In addition to reporting species, culture-independent detection methods ideally should report the subtype of a targeted pathogen. Serotyping is a commonly-used subtyping scheme. However, the genomic basis for serotype may involve many locii on multiple genes, making a direct PCR assay difficult to develop. While DNA sequencing may be useful to assess serotype from genomic data, it may also be possible to find other genomic markers that correlate strongly with serotypes of interest and yield a simple molecular test.
In this study, Daydreamer™ was utilized for in silico design of an identification assay for the Salmonella enterica serotype Typhimurium. A total of 265 whole-genome S. enterica genomes, including 24 with the Typhimurium serotype, were analyzed. Primers and probe sequences suitable for Life Technologies TaqMan® or similar chemistries were output, and subsequent BLAST analysis suggests that these designs will be sensitive and specific to the desired targets.
This study further demontrates that Daydreamer™ enables an in silico assay design process from genomic sequences that is rapid, robust, and suitable to a wide range of molecular assay design problems. Daydreamer™ is capable of utilizing platform-specific constraints as an integral part of its assay design process, resulting in an optimized design that is targeted exactly to the chemistry and platform to be utilized for a diagnostic. Pattern Genomics is dedicated to assisting diagnostic platform companies in leveraging next-generation DNA sequencing and our proprietary technology for rapid diagnostic development.
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