Next-Generation Sequencing Assays for Precision Medicine and Research

CleanPlex® is the most advanced amplicon-based NGS target enrichment technology. Start a new design and accelerate the development of your NGS amplicon panels.

– Sensitive Viral Detection
(<10 copies)

– Low Sequencing Cost
(2688 sample multiplexing)

– Full Genome Coverage
(>99% coverage at 1M reads)

– On Illumina and MGI
(Adding more platforms)

Customer Success Story on Custom RNA Viral NGS Panel

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

CleanPlex® Ready-to-Use NGS Panels

Accurate detection of somatic and germline mutations

Powered by a novel multiplex PCR background cleaning chemistry to effectively remove non-specific PCR products, resulting in high level of on-target and coverage uniformity performance and efficient use of sequencing reads.

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CleanPlex® UMI Ready-to-Use NGS Panels

Precise analysis of low-frequency variants

Incorporates unique molecular identifiers (UMIs) to enable error correction and are designed to work with cell-free DNA (cfDNA) and FFPE DNA for liquid biopsy and tumor profiling applications. 

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CleanPlex® Custom NGS Panels

Submit a design online and get your custom NGS panel in 4 weeks!

Designed and optimized by our expert scientists to meet your desired specifications. As many as 20,000+ amplicons per primer pool can be multiplexed in a single reaction to create small to large panels for any applications and for Illumina®, BGI/MGI, or Ion Torrent™ platforms. 

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A Universe of Possibilities

Solid Tumor Profiling

Hematologic Cancer Profiling

Liquid Biopsy – cfDNA Analysis

Liquid Biopsy – CTC Analysis

Cancer Risk Assessment

Tumor Mutational Burden

Genetic Disorders

Pharmacogenomics Profiling

CRISPR Editing Assessment

Molecular Breeding

Customer Success Story

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

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

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

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

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

Fruit and vegetable industries in the continental US are under constant threat by invasive pest fruit flies, many of which cannot be identified using morphology alone. When flies or their larvae are intercepted, regulatory agencies need to quickly identify what species they are dealing with and where they came from. USDA-ARS and University of Hawaii are developing genomic tools for these tasks. Paragon Genomics’ CleanPlex® technology allows us to target thousands of highly-informative genomic regions is a single panel, thus integrating species identification and source determination. The 2.5-hour library preparation time combined with robust reaction chemistry for low quality samples means that these tools can be used quickly and efficiently.

Julian R. Dupuis, PhD, Faculty, University of Hawaii at Manoa and USDA-ARS

Who’s Choosing CleanPlex

Researchers and assay developers from organizations, large and small, are expanding their genomics capabilities with CleanPlex

Introducing 100+ CleanPlex Pre-Designed NGS Amplicon Panels ….. Learn More.