Comprehensive DNA Signature Discovery and Validation

Abstract

DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46 Vibrio cholerae strains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu. Now that the genome sequences of hundreds of bacteria and viruses are known, we can design tests that will rapidly detect the presence of these species based solely on their DNA. Such tests have a wide range of applications, from diagnosing infections to detecting harmful microbes in a water supply. These tests can detect a pathogen in a complex mixture of organic material by recognizing short, distinguishing sequences—called DNA signatures—that occur in the pathogen and not in any other species. We present Insignia, a new computational system that identifies DNA signatures of any length in bacterial and viral genomes. Insignia uses highly efficient algorithms to compare sequenced bacterial and viral genomes against each other and to additional background genomes including plants, animals, and human. These comparisons are stored in a database and used to rapidly compute signatures for any particular target species. To maximize its utility for the community, we have made Insignia available as free, open-source software and as a Web application. We have also validated 50 Insignia-designed assays on a panel of 46 strains of Vibrio cholerae, and our results show that the signatures are both sensitive and specific.