One of the challenges of this approach is the frequent and unexpected amplification of contaminating template DNA, as observed in control reactions. Another potential problem with targeting 16S rRNA pathogen specific sequences is unexpected polymorphisms. Hence, naturally occurring variants may not be represented on the microarray, and failure to selleckchem detect the variants would represent false negatives [11]. Another common PCR based approach detects pathogen type by amplification of a specific set of genetic markers that are measured on an array that has several probes for genes from a set of organisms. Such tests have been

used for food-borne bacteria such as E. coli O157:H7 [12], viruses [13] and mixtures of pathogens [14]. The drawback of using this approach with multiplex PCR primers sets is the generation of spurious products [11]. Array based technologies using 70-mer oligonucleotide Selleck JQEZ5 probes derived from pathogen specific genes have similar factors that require consideration. For instance, viral detection using a microarray composed of 1,600 unique viral oligonucleotides (70-mers) derived from 140 distinct viral genomes has been previously demonstrated [15] as a powerful viral detection mechanism,

but the drawback of this strategy is that only the group of known pathogen-specific genes will be queried. Given the enormous spectrum of genetic possibilities, only a highly parallel field deployable technology that is universal in nature has near-term potential to address these needs. The initial vision for a universal DNA microarray was a matrix of oligonucleotide containing features with unique n-mer probes [16]. This matrix could in theory be used to query a biological sample for the presence of any nucleic acid sequence. This technique requires constructing an array that contains 4n features. Larger values of n infuse greater specificity into the arrayed probes, but as n increases the number of required features grows rapidly. This universality Mannose-binding protein-associated serine protease is obtained

by synthesizing a combinatorial n-mer array containing all 4n possible sequences of length n [17]. The key issue is to find a value of n that is large enough to afford sufficient hybridization specificity, yet small enough to be practically fabricated and analyzed. We have previously demonstrated the utility of a genome sequence-independent microarray for identifying genetic differences [18, 19]. The initial prototype of universal arrays used oligonucleotide probe lengths of 12 and 13 bases. From 412 possible probes, a subset of 14,283 probes was synthesized using in situ synthesis technology and digital optical chemistry (DOC) [20–22]. Fluorescently labelled genomic DNA was hybridized to produce unique informative patterns (i.e. bio-signatures) on a test set of pathogens and host (Bacillus subtilis, Yersinia pestis, Streptococcus peumoniae, Bacillus anthracis, and Homo sapiens).