hybseek: Pathogen primer design tool for diagnostic multi-analyte assays


C. Frech, K. Breuer, B. Ronacher, T. Kern, C. Sohn, G. Gebauer - hybseek: Pathogen primer design tool for diagnostic multi-analyte assays - COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, Vol. 94, No. 1, 2009, pp. 6


Recent diagnostic screening methods are limited in the number of micro-organisms and viruses that can be identified in parallel. Nucleic acid amplification testing (NAT) offers the opportunity to overcome this limitation, and especially solid-phase amplification (SPA) is a promising technique enabling highly parallelized assays. Multi-analyte NAT assays are in need of uniform and highly specific primer pairs for sometimes dozens of pathogens. Currently, no available primer or probe design tool allows an automated compilation of such primer sets; hence their design is an iterative, labor-intensive and often difficult procedure. We developed a novel rapid primer design strategy and a web-based service (hybseek) to compute highly pathogen-specific primer sets for DNA-based diagnostic multi-analyte assays. The degree of uniqueness is quantitatively expressed by a heuristic specificity score, which considers both amount and location of nucleotide mismatches. Results from qPCR-experiments confirm the feasibility of this design strategy and prove it highly useful when there is the need to discriminate between many and/or closely related pathogens.