CleanPlex Ready-to-Use NGS panels for targeted sequencing

Next Generation Sequencing (NGS) is a DNA sequencing technology which has revolutionised genomic research. Using NGS an entire human genome can be sequenced within a single day. CleanPlex NGS panels are powered by Paragon Genomics’ CleanPlex Technology, which uses a proprietary multiplex PCR background cleaning chemistry to effectively remove non-specific PCR products, resulting in best-in-class target enrichment performance and efficient use of sequencing reads. CleanPlex Ready-to-Use NGS Panels are expertly optimized to generate valuable insights.

Genetic disorders

Infectious disease



CleanPlex Technology

What is Targeted Sequencing (Resequencing) / Target Enrichment?

Targeted Sequencing or Resequencing is a method for only sequencing part of a whole genome or regions of interest without sequencing the entire genome of a sample. In order to only focus on specific or clinically relevant regions of a genome or DNA sample, it requires a pre-sequencing DNA preparation step called Target Enrichment where target DNA sequences are either directly amplified (amplicon or multiplex PCR-based) or captured (hybrid capture-based) and then subsequently sequenced using DNA sequencers.

Why Target Enrichment?

Whole genome sequencing (WGS) and its corresponding whole genome amplification (WGA) method are more suitable for research and discovery types of applications, while targeted sequencing and target enrichment are essential to many fast-growing clinical and industrial applications where cost and speed are more important.

CleanPlex NGS Target Enrichment Amplicon Sequencing Technology:

CleanPlex technology is an ultra-high multiplex PCR amplicon-based target enrichment technology for NGS targeted sequencing (amplicon sequencing as opposed to hybrid capture-based sequencing). It features a highly advanced proprietary primer design algorithm, an exceptionally uniform multiplex PCR amplification chemistry and an innovative, patented background cleaning chemistry. Together, they allow CleanPlex Ready-to-Use and Custom NGS Panels to break the limits of existing PCR amplicon-based and hybrid capture-based 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

CleanPlex multiplex PCR-based NGS 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 amplicon 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 Target Enrichment Panels’ ultra-high multiplexing capabilityhigh performancelow input requirementhigh sensitivitysingle-tube workflow, and cost-effective amplicon sequencing.  These remarkable features and benefits allow researchers and assay developers to discover more with less.

  • 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 input and resources to reduce costs

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