the industry.

NGP. As new technologies emerge, how do you continue to improve the sequencing market?
RB. Cogenics remains committed to providing the latest, most reliable, commercially relevant technology platforms and software available for generation and analysis of sequence data for all its services. Industrialization of the sequencing process and a high degree of automation provides Cogenics the ability to rapidly scale and to provide a highly competitive, consistently high quality service to all of its customers. The existence of both regulated and non-regulated sequencing units allows rapid prototyping and SOP generation in a non-regulated environment before passing to the regulated service group for full validation and release as a commercial service.

CM. We continue to improve 454 Sequencing in response to our customers needs. The GS FLX will feature increased read lengths, on average greater than 200 bases, that will allow even more applications to be rapidly developed.

We are enabling applications on the Genome Sequencer to support the specific research interests of our customers. For example, 454 Sequencing is ideally suited for exploring short RNA as scientists try to elucidate the cellular function of this recently identified class of molecules. A number of recent publications in journals such as Nature and Science have been a result of 454 sequencing.

NGP. With drug development being an expensive and timely process, how do you believe your technologies simplify complex laboratory processes and accelerate speed to make drug discoveries and increase drug approval?
CM. 454 Sequencing aids in both the research and approval processes for drug development. A good example is the work 454 Life Sciences performed for a major pharmaceutical company that had developed a new anti-infective drug. Prior to entering the clinic, they wanted to know if their drug worked through a different biological pathway than the current class of drugs. They sent us the pathogenic bacteria and several closely related, resistant strains. We quickly sequenced all of the bacterial strains and were able to identify a handful a genes with mutations, one of which was easily confirmed as the target; a target which is in a different pathway than that affected by current drugs. Discovery of new pathways directly linked to drug metabolism can lead to more successful drug development.

RB. The level of expertise in our organization allows Cogenics to contribute significantly to the acceleration and approval of new drugs. Cogenics provides a validated and regulated DNA sequencing service utilizing the latest relevant automated sequencing platforms. This service supports our customers’ needs for regulated sequencing required by the FDA in support of their INDs or to validate diagnostic tests that they are developing utilizing other, non-sequencing based, technology platforms. This, coupled with the companion services offered by Cogenics such as QPCR and traditional molecular biology techniques, allows the customer to have a single partner to support their regulatory needs in development of their products.

NGP. What direction do you predict the industry will take on the way pharmaceutical and biotech companies will be able to manage the production, analysis, and communication of DNA Sequencing?
CM. DNA sequence information will become increasingly important to the drug development industry as of the association of genetic variation to drug response becomes better understood. One example is research, published in the journal Nature Medicine in June, describing how the 454 Sequencing method identifies mutations in the Epidermal Growth Factor Receptor (EGFR) gene in tumor samples from patients with lung cancer. We hope our system will enable personalized medicine, such as identifying the early stages of drug resistance and facilitating a change in treatment that is tailored to a patient’s unique genetic response. The increase in all research and development data (including sequencing data) will be a challenge that we expect will be met over time via public and private resources.

RB. There are ever increasing demands placed on data quality and regulatory compliance applied to the development of pharmaceutical products by the regulatory authorities around the world. Commercial pressure to develop the next blockbuster is growing and customers continue to outsource their sequencing needs to commercial providers such as Cogenics to free talented scientists and internal resources for the investigation and development of new products. The potential of pharmacogenomics is also being recognized in allowing products to target specific subsections of the population, maximizing safety and efficacy.

The production of regulatory-compliant, commercial raw sequence data will continue to improve over the years with more sophisticated automation and the development of robust micro fluidic solutions. The miniaturization of sequencing reactions and the accompanying cost-savings and improved automation of reaction setup, along with data analysis will allow Cogenics to provide its customers with more cost effective sequencing solutions with a concomitant commitment to reduce the cycle times for data delivery.