In recent years, liquid biopsy approaches have emerged as powerful tools in oncology, enabling non‑invasive, real‑time insights into tumor dynamics. Among these technologies, droplet digital PCR (ddPCR) is gaining traction for molecular residual disease (MRD) detection and treatment monitoring. As the demand grows for clinically deployable assays to guide therapy decisions and track disease evolution, ddPCR-based solutions are shifting from research labs toward routine clinical use.
Technology Networks recently spoke with Dr. Gary Pestano, chief development officer at Biodesix, and Dr. Prithwish Pal, director of global product marketing at Bio‑Rad, to learn more about the advantages ddPCR offers in MRD detection, the development of a ddPCR-based ESR1 assay and the evolving role of liquid biopsy in cancer diagnostics.
Kate Robinson (KR):
Science Editor
Technology Networks
Kate Robinson is a science editor at Technology Networks. She joined the team in 2021 after obtaining a bachelor's degree in biomedical sciences.
What advantages does ddPCR offer for detecting MRD compared to other molecular methods?
Chief Development Officer
Biodesix
Dr. Pestano heads the Research and Development organization at Biodesix, a leading diagnostic solutions company. He is also the NYS CLEP Laboratory Director of the company’s corporate clinical testing laboratory in Louisville, Colorado. His greater than 20 years of experience in laboratory and assay development for high complexity molecular diagnostics for oncology includes genomic and proteomic approaches in support of Biodesix Nodify and IQLung blood-based tests. Most recently his work has focused on the detection and standardization of molecular testing for cell free nucleic acids as a part of a consortia led by the Friends of Cancer Research. As a critical part of product development Dr. Pestano has fostered innovative key collaborations with leading academic and industry partners across the globe. Prior to Biodesix, Dr. Pestano was at Ventana, a member of the Roche Group, where he led project teams in Pharma Services and in Assay Development. Dr. Pestano received his Ph.D. training at The Graduate Center, City University of New York and conducted his post-doctoral training in cancer immunology at the Dana Farber Cancer Institute, Harvard Medical School.
The most likely technology for comparison in the MRD setting is NGS. ddPCR offers a few key advantages over NGS in:
- Design and validation speed for specific targeted assays: For monitoring known and discovered specific molecular targets [e.g., a structural variant (SV) or single nucleotide variants including insertions and deletions (SNV/INDEL)], ddPCR assays are faster to design and validate, thus saving time to evaluate circulating variants.
- Workflow simplicity cost-effectiveness: the laboratory workflows are also simpler and less expensive to implement than for most NGS platforms, e.g., ddPCR has a streamlined workflow with automated options for extraction and droplet generation that aids lab personnel in easily implementing new bespoke assays.
- Data analysis: ddPCR offers multiplexing capabilities without requiring complex bioinformatics pipelines and technical support and knowledge curation modules as in most NGS platforms. This can make it more accessible for routine clinical diagnostics in many labs around the world.
Science Editor
Technology Networks
Kate Robinson is a science editor at Technology Networks. She joined the team in 2021 after obtaining a bachelor's degree in biomedical sciences.
How will the ESR1 assay support the development of targeted therapeutics and cancer treatment monitoring?
Director of Marketing
Bio-Rad
Prithwish Pal is the Director of Marketing at Bio-Rad Laboratories, where he leads a team for development of Digital Droplet PCR (ddPCR) assays for oncology applications across the patient journey continuum.
A ddPCR ESR1 circulating tumor DNA (ctDNA) assay will support targeted therapies and treatment monitoring by providing sensitive and quantitative detection of ESR1 mutations in liquid biopsies (plasma). An assay that incorporates a multiplicity of the prevalent variants could predict resistance to endocrine therapy and guide the selection of targeted drugs.
A highly multiplexed liquid biopsy assay like this one on the QX600 ddPCR system* would allow for the non-invasive, near real-time monitoring of tumor evolution, and potentially guide treatment switches to more effective options, thus improving patient outcomes.
*For Research Use Only. Not for diagnostic purposes.
Science Editor
Technology Networks
Kate Robinson is a science editor at Technology Networks. She joined the team in 2021 after obtaining a bachelor's degree in biomedical sciences.
How do you see liquid biopsy and ctDNA testing evolving over the next few years?
Chief Development Officer
Biodesix
Dr. Pestano heads the Research and Development organization at Biodesix, a leading diagnostic solutions company. He is also the NYS CLEP Laboratory Director of the company’s corporate clinical testing laboratory in Louisville, Colorado. His greater than 20 years of experience in laboratory and assay development for high complexity molecular diagnostics for oncology includes genomic and proteomic approaches in support of Biodesix Nodify and IQLung blood-based tests. Most recently his work has focused on the detection and standardization of molecular testing for cell free nucleic acids as a part of a consortia led by the Friends of Cancer Research. As a critical part of product development Dr. Pestano has fostered innovative key collaborations with leading academic and industry partners across the globe. Prior to Biodesix, Dr. Pestano was at Ventana, a member of the Roche Group, where he led project teams in Pharma Services and in Assay Development. Dr. Pestano received his Ph.D. training at The Graduate Center, City University of New York and conducted his post-doctoral training in cancer immunology at the Dana Farber Cancer Institute, Harvard Medical School.
Circulating nucleic acids/liquid biopsies are likely to continue to grow in the diagnostic space. We have seen tremendous gains in the last 10 years and only expect that the applications will accelerate.
We also expect that the complexity of molecular detection will expand from the initial SNV to more complex mutations including copy number amplification and deletions, and fusions (including RNA variants).
The applications will include a more comprehensive 'multiomic' approach that combines ctDNA with other markers like circulating tumor cells (CTCs), exosomes, fragments and methylation markers. Protein and RNA biomarkers (e.g., fusions, miRNA) will be included in these multiomic signatures.
The menu of assays and technologies will also become more sensitive and cost-effective due to advances in scaling technology, including miniaturization (microfluidics and nanotechnology).
Ultimately, we believe we are on track for enabling newer circulatory biomarkers (like ctDNA) to work in concert with the existing blood and tissue makers to enable earlier cancer detection and near real-time monitoring of treatment response.
Science Editor
Technology Networks
Kate Robinson is a science editor at Technology Networks. She joined the team in 2021 after obtaining a bachelor's degree in biomedical sciences.
What are the main hurdles in taking high-complexity molecular assays from validation to clinical deployment?
Director of Marketing
Bio-Rad
Prithwish Pal is the Director of Marketing at Bio-Rad Laboratories, where he leads a team for development of Digital Droplet PCR (ddPCR) assays for oncology applications across the patient journey continuum.
The major hurdles in moving a test from validation to widespread clinical deployment are in aligning the needs of assay developers with regulatory requirements, including support from pharma and biotech companies conducting clinical trials, and then with the conduct of clinical utility in demonstrating change in treatment decisions often necessary for gaining reimbursement.
Technology commercial channel access, customer training (technical expertise), and cost of technology and support can be other hurdles in deployment to clinical labs.
Science Editor
Technology Networks
Kate Robinson is a science editor at Technology Networks. She joined the team in 2021 after obtaining a bachelor's degree in biomedical sciences.
How will you prioritize which genomic markers to focus on for future ddPCR assays?
Chief Development Officer
Biodesix
Dr. Pestano heads the Research and Development organization at Biodesix, a leading diagnostic solutions company. He is also the NYS CLEP Laboratory Director of the company’s corporate clinical testing laboratory in Louisville, Colorado. His greater than 20 years of experience in laboratory and assay development for high complexity molecular diagnostics for oncology includes genomic and proteomic approaches in support of Biodesix Nodify and IQLung blood-based tests. Most recently his work has focused on the detection and standardization of molecular testing for cell free nucleic acids as a part of a consortia led by the Friends of Cancer Research. As a critical part of product development Dr. Pestano has fostered innovative key collaborations with leading academic and industry partners across the globe. Prior to Biodesix, Dr. Pestano was at Ventana, a member of the Roche Group, where he led project teams in Pharma Services and in Assay Development. Dr. Pestano received his Ph.D. training at The Graduate Center, City University of New York and conducted his post-doctoral training in cancer immunology at the Dana Farber Cancer Institute, Harvard Medical School.
For Biodesix, this is driven by the clinical need for the biomarker. We see tremendous application from early diagnosis, through early intervention (MRD), and in treatment guidance in the later stages of tumor progression and recurrence.
PP:
Director of Marketing
Bio-Rad
Prithwish Pal is the Director of Marketing at Bio-Rad Laboratories, where he leads a team for development of Digital Droplet PCR (ddPCR) assays for oncology applications across the patient journey continuum.
At Bio-Rad, we continue to keep a pulse on the needs of the oncology clinical research community, as well as the biomarker driven therapy development. We often work closely with academic key opinion leaders, and commercial leaders (such as Biodesix) to map and prioritize future ddPCR assays.
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