PanelPlex

PanelPlex™ is a multiplex PCR design software developed by DNA Software, intended for researchers and diagnostic developers working on cancer panels, antimicrobial resistance detection, and other applications requiring the detection of viruses, bacteria, and human targets. The software provides fully automated design of multiplex PCR assays and has been validated across numerous viral, bacterial, and human targets over more than two decades of development.

PanelPlex™ is designed to address common bottlenecks in multiplex panel development, including lengthy design cycles, knowledge gaps, and reliance on suboptimal or outdated tools. The software aims to reduce iterative experimental trial-and-error optimization, which typically adds six to nine months to the assay development process.

Core Capabilities

• Fully automated consensus design for multiple variants of DNA or RNA targets.
• Uses ThermoSleuth™ "playlists" to scan for off-target hybridizations that can cause false-positive results.
• Produces diagnostic-quality assay designs.
• Designs around a wide variety of potential artifacts.
• Supports scaling of multiplex PCR assay design to produce more assays with faster time to market.

Base Package Features

• Access to PanelPlex software through a secure web UI portal.
• Singleplex PCR primer and probe design for dozens of targets at a time in batch mode.
• Inclusion of assay background genomes to avoid unwanted amplifications.
• Support for fluorophores, quenchers, and tails in assay design oligos.
• Review of comprehensive PCR assay design results.
• Execution of up to two 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 users.

Available Add-On Packages

• Multiplexing Package: Designs multiplexed PCR assays with minimized cross-hybridizations and background sequence interference; supports addition of static control assay oligos; enables singleplex-to-multiplex design from predesigned singleplex oligos.
• Variant Package: Designs variant detection probes optimized for hybridizing small nucleotide variations (SNVs) in a target genome; supports multiple probes per target and inclusion of nucleotide modifications in primer and probe design.
• Shared Primers Package: Designs primers that function across multiple targets and in conjunction with alternate primer partners.
• Tiling Package: Designs multiplexed primers to generate tiled amplicons across a large target region.

PanelPlex™ is delivered through a hosted web-based platform, with each licensed seat accessing the software via a secure portal. DNA Software also offers direct consultation and demonstration sessions to help teams identify how the platform can address their specific assay design requirements.