As a result of recent progress in DNA sequencing technologies, which has generated datasets of unprecedented complexity and advanced our understanding of health, disease, and development, whole-genome sequencing has emerged as a highly anticipated goal. However, routine sequencing of whole genomes is still a challenging milestone, particularly for clinical applications.
A more affordable approach, target enrichment, involves capturing genomic regions of interest prior to sequencing. One example is whole-exome sequencing, in which next-generation technologies sequence only the coding regions, which represent slightly over 1% of the human genome and are thought to harbor a large proportion of the variation associated with human disease.
“A few years ago, I would have thought that targeted sequencing would be influential for only a few years, and that it would be replaced, as sequencing costs come down, by whole-genome sequencing, but that has not happened yet,” says Chad Nusbaum, Ph.D., co-director of the genome sequencing and analysis program at the Broad Institute.
Dr. Nusbaum and colleagues developed an approach called Solution Hybrid Selection capture, in which biotinylated RNA capture bait probes are generated and mixed with a library of randomly sheared DNA fragments amplified from human genomic DNA that are modified with sequencing adaptors. Hybridized fragments are captured on streptavidin beads, and the DNA is sequenced on a next-generation platform.
This method facilitated the extensive sequencing of targeted genomic loci of interest. After optimizing and further developing this application, investigators from Dr. Nusbaum’s lab recently described the first automated, highly scalable application to perform Solution Hybrid Selection capture in a cost-effective and highly efficient manner.
Several target-enrichment approaches have emerged in recent years. A factor that has catalyzed the expansion of this field is that as long as the costs remain significantly lower than the costs of sequencing whole genomes, more samples can be analyzed. “Since human genetics is all about statistics, and statistics is driven by the number of samples, targeted sequencing remains a significantly growing area,” says Dr. Nusbaum.
Among target-enrichment platforms, exome sequencing has received increasing attention. To a great extent, this can be explained by our better understanding of the direct biological implications of sequence variations within exons. “The remaining 97–98 percent of the genome, while it cannot be ignored and we need to learn more about it, is still difficult to understand in terms of biological and clinical implications,” emphasizes Dr. Nusbaum.
“We were interested in examining quantitative trait loci, and after localizing a specific genomic region identified by linkage analysis, we adopted the emerging technology of targeted resequencing,” says Jeremy B.M. Jowett, Ph.D., head of genomics and systems biology at the Baker IDI Heart and Diabetes Institute from Melbourne.