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Droplet Digital Polymerase Chain Reaction (ddPCR)

In 2024, MarinBio successfully passed the FDA inspection with no 483s and no observations and in 2025 passed the EU inspection

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Need ddPCR-based potency assays for biologics or viral vectors?

Leverage MarinBio’s ddPCR expertise to develop and qualify potency assays that measure transgene expression, viral genome integrity, or gene copy number with absolute accuracy

Preparing for release or stability testing with high precision?

Our validated 6-channel ddPCR methods deliver ultra-sensitive, absolute quantification for product release, biodistribution, and stability studies

Droplet Digital PCR (ddPCR) Services

Our digital droplet PCR (ddPCR) service leverages droplet-based sample partitioning and endpoint fluorescence analysis to deliver highly accurate and reproducible nucleic acid quantification across a wide range of applications.

Core Capabilities and Applications

Absolute Quantification
Direct copy number measurements without need for standard curves for:

  • Gene copy number variation (CNV) analysis with high-resolution discrimination
  • Viral load and vector copy number (VCN) determination
  • Reference standard characterization
  • Pharmacokinetic (PK) profiling

Gene and Cell Therapy Support

  • VCN assessment for cell therapies (e.g. CAR-T cells, gene-modified stem cells)
  • Biodistribution and shedding studies for gene therapy products
  • Cell and gene therapy vector quantification
  • Potency and lot release testing

Rare Event Detection
Superior sensitivity for reliable detection in complex matrices:

  • Rare mutation detection and low-frequency allele discrimination
  • Minimal residual disease (MRD) monitoring
  • Allele-specific expression (ASE) analysis
  • Subtle fold-change quantification (even <2-fold differences)

Key Performance Features

  • Precision: Minimal variation across replicates for robust, reproducible results suitable for regulatory submissions
  • Sensitivity: Detection of variants at frequencies <0.1% against high background
  • Accuracy: Absolute quantification eliminates standard curve variability and inter-lab discrepancies

Key Applications of ddPCR in Therapeutic Drug Development

Our ddPCR platform is ideally suited for a wide range of high-impact applications due to its absolute quantification and high sensitivity.

A scientist in a lab coat and gloves using a Bio-Rad QX600 Droplet Digital PCR system for therapeutic drug development analysis.

Gene Therapy

  • Vector Copy Number (VCN): Precise determination of the number of viral or non-viral vectors integrated into the genome.
  • Transgene Expression Quantification: Accurate measurement of the activity of the therapeutic gene.
  • Biodistribution in Tissues: Tracking the location and quantity of the therapeutic vector across different organs.
  • Replication-Competent Virus (RCL) Detection: Highly sensitive assay for detecting potentially dangerous, replication-competent viral particles.

Cell Therapy (e.g., CAR-T cells)

  • Vector copy number (VCN) assessment: Accurate determination average vector integrations per cell.
  • Transgene expression quantification: Precise measurement of the level of introduced gene expression in cells.
  • Cell therapy persistence and tracking: Monitoring the survival and quantity of therapeutic cells (like CAR-T cells) over time in the patient.

Translational Research (Small Molecule/Biologics)

  • Target Gene Modulation: Confirming the effect of a therapeutic compound even at very low-fold changes.
  • Verifying Gene Editing Events: Precise measurement of the efficiency and frequency of CRISPR-Cas or other gene editing outcomes.
  • High Precision Quantification for Regulatory/Pharmacodynamic Endpoints: Providing the quantitative accuracy needed for clinical trials and regulatory submissions.

Clinical Trial Applications

  • Biomarker detection and monitoring: ddPCR sensitively quantifies rare mutations, CNVs, and gene expression changes to support ctDNA-based response monitoring, MRD detection, and resistance tracking.
  • Patient stratification and selection: ddPCR enables accurate identification of patients with target genetic alterations for precision medicine trials.
  • Pharmacodynamic assessments: ddPCR measures drug-induced molecular changes with high precision, supporting dose optimization and mechanism-of-action studies.
  • Companion diagnostics development: ddPCR functions as a reference method for validating companion diagnostic assays during clinical development.

Drug Commercialization Applications

  • Quality control and manufacturing support: ddPCR ensures accurate viral vector quantification, cell line stability, and batch consistency to meet regulatory standards.
  • Post-market surveillance: ddPCR supports long-term monitoring of treatment response, resistance, and clinical outcomes in real-world settings.

Questions about Our Digital Droplet PCR (ddPCR) Services?

Contact us to discuss the specifics of your project. Our team of experienced scientists is ready to assist you with tailored solutions to meet your unique needs. Whether you need help with assay development, FDA IND, stability study,  lot release approval, or other scientific endeavors, we are here to support you.
Contact us to learn more about our cell based assay services

We will initiate your project as soon as the proposal is approved and signed by you. Our streamlined process ensures a quick start, minimizing delays and maximizing efficiency. Fill out the form below to email us or click our live chat option to speak with a MarinBio Scientist and get your project underway.

Yes, we have over 30 years of expertise in developing and validating cell based assays for FDA IND, lot release or stability study approval. Our team can also liaise directly with the FDA on your behalf, ensuring a smooth and compliant process. Please contact us to learn more about how we can assist you with your assay development and FDA approval needs.

MarinBio scientists are experienced and creative in designing, developing, validating assays. Some of the assays we perform are listed below, but there are many more that we created, developed and validated. Give us call so that we may help you.

MarinBio scientists conducting targeted protein degradation assays in advanced laboratory

Need help or have questions on cell based assays?

Give us a call at 415-883-8000

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