CleanPlex Amplicon Sequencing Technology for Targeted DNA and RNA-Seq

CleanPlex® is an ultra-scalable and ultra-sensitive NGS amplicon sequencing technology. It features a highly advanced proprietary multiplex PCR 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 traditional 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 DNA, FFPE RNA, cfDNA, cfRNA) and major sequencing platforms (Illumina, Ion Torrent, Genapsys, MGI DNBSeq)
  • Extreme sensitivity (down to single cell level direct amplification*)
  • Excellent panel size scalability from a few to over 20,000 amplicons in a single multiplex PCR pool
  • Detection of and analysis for single nucleotide variants (SNVs), small insertions and deletions (Indels), copy number variations (CNVs), gene fusions / splice variants, gene expression level, tumor mutational burden (TMB), microsatellite instability (MSI), internal tandem duplication (ITD), etc.

Specifically, amplicon sequencing technology offers a targeted approach that focuses on particular genes or specific genomic regions of interest.
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 or targeted gene sequencing is essential to many fast-growing clinical and industrial applications where cost and speed are more important.

One of the challenges the genomics community faces is the continued acquisition of large amounts of sequencing raw data that is yet to be fully and successfully translated and interpreted to help advance research, diagnose, and cure diseases on a wider scale. Even with current reduced sequencing costs, a whole genome sequencing approach can be practically used only in specific scenarios such as basic research, population genetics, or rare disease detection. A focused or targeted approach would be more appropriate for understanding disease progression and guiding therapy selection in clinical settings or massively screening DNA samples in industrial applications. In addition, sequencing an entire genome or exome can be prohibitively expensive in terms of laboratory operations and bioinformatics infrastructure for storing and processing large amounts of data. Therefore, targeted sequencing has become vital for the continued progress of precision medicine and research.

cleanplex DNA amplicon sequencing workflow

Figure 2. CleanPlex DNA Target Enrichment and Library Preparation Workflow

cleanplex RNA target enrichment library preparation workflow

Figure 3. CleanPlex RNA Target Enrichment and Library Preparation Workflow

View Data on CleanPlex® Technology for Amplicon Sequencing

Order a Free Trial Kit to Test 


Ultra-high Multiplexing Capability and High Performance Powered by Unique and Proprietary PCR Background Cleaning Technology

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 next generation sequencing library molecules, resulting in highly efficient use of sequencing reads.

cleanplex amplicon sequencing multiplex PCR background removal effect

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.

Interrogate More Targets Without Performance Compromise 

CleanPlex® Ready-to-Use and Custom NGS Panels are designed using our proprietary ParagonDesigner algorithm and optimized through an iterative process by our expert scientists to ensure maximum target design rate, as well as robust coverage uniformity, high on-target rate, and low amplification biasMore than 20,000 amplicons per primer pool can be multiplexed in a single CleanPlex reaction. Amplicon size can be tuned to specification to ensures high performance with the desired sample type. 

cleanplex amplicon sequencing panel scalability

Effective background removal for all multiplexing levels. Libraries were prepared with CleanPlex NGS Panels of varying sizes (7 to 8,000 amplicons) and examined on an Agilent® Bioanalyzer®. All libraries generated a clean peak indicating minimal formation of non-specific PCR products. The data shows that CleanPlex background cleaning chemistry is effective regardless of the level of multiplexing, which means new targets can be added without affecting performance.

cleanplex amplicon sequencing mapping rate vs panel size
cleanplex amplicon sequencing on-target rate vs panel size
cleanplex amplicon sequencing uniformity vs panel size

High performance regardless of panel size. Libraries were prepared with CleanPlex NGS Panels of varying sizes (15 to 1,500 amplicons) and sequenced on an Illumina® platform. Mapping rate was maintained above 96% and increased with the number of amplicons used per reaction, indicating that CleanPlex chemistry is even more effective on libraries prepared using larger numbers of amplicons. On-target rate was also higher than 96% for all panel sizes. Coverage uniformity, measured as % covered by at least 0.2X mean coverage, was maintained above 96%. 

Low Input and High Sensitivity

CleanPlex®‘s streamlined workflow minimizes sample loss to preserve genomic information in low-input and challenging samples, such as degraded FFPE DNA from tumor samples, cell-free DNA from liquid biopsies and single circulating tumor cell (CTC) from blood. High quality target-enriched libraries can be generated from as little as 1 ng of DNA and even down to 6 pg of DNA from a single CTC.

cleanplex amplicon sequencing uniformity vs panel sizeuniformity vs dna input

High performance even with low input amounts. Libraries were prepared with the CleanPlex OncoZoom Cancer Hotspot Panel (601 amplicons) using varying amount of input DNA and sequenced on an Illumina platform. CleanPlex technology was able to produce libraries with >95% coverage uniformity (measured as % covered by at least 0.2X mean coverage) using as little as 50 pg of input genomic DNA.

Direct Single Cell Targeted DNA Sequencing

CleanPlex NGS Panels can directly amplify single cells without pre-amplification such as whole genome amplification (WGA) while still maintaining high amplification uniformity. In addition, this avoids WGA bias and has much lower false positives and false negatives in terms of variant calls.

cleanplex single circulating tumor cell (CTC) targeted sequencing without WGA

Single cell targeted DNA sequencing with CleanPlex OncoZoom Cancer Hospot Panel. Single cell lysate obtained from RareCyte’s CTC assays and input as template into Paragon’s CleanPlex OncoZoom Cancer Hotspot Panel. Using this non-WGA method vastly improves: (A) coverage uniformity, and incidence of (B) false negative and false positive errors, when compared to single cell WGA products.

Detect Variants With High Confidence (Even Without Unique Molecular Identifiers – UMIs)

cleanplex amplicon sequencing error rate histogram

High quality sequencing data with low error rate. A library was prepared with the CleanPlex OncoZoom Cancer Hotspot Panel (610 amplicons) using 10 ng of Horizon Discovery HD780 cfDNA reference standard and sequenced on an Illumina platform to an average read depth of 8,500. A histogram of the frequency of random errors from sequencing shows that CleanPlex generated high quality data with the majority of random errors present at less than 0.2% frequency. This low level of background errors allows confident variant calling of mutations at 1% allele frequency.

CleanPlex amplicon sequencing variant calling concordance

High variant call concordance. Libraries were prepared with the CleanPlex OncoZoom Cancer Hotspot Panel (610 amplicons) using 10 ng of Horizon Discovery HD780 cfDNA reference standards and sequenced on an Illumina platform to an average depths ranging from around 1,100 to 9,800 reads per amplicon. The data shows that CleanPlex consistently detected validated variants at the expected frequency. The red lines represent the known allele frequencies of the eight mutations, and numbers are the averages of the detected frequencies for each allele with standard deviation error bars.

Fast, Single-Tube Workflow

CleanPlex® NGS Panels feature a rapid, single-tube workflow* that can be completed in 3 hours and requires only 75 min of hands-on time. High-quality target-enrich libraries can be easily and quickly prepared for faster time to results.

Single-tube workflow minimizes sample loss to preserve genomic information in the sample, and reduces the likelihood of errors and sample mix ups to ensure positive sample identification.

* Single-tube workflow. A single-tube workflow is followed when using a single-pool CleanPlex NGS Panel. For a multi-pool CleanPlex NGS Panel, the individual mPCR products from the primer pool-specific reactions are combined into one tube, and the remaining protocol is carried out using a single-tube workflow.

Simple Workflow Translates to High Reproducibility

CleanPlex NGS target enrichment library prep workflow reproducibility

High reproducibility. Eighteen CleanPlex libraries were generated by 3 operators and sequenced on an Illumina platform. The GC coverage of the libraries were plotted and compared against each other. The libraries produced highly reproducible GC coverage profiles, yielding a Pearson correlation coefficient of 97.26% ± 1.07%.

Cost-Effective Sequencing

The combination of low PCR background, low GC bias, and high mapping rate, on-target rate, and coverage uniformity means that very few sequencing reads are wasted on sequencing off-target sequences and non-specific PCR products and primer-dimers. It also means that fewer sequencing reads are required to ensure all targets are covered at a minimally required depth to make confident base calls. Overall, CleanPlex® NGS Panels allow efficient use of sequencing reads so that sequencing can be performed cost-effectively by allowing more samples to be sequenced at a time.

CleanPlex vs Ampliseq targeted sequencing uniformity and cost comparison

High performance translates to cost-effective sequencing. A 207-amplicon panel was used to generate target-enriched NGS libraries using either the CleanPlex or Competitor T’s library prep chemistry. Libraries were sequenced and analyzed for coverage uniformity across GC content. The results indicate that for a 207-amplicon panel, 60% less sequencing would be required using CleanPlex, which means 2.5X more samples can be sequenced on a flow cell. To achieve similar data quality, CleanPlex’s mean read depth could be reduced to 600X coverage while Competitor T’s would need to be increased to >1,500X coverage.

Sophia Genetics has compared CleanPlex technology with three other major amplicon-based technologies and published the results at the AMP (Association for Molecular Pathology) 2018 Annual Meeting. The following amplification plots show that CleanPlex has the best amplification uniformity (all amplicons’ read depths fall within 20% an 500% of mean depth while other technologies cannot achieve this). Besides amplification uniformity, Sophia Genetics also concluded that CleanPlex has high library conversion rate and reproducibility even on bad quality FFPE samples.

CleanPlex technology

Frequently Asked Questions

  • Amplicon sequencing is a powerful molecular biology technique that involves the amplification and sequencing of a specific DNA fragment or region of interest. It has a wide range of applications in various fields, including genomics, microbiology, ecology, and more. Common applications include rare variant detection- relevant in the field of oncology with ctDNA or cfDNA - which may be missed in whole-genome sequencing due to their low abundance.

  • CleanPlex® technology is a novel amplicon-based NGS target enrichment technology developed by Paragon Genomics. The technology inherits major advantages associated with traditional multiplex PCR methods while overcoming their key shortcomings such as PCR background noise, scalability (panel size), uniformity, and limitations from GC bias.

  • CleanPlex NGS Amplicon Sequencing enables researchers to conduct targeted sequencing, making it possible to identify and characterize specific genetic variants and mutations with high resolution. Specifically, researchers can identify a variety of genetic alterations with high levels of precision and accuracy that help track disease progression, identify potential therapeutic targets, and understand the genetic underpinnings of diseases.

    Additionally, with CleanPlex NGS amplicon sequencing, researchers have an important tool for advancing our understanding of various diseases and conditions that is cost-effective and efficient. Researchers can process a large number of samples in a single run, making it an ideal choice for projects involving extensive sample sizes or high-throughput screening. This scalability helps save on costs while accelerating progress.

    CleanPlex NGS Amplicon Sequencing empowers researchers to efficiently identify and explore diseases and genetics, and advance our understanding of medical conditions.