Comparative genomic hybridization study of Streptococcus pneumoniae

PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for Streptococcus pneumoniae remain a public health priority for every country in world today. The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance. Two hundread fifty five query strains were investigated in this study, with each query strain hybridized against the reference strain, tigr4. Each strain has a single dye experiment. Each oligo is spotted on the S.pneumoniae species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome of S. pneumoniae and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.