What Paragon Genomics, Inc. does

Paragon Genomics, Inc. is a privately held biotechnology company founded in 2015 and headquartered in Fremont, California. The company develops and commercializes CleanPlex, a proprietary multiplex PCR-based target enrichment and library preparation technology for amplicon-based next-generation sequencing (NGS). CleanPlex supports up to 20,000 amplicons per primer pool, delivers a 3–6 hour workflow, and operates with as little as 100 pg of DNA/RNA input, with short-amplicon design enabling performance on challenging samples including FFPE tissue, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), and single circulating tumor cells. The platform is compatible with the three major sequencing ecosystems: Illumina, MGI/DNBSEQ, and Ion Torrent. Companion technologies include the CleanPlex UMI (Unique Molecular Identifier) error-correction system for low-frequency variant detection below 0.5% allele frequency, the AccuFusion dual-primer RNA fusion detection chemistry, and the ParagonDesigner in-silico panel design algorithm.

The company's product portfolio spans ready-to-use NGS kits organized by application: infectious disease (SARS-CoV-2, respiratory virus research panel, emerging variants add-on), oncology (OncoZoom Cancer Hotspot, hereditary cancer, BRCA1 & BRCA2, TP53, UMI Lung Cancer, RNA fusion detection), genetic disorders (CFTR, mitochondrial disease), pharmacogenomics, and agrigenomics (AgriType Auto Targeted Library Kit). Supporting accessories include CleanMag magnetic beads, magnetic racks and plates, and indexed PCR primers for all three sequencing platforms. Paragon Genomics also offers custom NGS amplicon panel design via the ParagonDesigner online portal, with panels typically delivered within four weeks of design approval. The company has delivered more than 1,600 custom NGS panels to over 500 laboratories globally, and over 300 organizations are documented as partner organizations using CleanPlex panels.

The business model is product-sales-driven: revenue is generated primarily through one-time unit-priced kit sales (e.g., $335.40 for an 8-reaction SARS-CoV-2 kit up to $97,880 for a 1,152-reaction MGI hereditary cancer kit), supplemented by custom panel design services and OEM/white-label licensing arrangements. Go-to-market is sales-led with a direct e-commerce storefront, dedicated sales and technical support teams, free PhD-level custom panel consultation, channel distribution partnerships (notably Devyser, announced March 2023), OEM/white-label agreements, and active industry-conference presence (e.g., AMP 2025). Customer segments include academic and government research institutions (Broad Institute, NIH, USDA-ARS, Robert Koch Institute), major academic medical centers (MD Anderson, Mayo Clinic, UCSF, St. Jude, Boston Children's), pharmaceutical research (Novartis), and clinical diagnostics companies (Sophia Genetics, Berry Genomics, Dian Diagnostics, Interpace Diagnostics). All products are labeled for Research Use Only.

Name

Paragon Genomics, Inc.

Legal name

Paragon Genomics, Inc.

Website

https://paragongenomics.com

Company type

Private

Founded year

2015

Operating status

Operating

Headcount range

11–50 employees

Short description

Paragon Genomics develops and sells CleanPlex, a proprietary multiplex PCR-based target enrichment technology for next-generation sequencing, serving research institutions, clinical labs, diagnostics companies, and pharma with ready-to-use and custom NGS panels across oncology, infectious disease, genetic disorders, and pharmacogenomics.

Ownership category

akta.pro rank

Product category

NGS Library Preparation Reagents

NAICS

Analytical Laboratory Instrument Manufacturing (334516), Other Scientific and Technical Consulting Services (541690)

SIC

In Vitro & In Vivo Diagnostic Substances (2835), Laboratory Analytical Instruments (3826)

akta.pro primary industry

Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays) (HLAGAIAF)

akta.pro secondary industries

Molecular Diagnostics (PCR/qPCR, NGS-based assays) (HLAAALAA), Molecular & Genetic Testing (PCR/NGS/qPCR) (HLAGADAF), Multiplex & High-Throughput Diagnostics Platforms (microarrays, digital PCR, lab automation-enabled assays) (HLAAALAL)

Keywords

• Target enrichment kits
• NGS library preparation
• Multiplex PCR amplicon
• Next-generation sequencing
• Clinical genomics reagents

Headquarters

HQ city

Fremont

HQ country

United States

HQ region

North America

Offices1 record

Markets served

GTM type

B2B

Offering type

Hardware or Manufacturing

Cost components

Personnel, Technology or R&D, Operations, Marketing or Sales, Supply Chain, Infrastructure

Revenue model

1. CleanPlex NGS Kit Sales: Paragon Genomics generates revenue primarily through the sale of its CleanPlex brand multiplex PCR-based target enrichment and library preparation kits. These include ready-to-use panels for infectious disease, oncology, genetic disorders, pharmacogenomics, and custom panel offerings. Kits are sold in various pack sizes (8, 96, 384 reactions) and across sequencing platform formats (Illumina, MGI/DNBSEQ, Ion Torrent). Revenue is one-time per purchase, with no recurring subscription component for standard kits.
2. Custom NGS Panel Design and OEM Solutions: The company offers custom NGS amplicon panel design services through its ParagonDesigner online portal, with custom panels typically delivered within 4 weeks of design approval. Additionally, OEM business solutions and white-label arrangements allow other companies to embed Paragon Genomics technology under their own brands, generating licensing and service revenue.
3. Accessories and Consumables: Revenue is also generated from the sale of complementary accessories required for CleanPlex workflows, including CleanMag Magnetic Beads for purification, magnetic racks and plates, indexed PCR primers (dual-indexed and unique dual-indexed) for sample pooling and multiplexing, and other consumables.

Pricing tiers

Go-to-market motion3 records

Distribution channels5 records

Marketing channels8 records

Core offering

Paragon Genomics develops and manufactures the CleanPlex multiplex PCR-based target enrichment and library preparation kits used for amplicon-based next-generation sequencing (NGS). The company sells ready-to-use NGS panels covering infectious disease (SARS-CoV-2, respiratory virus), oncology (cancer hotspots, hereditary cancer, BRCA1/2, TP53, RNA gene fusions), genetic disorders (CFTR, mitochondrial disease), and pharmacogenomics, plus accessories (magnetic beads, indexed primers) and custom NGS panel design services enabled by the proprietary ParagonDesigner algorithm.

Product overview

Paragon Genomics is a biotechnology company offering CleanPlex, a comprehensive multiplex PCR-based amplicon sequencing technology platform. The portfolio includes ready-to-use NGS kits organized by application area: infectious disease panels (SARS-CoV-2, Respiratory Virus), oncology panels (OncoZoom Cancer Hotspot, Hereditary Cancer, BRCA1 & BRCA2, TP53, UMI Lung Cancer), genetic disorder panels (CFTR, Mitochondrial Disease), pharmacogenomics panels, and AgriType library kits. Supporting accessories include CleanMag magnetic beads, magnetic racks/plates, and indexed PCR primers for Illumina, Ion Torrent, and MGI DNBSEQ platforms. The technology enables ultra-high multiplexing (up to 20,000 amplicons per pool), fast workflows (3-6 hours), low DNA input requirements (as low as 100 pg), and compatibility with major sequencing platforms (Illumina, MGI DNBSEQ, Ion Torrent).

Differentiator

Problem solved

Functional benefit

Brands

• CleanPlex: Multiplex PCR-based target enrichment and library preparation technology for amplicon sequencing
• AccuFusion
• AgriType
• CleanMag
• ParagonDesigner

Products and services

• CleanPlex SARS-CoV-2 Kit Amplicon-based SARS-CoV-2 NGS panel designed for COVID-19 coronavirus research and surveillance, enabling complete genome sequencing of the SARS-CoV-2 virus with 99% genome coverage, 99% reduction in sequencing cost versus shotgun metagenomics, and detection down to 1 copy with high confidence. Targets research and surveillance laboratories using Illumina sequencing platforms.
• CleanPlex SARS-CoV-2 FLEX Kit Enhanced amplicon-based SARS-CoV-2 FLEX NGS panel built upon the original SARS-CoV-2 Panel with additional components for robust variant calling. Features degenerate primer designs for consistent coverage across variable strains and includes human positive control as library preparation control.
• CleanPlex for MGI SARS-CoV-2 Kit Amplicon-based SARS-CoV-2 NGS panel designed for MGI DNBSEQ platforms, enabling complete genome sequencing of SARS-CoV-2. Offers 98% reduction in sequencing cost with only 0.2M reads per sample required.
• SARS-CoV-2 Emerging Variants Panel Add-on v2 Add-on panel primers for use with the original SARS-CoV-2 Kit or FLEX Kit, providing robust coverage of emerging variants including delta, mu, and omicron sub-lineages (BA.1, BA.2, BA.2.12.1, BA.2.75, BA.3, BA.4, BA.5).
• CleanPlex Respiratory Virus Research Panel V2 Amplicon-based respiratory virus panel for detection, research, and surveillance of key respiratory pathogens including SARS-CoV-2, Influenza (Flu A/B), and RSV (A/B). Enables complete genome sequencing of SARS-CoV-2 with subtype-level identification for influenza and RSV through 149 strategically designed primers.
• CleanPlex OncoZoom Cancer Hotspot Kit Multiplex PCR-based targeted resequencing assay for rapid cancer profiling of somatic mutations across hotspot regions of 65 oncogenes and tumor suppressor genes. Targets 2,900+ hotspots with starting input of just 100 pg genomic DNA in a 3-hour single-tube workflow.
• CleanPlex for MGI OncoZoom Cancer Hotspot Kit Multiplex PCR-based targeted resequencing assay for DNBSEQ platforms, designed for rapid detection of somatic mutations across hotspot regions of 65 oncogenes and tumor suppressor genes.
• CleanPlex Comprehensive Hereditary Cancer Panel Pre-designed multiplex PCR/amplicon-based targeted sequencing assay for examining germline variants across 88 genes associated with comprehensive hereditary cancer. Targets all exonic regions and flanking intronic sequences with 10 ng DNA input in 3 hours.
• CleanPlex Hereditary Cancer Kit v2 Targeted resequencing assay for analyzing 37 genes associated with increased risk of hereditary cancers including breast, ovarian, uterine, skin, prostate, gastric, colorectal, and pancreatic cancers. Features streamlined 3-hour workflow with 20 ng DNA input.
• CleanPlex BRCA1 & BRCA2 Kit v3 Multiplex PCR-based targeted resequencing assay for evaluating somatic and germline variants across BRCA1 and BRCA2 genes. Targets all exonic regions with 20 bp flanking intronic sequences. Detects somatic mutations as low as 1% variant allele frequency.
• CleanPlex for MGI BRCA1 & BRCA2 Kit Multiplex PCR-based targeted resequencing assay for DNBSEQ platforms designed to simplify evaluation of somatic and germline variants across BRCA1 and BRCA2 genes.
• CleanPlex TP53 Kit Multiplex PCR-based targeted resequencing assay for evaluating somatic and germline variants across the TP53 gene. Targets all exonic regions and flanking intronic sequences with 20 ng DNA input in a 3-hour workflow.
• AccuFusion RNA Lung Cancer Kit Dual primer amplification method for focused detection of 280+ known gene fusions associated with non-small cell lung cancer (NSCLC). Fusion genes include ALK, CIT, EML4, FGFR1, MET, NRG1, NTRK1, NTRK3, PDGFRA, RET, ROS1, TACC3. Uses 10 ng RNA input with 6-hour workflow.
• CleanPlex CFTR Kit Multiplex PCR-based targeted resequencing assay for evaluating germline variants across the CFTR gene for cystic fibrosis research. Targets all exonic regions and flanking intronic sequences with 10 ng DNA input.
• CleanPlex Mitochondrial Disease Kit Multiplex PCR-based targeted resequencing assay for evaluating the entire human mitochondrial genome. Provides complete coverage of all 37 genes of the ~17 kb mitochondrial genome with just 2 ng DNA input in 3 hours.
• CleanPlex Pharmacogenomics Kit Ready-to-use multiplex PCR/amplicon-based targeted sequencing assay designed to examine the most important and actionable PGx variants. Genes include CYP2D6, CYP2C19, CYP2C9, DPYD, TPMT, VKORC1, and 24 others. Uses 10 ng DNA input with 3-hour workflow.
• CleanPlex UMI Lung Cancer Kit Targeted resequencing assay for rapid and high-confident detection of low-frequency variants across hotspot regions of 23 genes associated with lung cancer. Powered by CleanPlex UMI technology with unique molecular identifiers for PCR and sequencing error correction. Detects variants below 0.5% allele frequency with 30 ng DNA input.
• AgriType Auto Targeted Library Kit, 1-Pool Targeted genotyping by sequencing solution for large-scale agrigenomics projects. Powered by advanced primer design algorithm and ultra-high multiplex PCR-based target enrichment chemistry. Targets up to 7,000 relevant amplicons per pool for marker assisted selection, genomic selection, and QTL screening.
• CleanMag Magnetic Beads High-throughput purification of PCR amplicons for removal of excess primers, nucleotides, salts, and enzymes. Formulated for use with CleanPlex and CleanPlex UMI NGS Panels and compatible with various DNA and RNA NGS library preparation chemistries.
• CleanMag Magnetic Rack Magnetic rack designed for maximum magnetic bead-based nucleic acid purification performance from 0.2 mL PCR tubes and strips. Processes up to 24 samples from 8- or 12-tube PCR strips.
• CleanMag Magnetic Plate Magnetic plate designed for maximum magnetic bead-based nucleic acid purification in manual and automated workflows using full, 1/2, and non-skirted PCR plates, and 0.2 mL PCR strips. SBS compliant.
• CleanPlex Plated Dual-Indexed PCR Primers for Illumina High-quality ready-to-use PCR primers for Illumina library construction compatible with all CleanPlex and CleanPlex UMI NGS Panels. Features combinatorial indexing with 8 x 12 index combinations enabling up to 2,688 sample multiplexing per flow cell.
• CleanPlex Plated Unique Dual-Indexed PCR Primers for Illumina High-quality ready-to-use PCR primers for Illumina library construction with unique dual indexing to mitigate index hopping concerns on Illumina patterned flow-cells. 96 unique index pairs per set, combinable for 384 total UDI options.
• CleanPlex Plated Single-Indexed PCR Primers v2 for Ion Torrent High-quality ready-to-use PCR primers for Ion Torrent library construction compatible with all CleanPlex NGS Panels. Features 96 index pools per set for sample multiplexing.
• CleanPlex for MGI Plated Single-Indexed PCR Primers High-quality ready-to-use PCR primers for DNBSEQ library construction compatible with all CleanPlex for MGI NGS Panels. Features 96 unique index pools for sample multiplexing.
• Custom NGS Panel Design Service (ParagonDesigner) Custom NGS amplicon panel design service powered by the proprietary ParagonDesigner algorithm, including free PhD-level consultation. Custom panels are typically delivered within 4 weeks of design approval and can be used across Illumina, MGI DNBSEQ, and Ion Torrent platforms for applications in agrigenomics, oncology, inherited diseases, infectious diseases, and pharmacogenomics.

Quantifiable outcome

• 99% reduction in sequencing cost — only 50K reads per sample required versus 10M reads required by shotgun metagenomics methods (SARS-CoV-2 standard kit)
• +11 more outcomes

Named customers19 records

Segments8 records

Ideal customer profiles5 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Integration4 records

Feature9 records

Partnerships

Three partnerships are on record, tiered core and secondary.

• Genetica Consulting ServicescoreStrategic or Co-development Partner · 14 November 2025Developed in collaboration with Genetica Consulting Services, Paragon Genomics launched the CleanPlex Pharmacogenomics (PGx) NGS Panel at AMP 2025. The assay is designed to identify genetic biomarkers associated with drug response using high-throughput sequencing technology.
• SynthegocoreStrategic or Co-development Partner · 19 June 2025Synthego and Paragon Genomics combined their technologies to develop a high-throughput method for evaluating novel nuclease activity in gene editing applications. The method integrates Synthego's Halo Platform for synthetic sgRNA and automation with Paragon Genomics' CleanPlex amplicon sequencing technology to enable direct side-by-side comparison of nucleases including SpCas9 against other novel nucleases. This workflow reduces hands-on time for library preparation and supports rapid evaluation of editing activity and indel profiles at numerous genomic targets.
• DevysersecondaryChannel Partner/ Reseller/ DistributorDevyser is a distribution partner for Paragon Genomics, distributing CleanPlex products in certain markets. The partnership was announced in March 2023.

Scale indicators3 records

Recent moves7 records

Expansion highlights6 records

Direct peers

• New England Biolabs (NEB): NEB's NEBNext product line for NGS library prep and target enrichment overlaps with CleanPlex across amplicon and hybrid-capture workflows for research and translational genomics labs.
• Qiagen: Qiagen's QIAseq targeted NGS panels (DNA and RNA) and GeneRead DNAseq products directly compete with CleanPlex ready-to-use and custom panels in oncology, inherited disease, and infectious disease workflows.
• Twist Bioscience: Twist Bioscience offers custom NGS target enrichment panels (Twist Alliance panels) using a DNA synthesis-based workflow that competes directly with CleanPlex custom amplicon panels for targeted sequencing applications.
• Integrated DNA Technologies (IDT): IDT's xGen Amplicon and Lockdown NGS target enrichment products compete with CleanPlex in amplicon-based library prep for Illumina and other platforms, serving the same research and clinical research lab buyer.

Emerging players

• Sophia Genetics: Sophia Genetics is both a Paragon customer/partner and a developer of NGS-based clinical interpretation software and IVD workflows for oncology and rare disease, adjacent to Paragon's target enrichment kit business.
• Devyser: Devyser is a Swedish diagnostics company offering NGS-based hereditary and oncology kits, and is also Paragon Genomics' distribution partner. Overlap exists in hereditary cancer and CFTR amplicon NGS kits.

Broad incumbents

• Illumina: Illumina's AmpliSeq for Illumina, TruSeq, and connected content products compete with CleanPlex across amplicon and library prep workflows. As the dominant NGS instrument vendor, Illumina is both a partner (platform) and a competitor (consumables).
• Bio-Rad Laboratories: Bio-Rad offers ddPCR and NGS-related consumables (e.g., QX200 systems, SureCell workflows) that compete with CleanPlex in droplet-based and targeted DNA/RNA quantification and library prep applications.
• Thermo Fisher Scientific: Thermo Fisher's Ion Torrent AmpliSeq and Oncomine NGS products compete with CleanPlex, particularly for Ion Torrent platform users and in clinical oncology research applications.
• Agilent Technologies: Agilent's SureSelect and HaloPlex hybrid-capture and amplicon NGS target enrichment products compete with CleanPlex, particularly in clinical research and exome-scale applications, as part of Agilent's broader diagnostics and life sciences portfolio.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat6 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/paragongenomics
• YouTubeyoutube.com/channel/UCQoePob-EWW5cBz96Mo9QvA
• Facebookfacebook.com/paragongenomics
• LinkedInlinkedin.com/company/paragon-genomics-inc.

Revenue estimate

Valuation estimate

Number of profiles

Profiles2 records

Funding overview

Funding rounds1 record

Investors5 records

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Paragon Genomics, Inc.