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Case Studies

Pattern Genomics has kicked off a study involving enterovirus.  In order to help our collaborator visualize the data, we have produced multiple sequence alignments in regions of interest.  Multiple sequence alignments are complex to produce, and as every well-trained bioinformatician knows, no efficient algorithm can guarantee finding an optimal alignment on a large data set [...]

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salmonella_scaled

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 [...]

Filed Under: Case Studies

Clostridium difficile

This case study focuses on providing a more in-depth view of how the Daydreamer™ software enables rapid PCR assay design.  Clostridium difficile is a common HAI.  Phenotypic testing for C. difficile generally involves looking for the presence of at least one of two unique toxins typically produced by the infection, commonly called Toxin A and Toxin B. [...]

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This case study demonstrates how Pattern Genomics is capable of designing a complex PCR detection assay and validating it on reference samples.  Our in silico approach to assay design saves substantial time and effort over the traditional approach of searching the literature, engaging disease-specific researchers, and trial-and-error wet lab work.  The result is a primer set [...]

Filed Under: Case Studies