Consensus

Consensus™ is a PCR assay design tool developed by DNA Software, intended for researchers and organizations working with infectious disease diagnostics, genomic targets, and mRNA profiling. It provides automated design of PCR assays targeting viruses, bacteria, fungi, and parasites, and has been validated for the detection of thousands of viral, bacterial, and human targets.

The tool is suited for applications including detection of infectious disease variants, identification of bacterial and viral strains, human genomic target analysis, and consensus design across large sequence panels — for example, detecting all variants of pandemic 2009 influenza A virus or generating a single set of universal primers covering all known FluA variants. Consensus™ is positioned as an alternative to freeware and outdated design tools, particularly for organizations where assay design is mission-critical.

Design Algorithm Capabilities

• Uses a novel assay design algorithm built on empirically-derived thermodynamic parameters that calculate oligo hybridizations from first principles, rather than derivative complementarity rules.
• Accounts for a wide range of potential PCR artifacts, including false negatives caused by target secondary structure, undesired primer-primer interactions, false primer-amplicon interactions, false amplicons to background genomes, and low coverage due to sequence variations.
• Handles large sequence playlists such as the entire human genome, human RefSeq, human microbiome, bacterial diversity panels, soil microbes, and all known viruses.
• Includes many pre-imported sequences for common use cases.

Workflow and Development Efficiency

• Designs are intended to work without extensive laboratory iteration, reducing the number of lab development cycles required to arrive at a viable assay.
• Reported to save an average of 3–8 months in development time, and regularly saves organizations 6 or more months of work through the use of inclusivity and exclusivity panels for diagnostic-quality assays.
• Supports custom platform, laboratory, and business requirements, including multiplexing, to optimize designs for high-volume commercial laboratory use and reduce per-assay costs at scale.

Base Package Features

• Access to Consensus software through a secure web UI portal.
• Design of singleplex PCR primers and probes optimized to assay a target of homologous sequences.
• Inclusion of assay background genomes to build designs that avoid unwanted amplifications.
• Support for fluorophores, quenchers, and tails in assay design oligos.
• Review of comprehensive PCR assay design results.
• Execution of up to 2 concurrent PCR assay design jobs.
• Up to 100 hours of hosted hybridization analysis with unlimited results storage.
• Sharing of target sequences and analysis results with other licensed users.

Consensus™ is accessed via a hosted web UI, with each licensed seat providing individual user access. DNA Software also operates PCRassays.com for PCR kit procurement, which may complement assay designs produced within the Consensus™ platform.