The most advanced amplicon-based NGS target enrichment technology

CleanPlex® technology is an ultra-high multiplex PCR-based target enrichment technology for next-generation sequencing (NGS). It features a highly advanced proprietary primer design algorithm and an innovative, patented background cleaning chemistry. Together, they allow CleanPlex Ready-to-Use and Custom NGS Panels to break the limits of existing target enrichment technologies.

 

Feature Highlights:

  • Super high amplification uniformity and super low PCR background noise (more accurate variant calling or less sequencing cost)
  • Single-tube and 3-hour workflow with minimal hands-on time (easy automation)
  • Compatible with difficult samples (degraded FFPE, cfDNA) and major sequencing platforms (Illumina, Ion Torrent, MGISeq)
  • Extreme sensitivity (down to single cell level direct amplification*)
  • Excellent panel size scalability from a few amplicons to over 20,000 amplicons in a single multiplex PCR pool

*based on data from our collaborator RareCyte

CleanPlex multiplex PCR-based target enrichment workflow. CleanPlex Ready-to-Use and Custom NGS Panels allow high-quality target-enriched NGS libraries to be easily and quickly prepared for sequencing. 

CleanPlex background cleaning chemistry. The CleanPlex chemistry involves 3 simple steps, each consisting of a thermal cycling or incubation reaction followed by a library purification using magnetic beads. The streamlined protocol can be completed in just 3 hours. In step 1, targets of interest are amplified in a multiplex PCR reaction. In step 2. primer-dimers, non-specific PCR products, and complex molecular-debris are biochemically removed in a digestion reaction. In step 3, libraries are barcoded with sample indexes and amplified in a PCR reaction.

High performance powered by background cleaning

Non-specific PCR products and primer-dimers are biochemically removed using the proprietary CleanPlex digestion chemistry. This ensures that only DNA sequences of interest are converted into NGS library molecules, resulting in highly efficient use of sequencing reads.

Effective removal of PCR background. Libraries were prepared using the CleanPlex OncoZoom Cancer Hotspot Panel with (blue trace) or without (red trace) using the CleanPlex digestion reagent and examined using an Agilent® Bioanalyzer®. Without CleanPlex digestion, significant PCR background was formed, which would result in low mapping rate and poor on-target rate and require more sequencing reads to obtain adequate data. With CleanPlex digestion, nearly no background was generated, producing a sharp and clean library peak in the Bioanalyzer trace. The proprietary CleanPlex digestion chemistry is essential for removing undesired side products formed during multiplex PCR  amplification of target sequences.

Discover more with less™

The combination of superior primer design and innovative library preparation chemistry give rise to CleanPlex NGS Panels’ ultra-high multiplexing capability, high performance, low input requirement, high sensitivity, single-tube workflow, and cost-effective sequencing.  These remarkable features and benefits allow researchers and assay developers to discover more with less.

Discover More 

Discover more with CleanPlex NGS Panels

• Multiplex 20,000+ amplicons per reaction
• High target design rate
• High coverage uniformity
• High on-target rate
• High sensitivity (1% LOD with 10 ng input)

Use Less

Use less input and resources to reduce costs

• Inputs as low as 10 ng
• Fast 3-hour protocol
• Simple, streamlined workflow
• Efficient use of NGS reads

View more data on CleanPlex® technology