From functional genomics to translational cancer studies, CleanPlex® gives researchers fast, high-quality targeted sequencing to accelerate discovery. With a streamlined, approximately 3-hour workflow and flexible panel design options, CleanPlex supports a wide range of academic applications — from standard research to disease-focused projects.
By enabling accurate analysis of genetic variants, biomarkers, and complex pathways, CleanPlex panels help bridge the gap between early-stage discovery and translational research. Whether used to explore gene function, validate new hypotheses, or generate data for clinical collaborations, CleanPlex provides the speed, sensitivity, and scalability needed to advance academic innovation.
Products Most Used in Academic & Translational Research
CleanPlex Ready-To-Use Panels
Our portfolio of ready-to-use panels includes OncoZoom, TP53, BRCA1/2, Hereditary Cancer, Fusion/AccuFusion, TMB 500, and more. Each panel is optimized for high coverage uniformity and reliable performance, giving researchers the ability to quickly generate high-quality data for studies ranging from standard research to translational applications.
Custom NGS Panel Design
CleanPlex® Custom Panels provide researchers the flexibility to design assays around their unique study needs. Custom panels support mutational profiling, gene expression analysis, or fusion detection, with rapid delivery timelines and expert consultation to guide every step from design to implementation.
Workflow Fit
Our workflow helps academic and translational researchers move efficiently from concept to results, with flexibility to adapt across projects.
Target Selection
Choose from ready-to-use oncology and hereditary cancer panels, or design a custom panel focused on specific genes, variants, or pathways.
CleanPlex® Library Preparation (~3 hours)
Generate high-quality sequencing libraries in a simple, single-tube workflow that delivers fast turnaround and works reliably with challenging sample types.
Sequence & Analyze
Libraries are compatible with major sequencing platforms, making it easy to generate data across diverse projects.
Pipelines for Variant Calling and Biomarker Assessment
Streamlined analysis pipelines support accurate variant calling, fusion detection, and biomarker evaluation, helping researchers translate findings into meaningful insights.
Testimonials
“Cost-effectiveness, accessibility, and usability made Paragon Genomics the right fit. CleanPlex panels helped us streamline our NGS workflow, enabling our team to scale oncology testing with confidence. The uniformity and data quality are excellent, and being able to go from sample to sequencing-ready libraries in under 6 hours is a game-changer.”
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, PhD, Director of Bioinformatics, Children's Hospital Los AngelesParagon Genomics has streamlined our workflow, from assay design and optimization to laboratory implementation. Their expertise helped us successfully implement a fully automated process using a custom-designed CleanPlex UMI panel, enabling low variant allele frequency (VAF) detection critical for our projects. Paragon’s excellent bioinformatics services and customer support services were key to achieving our goals.”
Ian Mongrain, Director of Operations, Montreal Heart Institute - Pharmacogenomics CentreWhen we decided to choose a targeted sequencing 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, Associate Professor, University of California San FranciscoWe’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 HarvardParagon 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, AnnoroadWe 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-ARSWhy CleanPlex for Academic & Translational Research
CleanPlex® Technology provides academic and translational researchers with a fast, cost-effective workflow that delivers results in as little as 3–6 hours. This efficiency enables more experiments, quicker validation of hypotheses, and faster progress from discovery to publication.
With excellent sensitivity and uniformity across targets, CleanPlex panels generate reliable data even from low-input or challenging samples. Researchers can trust their results to be consistent across studies and replicable across labs. CleanPlex solutions are also scalable and compatible with major sequencing platforms, making them easy to adopt for projects of any size — from small exploratory studies to large multi-institution collaborations.
