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Xing, Guoliang; Mei, Gangwu; Vallaeys, Tatiana; Berthet, Nicolas; Filliol, Ingrid; Retief, Jacques; Mittman, Michael; Williams, Alan; Davies, Christopher; Old, Iain; Cole, Stewart; Kennedy, Giulia
High-density oligonucleotide arrays, commonly referred to as "DNA microarrays" or "chips", allow researchers to rapidly access large quantities of genetic information in a single experiment. These chips have been used to study large-scale transcription of genes, to genotype single-nucleotide polymorphisms (SNPs) and to resequence genomic DNA. Previous work has shown that viral and bacterial pathogens can be resequenced using oligonucleotide microarrays. Genomic sequence variation can be identified, allowing for accurate species and sub-species determination. Detection of known polymorphisms as well as de novo identification of novel mutations can also be used to construct phylogenetic trees of these organisms. We are using microarrays which contain 300,000 bp of sequence information to simultaneously identify 28 bacteria and 42 viruses on a single microarray. These pathogens have been identified by the National Institute of Allergy and Infectious Disease (NIAID) to be the largest threat to human health in the United States; however these arrays are applicable to studying infectious agents from around the world. Data will be presented describing the design of a high-density microarray useful for identification of medically important bacteria and pathogens in clinical samples. |
