Near-Term Technology Development for Genome Sequencing

Article excerpt

The purpose of this Request for Applications (RFA) is to solicit grant applications to develop novel technologies that will substantially reduce the cost of genomic DNA sequencing. Current technologies are able to produce the sequence of a mammalian-sized genome of the desired data quality for $10-50 million; the goal of this initiative is to reduce costs by at least two orders of magnitude. It is anticipated that emerging technologies are sufficiently advanced that, with additional investment, it may be possible to achieve proof of principle or even early stage commercialization for genome-scale sequencing within five years. A parallel RFA HG-04-003 ( RFA-HG-04-003.html) solicits grant applications to develop technologies to meet the longer-term goal of achieving four-orders of magnitude cost reduction in about ten years.

The ability to sequence complete genomes and the free dissemination of the sequence data have dramatically changed the nature of biological and biomedical research. Sequence and other genomic data have the potential to lead to remarkable improvement in many facets of human life and society, including the understanding, diagnosis, treatment and prevention of disease; advances in agriculture, environmental science and remediation; and the understanding of evolution and ecological systems.

The ability to sequence many genomes completely has been made possible by the enormous reduction of the cost of sequencing in the past two decades, from tens of dollars per base in the 1980s to a few cents per base today. However, even at current prices, the cost of sequencing a mammalian-sized genome is tens of millions of dollars and, accordingly, we must still be very selective when choosing new genomes to sequence. In particular, we remain very far away from being able to afford to use comprehensive genomic sequence information in individual health care. For this, and many other reasons, the rationale for achieving the ability to sequence entire genomes very inexpensively is very strong.

There are many areas of high priority research to which genomic sequencing at dramatically reduced cost would make vital contributions. 1) Expanded comparative genomic analysis across species, which will yield great insights into the structure and function of the human genome and, consequently, the genetics of human health and disease. Studies to date that have been able to compare small regions of several genomes, and "draft" versions of full genomes, have clearly demonstrated the need for much more complete data sets. While some of the needed data will be obtained over the next two or three years using existing DNA sequencing technology, and while costs will continue their gradual decline, the cost of current approaches to sequence acquisition will continue to limit the amount of useful data that can be produced. 2) Studies of human genetic variation and the application of such information to individual health care, which will also require much cheaper sequencing technology. Today, genetic variation must be assessed by genotyping the relatively few known differences at a relatively small number of loci within the human population. A richer and better characterized catalog of such variable sites is being generated to support more detailed and powerful analyses.

While these methods are, and will become even more, powerful and likely to provide a significant amount of important new information, they are nevertheless only a surrogate for determining the full, contiguous sequence of individual human genomes, and are not as informative as sequencing would be. For example, current genotyping methods are likely to miss rare differences between people at any particular location in the genome and have limited ability to determine long-range information (e.g., genomic rearrangements). Therefore, new methods based on complete genomic sequencing will be needed to use genomic information for individual health care in the most effective manner possible. …