tailieunhanh - Báo cáo khoa học: Human-blind probes and primers for dengue virus identification Exhaustive analysis of subsequences present in the human and 83 dengue genome sequences

Reliable detection and identification of pathogens in complex biological samples, in the presence of contaminating DNA from a variety of sources, is an important and challenging diagnostic problem for the development of field tests. The problem is compounded by the difficulty of finding a single, unique genomic sequence that is present simultaneously in all genomes of a species of closely related pathogens and absent in the genomes of the host or the organisms that contribute to the sample background. . | iFEBS Journal Human-blind probes and primers for dengue virus identification Exhaustive analysis of subsequences present in the human and 83 dengue genome sequences Catherine Putonti1 Sergei Chumakov2 Rahul Mitra3 George E. Fox4 Richard C. Willson4 5 and Yuriy Fofanov1 4 1 Department of Computer Science University of Houston Houston TX USA 2 Department of Physics University of Guadalajara Guadalajara Jalisco Mexico 3 Genomics USA Houston TX USA 4 Department of Biology and Biochemistry University of Houston Houston TX USA 5 Department of ChemicalEngineering University of Houston Houston TX USA Keywords dengue diagnostic assay flavivirus microarray pathogen identification Correspondence C. Putonti University of Houston 218 PGH Houston TX 77204-3058 USA Fax 1 713 7431250 Tel 1 713 7433992 E-mail putonti@ Received 5 September 2005 revised 22 November 2005 accepted 23 November 2005 doi Reliable detection and identification of pathogens in complex biological samples in the presence of contaminating DNA from a variety of sources is an important and challenging diagnostic problem for the development of field tests. The problem is compounded by the difficulty of finding a single unique genomic sequence that is present simultaneously in all genomes of a species of closely related pathogens and absent in the genomes of the host or the organisms that contribute to the sample background. Here we describe host-blind probe design - a novel strategy of designing probes based on highly frequent genomic signatures found in the pathogen genomes of interest but absent from the host genome. Upon hybridization an array of such informative probes will produce a unique pattern that is a genetic fingerprint for each pathogen strain. This multiprobe approach was applied to 83 dengue virus genome sequences available in public databases to design and perform in silico microarray experiments. The resulting patterns allow one to unequivocally .