Genomic Advances of the 2000s Will Demand an Informatics Revolution in the 2010s

We have witnessed some of most striking technological and scientific innovations in humankind during the first decade of the new millennium. While such claims perhaps seem cliché in an age where the media constantly report on new findings that really do not warrant our full attention, several discoveries and innovations in the recent history of genomics were truly groundbreaking and will have long-lasting implications.

The expanding applications of genomic technology that will help us better understand causes and treatments of common human diseases, global warming, and hunger will become clear in the coming decades. The innovations most impressive to me in the past decade were those that have begun to shake many of the foundations upon which the life sciences and biomedical research have been built. Here are what I consider four of those more impressive discoveries:

1) The discovery that environmental stress can induce heritable DNA-based changes.

2) The maturation of highly parallel sequencing and genotyping technologies that have revolutionized our ability to associate changes in DNA with disease.

3) The discovery of whole new classes of RNA that do not carry out instructions from genes, yet are still critical to cellular and higher order biological processes.

4) The development of third-generation DNA sequencing that will lead to greater insights about underlying biology.

As our ability to capture data from entire genomes increases exponentially, this is creating a huge software and computing challenge. Life sciences and biomedical researchers will need novel solutions (a yet to come fifth innovation):

5) The translation of the deluge of data coming from the new discoveries and technologies into actionable results that can impact human wellbeing.

This will be a big trend to watch in the coming decade, but more on that later. First, I want to explain a little about why I’m singling out these four particular discoveries and technologies as groundbreaking:

1. Environmental stresses can induce heritable DNA-based changes.

In 2005 Michael Skinner, a professor at Washington State University, published a paper in Science demonstrating that in response to exposure to an endocrine disruptor (a common environmental toxin), DNA can be chemically modified in certain locations and that these modifications can affect the ability of the biological machinery within the cells in every bodily organ to read the modified DNA. Reading DNA is a necessary first step for cells to manufacture the proteins

Author: Eric Schadt

Eric Schadt is the director of the Mt. Sinai Institute for Genomics and Multi-Scale Biology in New York, and the chief scientific officer for Pacific Biosciences, a company developing new gene sequencing technologies. He is also a founding member of Sage Bionetworks- an open access genomics initiative designed to build and support databases and an accessible plaform for creating innovative dynamic disease models. Dr. Schadt joined Pacific Biosciences in May 2009 from Rosetta Inpharmatics, a subsidiary of Merck & Co., Inc. in Seattle, where he was Executive Scientific Director of Genetics. Dr. Schadt's work at Rosetta involved the generation and integration of very large-scale sequence variation, molecular profiling and clinical data in disease populations to construct the molecular networks that define disease states and link molecular biology to physiology in ways that can impact clinical medicine. Dr. Schadt has contributed to a number of discoveries relating to the genetic basis of common human diseases such as diabetes and obesity, which have been widely published in leading scientific journals. His research has provided novel insights into what is needed to master diverse, large-scale data collected on normal and disease populations in order to elucidate the complexity of disease and make more informed decisions in the drug discovery arena. Prior to joining Rosetta, Dr. Schadt was a Senior Research Scientist at Roche Bioscience. He received his B.A. in applied mathematics and computer science from California Polytechnic State University, his M.A. in pure mathematics from UCLA, and his Ph.D. in bio-mathematics from UCLA.