● Breaking
CleanPlex converts degraded DNA into sequencing-ready libraries in ~5 hours 300+ labs worldwide run Paragon Genomics panels $8M oversubscribed Series A closed September 2017 SARS-CoV-2 panel scaled to 20,000+ samples per run Founded 2015 in the San Francisco Bay Area Panels compatible with Illumina, Ion Torrent and MGISEQ
Company Profile Biotechnology Fremont, California

Paragon Genomics sells the pickaxes of precision sequencing.

A 16-person biotech that makes the reagent kits letting other people's sequencers actually work - and quietly put its CleanPlex chemistry inside the Broad Institute, Mayo Clinic and the USDA.

Above: the company wordmark. No sequencing machines here - just the chemistry that decides whether your data is any good. It is the least glamorous part of genomics, which is exactly why it is a business.

2015Founded
$8MSeries A
300+Labs served
~5 hrsSample to library

The Feature

A boring problem worth a whole company

Here is a fact about genomics that does not make it into press releases: the sequencing machine is often the easy part. You can buy a sequencer. What you cannot buy off a shelf - or at least, what you could not easily buy in 2015 - is a reliable way to prepare a difficult sample so the sequencer reads only the regions you care about, cleanly, cheaply, and without drowning your data in noise. That preparation step, called targeted enrichment and library prep, is unglamorous chemistry. It is also where a lot of experiments quietly die.

Paragon Genomics is a company built on that boring, load-bearing step. Founded in 2015 in the San Francisco Bay Area by Tao Chen and Zhitong Liu, and now headquartered in Fremont, California, it makes reagent kits - not machines - for targeted next-generation sequencing. Its flagship technology is called CleanPlex, and the pitch is straightforward enough that you can explain it at a dinner party: take a tiny or degraded DNA or RNA sample, and turn it into a sequencing-ready library in about five hours, with much less of the background junk that makes older methods frustrating.

The clever bit - and the thing that makes CleanPlex a product rather than a protocol - is a patented "background-cleaning" chemistry. Amplicon-based methods, which use multiplex PCR to copy the regions of interest, are fast and work with very little starting material. But they generate non-specific PCR products - noise. The competing approach, hybrid capture, is cleaner but slower and fussier. Paragon's scientists decided they did not want to pick. CleanPlex pairs a proprietary primer-design algorithm and a uniform amplification chemistry with a step that scrubs away the non-specific products, aiming for the speed of amplicon with cleanliness closer to capture.

"CleanPlex was created to bridge the gap between amplicon- and hybrid capture-based methods - a better tool to prepare NGS libraries for targeted sequencing." — Paragon Genomics technical note

If that sounds like an incremental improvement, consider who buys it. Paragon says more than 300 organizations globally use its panels, and the customer list reads like a directory of serious science: the Broad Institute, MD Anderson Cancer Center, Mayo Clinic, St. Jude Children's Research Hospital, Boston Children's Hospital, Novartis, plus government and academic labs at the University of California, the USDA, the CDC and the Chinese Academy of Sciences. When your reagent shows up in the methods sections of that many good papers, you are no longer selling a chemistry kit. You are selling a dependency.


The Toolkit

What you can actually do with it

Paragon sells two things: ready-to-use panels for common jobs, and custom panel design for when you have your own gene list. Both come down to the same promise - read the regions that matter, skip the rest, and do it from hard samples.

DNA · RNA

CleanPlex Panels

Ready-to-use targeted panels that convert DNA or RNA into sequencing-ready libraries through a fast multi-step workflow. The everyday workhorse for oncology and disease research.

High sensitivity

CleanPlex UMI

Adds unique molecular identifiers to catch low-frequency variants - the rare mutations in circulating tumor DNA that ordinary depth would miss.

Oncology

OmniFusion

An assay for detecting gene fusions from RNA, a recurring need in cancer research where fusion events drive tumors.

Your gene list

Custom Panel Design

Send the targets; get back a validated assay. Paragon productized the expertise of panel design so a lab does not have to become a chemistry shop.

2020 · Surveillance

CleanPlex SARS-CoV-2

A whole-genome COVID-19 panel shipped within weeks of the pandemic's onset, later scaled to pool 20,000+ samples in a single run.

Any platform

Platform-agnostic

Libraries run on Illumina, Ion Torrent and MGISEQ alike - so labs are not locked into one instrument vendor.


Case Study · 2020

The five-hour pandemic response

In March 2020, while a lot of companies were figuring out how to work from home, Paragon shipped a CleanPlex SARS-CoV-2 panel covering the entire viral genome, with a workflow that ran in roughly five hours. By July it had a higher-throughput version aimed at pooling more than 20,000 samples in a single sequencing run - the kind of scale that makes genomic surveillance a public-health tool rather than a boutique service.

The sensitivity mattered. The panel could detect a single viral copy in a sample, where a typical RT-PCR assay's limit of detection is usually five copies or more. And in 2021, independent peer-reviewed publications confirmed the panel accurately identified variants of concern, including the Alpha and Delta lineages. For a small reagent company, that is roughly the best outcome available: not a marketing claim, but other people's data.

Detection sensitivity — viral copies needed

CleanPlex
1 copy
Typical RT-PCR
~5 copies

Lower is more sensitive. Source: company materials, 2020.


The Money

Small, focused, and selling consumables

The business model is the classic "sell the pickaxes" play, and it is a good one. Paragon does not sequence anyone's genome and does not sell instruments. It sells consumable reagent kits and custom design services, ordered B2B - including through its own website - to research institutions, clinical labs, diagnostics companies and agricultural genomics groups. Consumables get reordered. Dependencies compound.

The capital story is refreshingly small. In September 2017 the company raised an oversubscribed $8 million Series A led by Cowin Venture Capital and Fosun Industrial, with participation from Cloudstone Venture, HEDA Ventures and Wisemont Capital. That is, as far as public records show, the extent of the outside funding - no billion-dollar valuation, no hype cycle. With a team of roughly 16 people and estimated revenue around $4.5 million, Paragon looks like what a focused life-science tools company is supposed to look like: modest headcount, real customers, a defensible product.

Fun facts & footnotes

The amusing part

  • It sells no sequencers - only the reagent kits that make other companies' sequencers useful.
  • Its COVID panel could detect a single viral copy, more sensitive than the usual RT-PCR limit of five.
  • CleanPlex libraries run on Illumina, Ion Torrent and MGISEQ, so labs aren't locked to one instrument.
  • A ~16-person team's chemistry appears in research from the Broad, Mayo Clinic and St. Jude.

The Founders

Two scientists, one dependency business

Co-Founder & CEO

Tao Chen

The scientist-turned-operator behind Paragon. Chen founded the company in 2015 and, per his own profile, later attended Harvard Business School - a familiar arc for technical founders who learn the business isn't the technology, it's the customer's whole day.

Co-Founder, President & CTO

Zhitong Liu

The technical counterpart, credited as co-founder and chief technology officer. The CleanPlex chemistry - primer design, uniform amplification, background cleaning - is the kind of R&D-heavy product that needs a founder living in the lab.


The Record

A decade of compounding, quietly

2015

Founded

Tao Chen and Zhitong Liu start Paragon Genomics in the San Francisco Bay Area to build better targeted-sequencing tools.

2016

CleanPlex launches

The patented amplicon-based target-enrichment chemistry and first NGS panels reach the market.

2017

$8M Series A

An oversubscribed round led by Cowin Venture Capital and Fosun Industrial funds scale-up of the CleanPlex line.

2018

CleanPlex UMI

Unique-molecular-identifier panels arrive for high-sensitivity detection of low-frequency variants.

2020

SARS-CoV-2 panel

A whole-genome COVID-19 surveillance panel ships within weeks and later scales to 20,000+ samples per run.

2021

Variant validation

Independent publications confirm the panel accurately identifies SARS-CoV-2 variants of concern, including Alpha and Delta.


The Competition

Who else sells shovels

Paragon is not alone in the target-enrichment aisle. It competes with much larger names: Illumina's AmpliSeq, Twist Bioscience, IDT, Agilent's SureSelect, QIAGEN, and Roche's KAPA products. The interesting question for a company this size is not whether it can out-spend those firms - it cannot - but whether a focused, well-engineered chemistry that handles the hard cases can keep winning labs one validated experiment at a time. So far, 300-plus of them suggest it can.

There is a tidy lesson buried in all of this, and it is the kind that outlasts any single product. The durable businesses in a gold rush are usually not the prospectors. They are the people selling the tools - the reagents, the kits, the boring middle of the workflow that everyone needs and nobody wants to build themselves. Paragon Genomics found one of those middles and made it a company.


Reader Questions

FAQ

What does Paragon Genomics make?
It develops and sells CleanPlex targeted next-generation sequencing panels and custom NGS assay-design services - reagent kits that prepare DNA and RNA samples for targeted sequencing.
What is CleanPlex technology?
A patented amplicon-based target-enrichment method combining a proprietary multiplex PCR primer-design algorithm, uniform amplification chemistry, and a background-cleaning step that removes non-specific PCR products - giving cleaner data from low-input or degraded samples.
Who founded Paragon Genomics and when?
It was founded in 2015 by Tao Chen (Co-Founder & CEO) and Zhitong Liu (Co-Founder, President & CTO), and is headquartered in Fremont, California.
How much funding has it raised?
An oversubscribed $8M Series A in September 2017, led by Cowin Venture Capital and Fosun Industrial, with participation from Cloudstone Venture, HEDA Ventures and Wisemont Capital.
Who uses Paragon Genomics products?
More than 300 organizations worldwide, including the University of California, USDA and CDC, plus institutions such as the Broad Institute, MD Anderson, Mayo Clinic and St. Jude Children's Research Hospital.

Connect & Explore

Links, socials & watch

Watch — CleanPlex workflow & product demos on YouTube →