Pattern Genomics’ Approach to Assay Design

How does one design a molecular diagnostic today?  There are plenty of off-the-shelf techniques and proprietary methods for sample processing, chemistry, and detection of analytes.  But a key part of a targeted molecular diagnostic is the primer and probe set that is sensitive and specific to the desired target.  Where does this set come from?  Basic research?  Expert knowledge?  Trial-and-error?  All three?  The difficulty in finding optimal primers and probe designs is often downplayed when planning a new assay, leading to delays, cost over-runs, and unnecessary redesigns.

Pattern Genomics proposes a new, data-driven approach to assay design that is enabled by next-generation DNA sequencing and our proprietary Daydreamer™ platform.  The process is outlined in the figure below.


1. Sequence

All relevant, raw DNA sequencing data are gathered, assembled and optionally annotated.


2.  Analyze

Data and detailed assay-specific constraints are loaded into Daydreamer™ and the results are visualized and curated.


3. Validate

Design is tested on reference samples.  Any discrepant samples can be sequenced and included in a re-run of the analysis.


4. Done

That’s it!  The entire process can be completed in weeks, limited only by data availability and lab requirements.

By incorporating dozens or even hundreds of sequences into the analysis, Daydreamer™ is able to find a robust combination of markers that uniquely identify the assay targets and avoid cross-reactivity.  Daydreamer™ is designed for efficiency, and the input sequences may be as large as whole genomes, meaning that the analysis is unbiased by pre-selection of genes or a particular reference sequence.  With an embedded constrained optimization engine, Daydreamer™ is able to find compact sets of primers and probes that meet the exact design criteria specified by the user.  Melting temperatures, sequence composition, amplicon lengths, limits on primer-primer interactions, etc. can all be specified.  Daydreamer™ is modular and easily extended, for example to incorporate platform-specific assay formats.  Finally, when designing an assay, it is impossible to predict the future evolution of the targets.  But in the case that emerging strains are not properly handled by an existing design, it is easy to sequence the new strains and add them into the analysis, providing an efficient path to assay updates.

Contact us to find out more about how Pattern Genomics and Daydreamer™ can help you meet your objectives.