Genomic Scientist

CleanPlex® Amplicon Sequencing

The Most Advanced NGS Target Enrichment Solution

High Quality | Rapid Workflow | Customizable


AgriType® for AgriGenomics

High-throughput Genotyping by Sequencing for Molecular Breeding

Accurate | Cost-effective | Automation-friendly


CleanPlex® for Precision Oncology

Targeted Oncology NGS Panels for Precision Cancer Testing

Single Cell Compatible | Fusion Detection | NGS Platform Agnostic

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High-Sensitivity SARS-CoV-2 Amplicon Sequencing Kits for COVID-19 Surveillance

Proven Ability to Sequence Single Viral Genomes from Wastewater Samples

Edwin Oh on wastewater SARS-CoV-2 sequencing for COVID-19 surveillance

Prof. Oh from the University of Nevada along with his colleagues from the University of Arizona performed a WGS study to detect SARS-CoV-2 variants in wastewater using CleanPlex SARS-CoV-2 FLEX Panel. Compared to hybrid capture and other amplicon-based technologies, the lab was able to show that NGS libraries prepared with CleanPlex had the specificity and sensitivity to sequence single viral genomes. Read the paper here

Testimonials on CleanPlex COVID-19 NGS Kits

“I was very impressed by how well the CleanPlex SARS-CoV-2 panel worked when we evaluated it back in March. Working with Paragon Genomics, we were able to leverage the panel to quickly launch a SARS-CoV-2 whole-genome sequencing assay and used it effectively for a number of genomic epidemiology studies.”

Xiaowu Gai, Ph.D., Director of Bioinformatics, Children's Hospital Los Angeles

“The laboratory, bioinformatics and administrative staff at Paragon Genomics have helped save time and effort on numerous occasions during our COVID-19 project development. Supportive collaboration with PG has played an integral role in learning more about transmission dynamics of this dangerous new coronavirus.”

Peter ZimmermanPeter Zimmerman, Ph.D,, Professor, Department of Pathology, Case Western Reserve University

500+ Custom Next-Generation Sequencing (NGS) Panels Delivered to 300+ NGS Labs

Custom Panel Consultation
Ready-to-Use NGS Assays
Custom and OEM Solutions

CleanPlex Amplicon Sequencing Technology

Targeted DNA or RNA-Seq

    • 3-hour workflow
    • Low DNA/RNA input
    • Up to 20,000 amplicons per pool
    • Unique PCR background cleaning

Learn more >

ctDNA Liquid Biopsy

    • 3.5-hour workflow
    • No fragmentation
    • Ultra sensitivity (0.1%)
    • Unique molecular barcoding chemistry

Learn more >

RNA Gene Fusion Detection

    • 6-hour workflow
    • Detect novel gene fusions
    • Optimized reverse transcription
    • Built on single primer chemistry

Learn more >


Take CleanPlex in-house for your genomic testing or research projects

Infectious Disease

infectious disease research and testing, pathogen detection via NGS targeted amplicon sequencing

Precision Oncology

Tumor profiling using NGS targeted sequencing

Inherited Disease

inherited diseases and genetic disorders research via NGS targeted amplicon sequencing

Molecular Breeding

agrigenomics and molecular breeding via NGS targeted amplicon sequencing

Customer Testimonials on CleanPlex Technology

I was very impressed by how well the CleanPlex SARS-CoV-2 panel worked

“I was very impressed by how well the CleanPlex SARS-CoV-2 panel worked when we evaluated it back in March. Working with Paragon Genomics, we were able to leverage the panel to quickly launch a SARS-CoV-2 whole-genome sequencing assay and used it effectively for a number of genomic epidemiology studies. As a human geneticist and informaticist, I am also excited about the availability of the CleanPlex ACE2/TMPRSS2 germline + eQTL panel. We have sequenced thousands of positive COVID 19 samples, which revealed a tremendous amount of viral genetic diversity. It is therefore most interesting now to study the host genetic variants, especially in the ACE2 and TMPRSS2 genes that are the two most essential genes for SARS-CoV-2 infection. The interplay of human host genetic variants in these genes, along with the SARS-CoV-2 mutations and haplotypes, may well determine how severe the infection is and the resulting clinical phenotypes.”

Xiaowu Gai, PhD, Director of Bioinformatics, Children's Hospital Los Angeles

Affordable and easy-to-use product

“When we decided to choose a target enrichment platform, we had several choices and I am delighted that we chose Paragon Genomics. Paragon Genomics has enabled us to move our sequencing in-house with an affordable and easy-to-use product. They assisted us every step along the way from choosing the amplicons, to guiding us through library preparation to assisting with analysis. I strongly recommend their CleanPlex® amplicon-based targeted sequencing approach and could not be happier with their product.”

Elliot Stieglitz, MD, Assistant Professor, University of California San Francisco

Complete viral genomes from clinical samples with low viral content

“We’re using Paragon’s CleanPlex and CleanPlex UMI technologies to sequence RNA viruses. These technologies enable us to rapidly and cost-effectively obtain complete viral genomes from clinical samples with low viral content. Further analyses of viral genomes, including the identification of minor variants, elucidates viral diversity and evolution. Paragon has enthusiastically worked with us to tackle this new application; they have diligently designed panels to our specifications, meeting with us frequently to optimize the design.”

Aaron Lin, PhD; Erica Normandin; Kim Lagerborg, The Broad Institute of MIT and Harvard

Great PCR uniformity and on-target rate

“Paragon Genomics designed a high-quality NGS custom panel for us within two weeks. Its CleanPlex® targeted library technology is fast and easy to use with great PCR uniformity and on-target rate. We are very satisfied by CleanPlex product performance and the superb technical and customer support provided by the Company.”

Chongjian Chen, PhD, CEO, Annoroad

Robust and work directly from the start

“As a service provider and distributor company, it is crucial for us to fulfill inquiries coming from our customer in a fast and reliable manner. Paragon Genomics’ custom design and production pipeline has shown itself very useful to expand our portfolio and services in a very short time. Their CleanPlex® assays are robust and work directly from the start with a uniform coverage distribution and the ability to design single gene or small gene panels as well as larger panels makes CleanPlex a flexible tool.”

Damla Erdogan, Business Development Manager, Gen Era Diagnostics

A ‘future proof method’ and a ‘one and done’ approach

“We are looking for a ‘future proof method’, a better way to do high throughput screening at a species level diagnosis. Paragon Genomics has developed a rapid 2.5-hour library preparation allowing multi-gene methodology, letting us look at lots of unique loci across multiple genomes. It offers a ‘one and done’ approach instead of many different disconnected experiments.”

Scott Geib, PhD, Research Entomologist, USDA-ARS

Who’s Choosing CleanPlex NGS Panels

300+ organizations globally are using CleanPlex for their targeted sequencing applications