Dr. Elaine Mardis, The Genome Institute’s Co-Director and Director of Technology Development, in front of Pacific Biosciences’ third generation instrument.
Sequencing technology has exploded since the completion of the Human Genome Project, the international effort to sequence every letter, or ‘base,’ of our body’s DNA. Dr. Elaine Mardis, The Genome Institute’s Co-Director and Director of Technology Development, is intimately involved with this technology and has watched its influence grow within the field of genomics. Dr. Mardis summarizes her views on sequencing technology and its impact on biomedical research over the last decade in a perspective published in the journal Nature’s 10th anniversary issue celebrating the first draft of the human genome. She writes in the article that since the announcement, “the ensuing 10 years has been marked by dramatic improvements to sequencing technology that have catapulted sequencing to the forefront of biological experimentation and have revolutionized the way that we approach genome-wide questions.”
The first widely used form of DNA sequencing technology was based on a method that is still in use today (with some updates and automation). Called Sanger sequencing, it relies on a technique known as capillary electrophoresis, which separates fragments of DNA by size and then sequences them by detecting the final fluorescent base on each fragment. Compared to more recently developed technologies, this method is slow and expensive, but it is highly accurate, which is why it remains a valuable tool. This is the technology that was used to sequence the DNA from the Human Genome Project.
The advent of newer technologies has brought fierce competition among various sequencing methods and companies, each of which have their own advantages and disadvantages. The newer or ‘next generation’ sequencing technologies are far faster and cheaper than Sanger sequencing, since they occur in a massively parallel manner (meaning many strands of DNA are sequenced at once). This kind of sequencing generates far more data per instrument run than the Sanger method. But one major disadvantage lies in the technologies’ read lengths: The number of DNA bases per sequenced fragment is much lower than Sanger reads. Also, increased data generation - while on the surface may seem like an advantage - does present its own problems.
The availability of massive amounts of data from the next generation sequencing technologies has prompted the need for larger data storage facilities and the ability to analyze and manipulate much larger data sets than in the past. The analysis task falls in large part to those in the field of bioinformatics – which applies statistical and computational analysis to the study of genetic information. This field is key to understanding what the large amounts of data coming off the sequencers actually means and how best to apply it in the real world. The applications of being able to generate such large amounts of data in a relatively short time are widespread.
One of the fields of study to benefit most from advanced sequencing technologies is cancer. The newer technologies can now sequence an entire human genome in just over a week. This kind of speed makes it more feasible to sequence multiple patients’ normal and tumor genomes to understand more about how the disease progresses. “Within a given cancer patient we have this unique ability to compare the genome they were born with to the genome that develops in their cancer cells,” says Dr. Mardis. By looking at the changes in the DNA between a patient’s normal and tumor genomes, this research is already beginning to help inform both cancer diagnosis and treatment.
Yet as Dr. Mardis points out, this kind of work is still extremely expensive and resource-intensive, and the number of people it can help remains small. “Doing this work is extraordinarily time consuming because you want to get it right and you also need a broad brush of expertise – not only for the analysis of the data, but for the interpretation of the data.” she says. There are also issues to consider when disclosing the results of this sort of research to the patient. “It’s this kind of a ‘brave new world.’ There are many ethical considerations that come into play when we have to deliver the information back to people.”
In her perspective, Dr. Mardis describes this complicated interplay of sequencing, analysis and interpretation of data in terms of a car. Sequencing technology is like the engine powering the car that allows us to explore the human genome. But a car requires more than just an engine to run – it needs the fuel (DNA), parts (automation) and something to direct it (bioinformatics) to its destination (biological discovery). Because of this complicated interplay, it’s often very difficult to evaluate a new technology. For this reason Dr. Mardis leads The Genome Institute’s Technology Development group. Their main goal is to take a new technology for a ‘test drive’ to determine how well it works and whether it fits into the institute’s larger project goals. “People really look to us for that initial validation of the technology,” says Dr. Mardis. She adds: “We’re obligated, in some ways, to try every technology and to evaluate it. And that’s why I’m happy that we have a devoted group that does nothing but that.”
With the rise of massively parallel sequencing, there has been a drive to improve on the initial technology. The latest sequencers, called ‘third generation,’ are now capable of sequencing DNA directly – eliminating much of the sample preparation that was necessary for Sanger and next generation sequencing. While these technologies are still not able to sequence an entire human genome in one run, they have the potential to become powerful diagnostic tools. One use may be to sequence the smaller genomes of infectious agents from viral and bacterial outbreaks.
As sequencing technology and analysis marches along, so do the potential applications. Along with the study of cancer and infectious disease, the new technologies are being used to catalog the complement of microbes inhabiting our bodies, understand the cells that make up our tissues and compare the genomes of vast numbers of species to learn more about evolution and disease. This research is beginning to fulfill the initial promise of the Human Genome Project. Dr. Mardis summarizes such progress in her Nature perspective: “Taken together, these unprecedented sequencing and analysis capabilities have inspired new areas of inquiry, have solved major questions about the regulations, variability, and diaspora of the human genome, and have introduced a genomic era in medical inquiry and (ultimately), practice, that will bring about the originally envisioned impact of the Human Genome Project.”