Introduction to Next Generation Sequencing and Genotyping Issue


Victor M. Ugaz

During the fall of 2005 I found myself teaching an elective course on the topic of microfabrication and microfluidics technology. Since this is a relatively fast moving field, I find it necessary to review the literature each time I teach the class so that I can make sure to incorporate examples that are up to date and reflect the current state of the art. It was at this time that I came across literature describing new methods that could be used to perform DNA sequencing. These approaches had been developed during the early 2000s and were just reaching a stage where commercial implementation was on the horizon, with key breakthroughs in polony and pyrosequencing based approaches having been published earlier in 2005 in the journals Science and Nature, respectively. As I read more, I was struck not just by how amazingly innovative the technology was, but also by the incredible implications it could have if successful. This was something new and exciting, something that I wanted to learn more about and share with others. Motivated by this interest, I eagerly developed a lecture for my class as a “forward looking” example of how miniaturization can have a revolutionary impact.

Although not personally involved in DNA sequencing work, I was familiar with the challenges and limitations facing conventional Sanger methods through my postdoctoral research dealing with microchip-based gel electrophoresis. Pioneering efforts to develop high-performance capillary electrophoresis systems during the 1990s were a major force behind the success of the Human Genome Project. But it was also becoming clear that a significantly improved toolbox would be needed before DNA sequencing could become anything close to routine. This sentiment was famously echoed in 2003 by Francis Collins’ call for renewed efforts toward the goal of rapid and affordable genome-scale sequencing—the “$1000 genome.” Further refinement of existing methods would be an obvious step in this direction, but there were also new ideas on the horizon. In a radical departure from the Sanger-based paradigm, visions of reconstructing a DNA sequence by detecting tiny changes in light, pH, and electric current associated with each individual base had been proposed. And as far-fetched as they may have sounded initially, by 2005 many of these innovative ideas were beginning to show real promise.

On the last day of class, December 2, 2005, I stood in front of the students and told them what they were about to see was something that would profoundly impact their lives within the next decade. I remember thinking that I should write that prediction down on a piece of paper and seal it in a dated envelope so I could later prove that really I said it (regrettably, I didn't follow through on the idea). The students, mostly chemical engineers, probably didn't view the lecture with nearly the same enthusiasm, but I didn't care. This was one of the few times I can remember being absolutely certain I was witnessing something big. In January of 2012, after not teaching this material for several years, I once again had the opportunity to give a lecture about next generation sequencing. As I went back to look at my original materials, I was astounded by how far the field had come in such a short time. Sequencing has become routine in many areas of research. Colleagues of mine a few doors down the hall now have these instruments in their labs. Like television, smartphones, and personal computers, it is becoming harder and harder to remember how we were ever able to manage without them.

It is rare to have a front row seat to watch an entire field emerge, grow, and begin to mature within the span of a decade. To me this is one of the most exciting things about the field of next generation sequencing, and it is in this spirit that we are delighted to present an outstanding collection of papers dedicated to this topic. We have assembled a diverse mix of reviews, technology-focused, and application-oriented papers that convey both the current state of the field and a glimpse of future directions. The review and technology-focused contributions are weighted toward nanopore-based methods, reflecting the rapid pace of recent progress in this area. The application-oriented papers cover a broader range of topics, but one aspect that stands out is the capability to study genetic variation. These broader studies are particularly demanding because sufficient data must be collected in order to establish meaningful correlations. “Traditional” electrophoresis-based approaches have also continued to evolve to address these needs, and can often compliment newer NGS methods in a synergistic way. In this spirit, we have also highlighted selected works focused on analysis of genetic variation to showcase the impact of more accessible sequencing technologies.

A unique feature of this collection is that our contributors have endeavored to make their work accessible to a broad range of readers. If you are new to the field this resource will be a good starting point to quickly get up to speed. If you are already involved in research related to next generation sequencing, this collection provides a broad snapshot of developments you may have missed because they are at the periphery of your main focus area. Of course none of this would have been possible without the efforts of our contributors, and we gratefully thank them for sharing their work and insights. We hope you find this collection as enjoyable to read as it was for us to prepare.


Best wishes,

Victor M. Ugaz