Organism Identification using a Genome Sequence-Independent Universal Microarray Probe Set

Abstract

There has been increasing interest and efforts devoted to developing biosensor technologies for identifying pathogens, particularly in the biothreat area. In this study, a universal set of short 12- and 13-mer oligonucleotide probes was derived independently of a priori genomic sequence information and used to generate unique species-dependent genomic hybridization signatures. The probe set sequences were algorithmically generated to be maximally distant in sequence space and not dependent on the sequence of any particular genome. The probe set is universally applicable because it is unbiased and independent of hybridization predictions based upon simplified assumptions regarding probe-target duplex formation from linear sequence analysis. Tests were conducted on microarrays containing 14,283 unique probes synthesized using an in situ light-directed synthesis methodology. The genomic DNA hybridization intensity patterns reproducibly differentiated various organisms (Bacillus subtilis, Yersinia pestis, Streptococcus pneumonia, Bacillus anthracis, and Homo sapiens), including the correct identification of a blinded "unknown" sample. Applications of this method include not only pathological and forensic genome identification in medicine and basic science, but also potentially a novel method for the discovery of unknown targets and associations inherent in dynamic nucleic acid populations such as represented by differential gene expression.

Broad spectrum microarray for fingerprint-based bacterial species identification

“…With the advent of microarrays it became obvious that attempts should be made to exploit these new tools for fingerprint-based taxon characterisation. Eventually, a strategy similar to the one developed at our laboratory with a microarray containing 14,283 anonymous probes was successfully applied to identify bacterial and other genomes [19]. Together with the data shown here this supports our conclusion that fingerprint-based species identification is a powerful tool.…”

DNA Chip Analysis in Diverse Organisms with Unsequenced Genomes

“…In some cases DNA chips from closely related species have been applied successfully [8][9][10][11][12] but even closely related arrays often are unavailable. A number of attempts also have been made to develop universal arrays based on short oligonucleotide probes [13] or genomic shotgun arrays prepared with PCR amplified fragments [14][15][16]. Both, however, still require substantial resources and tend to be limited with respect to sequence diversity.…”

An information theoretic method of microarray probe design for genome classification

“…Almost all previous microarray classification methods use ways to detect particular genomic regions rather than using the genome sequence statistics and built-in Nmer signatures. Only recently, in [3], have shorter Nmers (12/13-length) been proposed for microarray placement detection, but since the N-mers were sequence-independent, this research did not go further.…”

“…Almost all previous microarray classification methods use ways to detect particular genomic regions rather than using the genome sequence statistics and built-in Nmer signatures. Only recently, in [3], have shorter Nmers (12/13-length) been proposed for microarray placement detection, but since the N-mers were sequence-independent, this research did not go further.With the volume of genomes being sequenced, we can now develop genomic fingerprints based on the composition and develop information theoretic measures can to discriminate and classify particular species. Information theoretic measures have recently been shown useful to construct evolutionary histories of genomes [6].…”

“…Unfortunately, in genomes with high mutations, such as HIV virii, PCR needs more than a few identifiers [2]. Many pathogens contain mobile genetic elements that can potentially interfere with proper identification using single loci detection systems and therefore, many loci are needed.With the advent of microarrays, there have been several methods developed [3,4,5]. In [4], each probe selected is a substring of a gene, which acts as its fingerprint.…”