NEW YORK – While digital PCR has been around for more than three decades and has established itself as a valuable research tool, its use in clinical diagnostics had continued to be a goal more than a reality.
But in the cancer space, at least, there are hints that clinicians may be more open to adopting digital PCR to diagnose and manage disease, potentially creating a new paradigm in cancer care.
Vendors have fine-tuned their development strategies around dPCR cancer assays in the past few years while also gaining traction through partnerships and support of third-party kit developers and service providers. These dPCR users in turn have observed that the technology's benefits — absolute quantitation combined with ever-increasing multiplexing capabilities and lower cost compared to sequencing — are starting to strike a chord in clinical cancer.
Underlying the ongoing clinical pivot for dPCR system makers like Bio-Rad Laboratories, Qiagen, Roche, and Thermo Fisher Scientific is their continued curation of expansive research-use dPCR assay menus. Many of these firms have also launched dedicated diagnostics instruments and are pursuing regulatory approval for their tests and supporting users of their systems to do the same.
Growing evidence that dPCR is effective and efficient for cancer diagnosis, prognosis, and monitoring is driving its adoption, experts say, citing liquid biopsy, treatment response, minimal residual disease testing, and human papilloma virus-related head-and-neck cancer monitoring as exemplary cases.
One reason that digital PCR is increasingly being adopted in clinical applications is that it is "highly effective at identifying rare cancer-associated genetic changes that might be otherwise missed," said Chris McKee, CEO and founder of test maker GT Molecular.
Clinicians are appreciating that the technology enables noninvasive cancer detection and assessment through liquid biopsy applications, McKee said, while MRD monitoring can track cancer recurrence or treatment resistance, allowing for early intervention.
Importantly, digital PCR can do these jobs faster and more cost-effectively than next-generation sequencing approaches, he said.
Steve Kulisch, Bio-Rad's VP of global marketing, noted that in addition to closely monitoring market needs and trends to help focus product development, his firm is growing the space through clinical research collaborations that generate evidence and help develop new applications.
Similarly, Bio-Rad recently provided reagents and an instrument through a formal collaboration with a team at New York University that developed a 20-minute dPCR protocol using the QX200, potentially enabling molecularly guided brain tumor surgery.
In clinical oncology overall, however, the use of different analytical methodologies continues to be dynamic, and the appropriateness and utility of dPCR versus qPCR, proteomics, or sequencing is the subject of ongoing clinical research. As sequencing- and qPCR-based oncology testing is also burgeoning, most experts seem to see these analytical methodologies playing nicely together in the care continuum.
"Different technologies can be used to answer different questions, for different samples, and in a complementary way," explained Kay Eron, VP and general manager for dPCR platforms in Thermo Fisher's life sciences solutions group. For example, NGS testing supports comprehensive gene target screening, while dPCR can subsequently be deployed for personalized biomarker quantification.
Jonathan Arnold, VP and head of Qiagen's precision medicine franchise, said competition from other methods is not dampening dPCR's uptake. Instead, "we're seeing accelerating momentum," Arnold said, in part because dPCR "offers a unique combination of ultrahigh sensitivity, absolute quantification, shorter turnaround times, and greater cost-effectiveness compared to NGS."
Digital PCR is also much more reproducible within and between labs and experiments than qPCR, according to Wim Trypsteen at the Ghent University Digital PCR Center (DIGPCR). Initial results from a comparison study by Trypsteen and his team show this holds across all major dPCR platforms, an attribute of the method that potentially benefits customers.
Although Trypsteen sees broader adoption of dPCR in clinical oncology currently impeded by knowledge gaps among providers, payors, and potential customers, the balance is starting to shift, he said.
Quantitation and multiplexing
Qiagen launched its first digital PCR platform, the QiAcuity instrument, in 2020. Since then, the firm's strategies have evolved significantly to track with market needs, according to Carola Schade, VP and head of Qiagen's dPCR business.
"Initially, dPCR was seen primarily as a high-precision research tool," Schade said. "In recent years, we've seen strong clinical demand for dPCR's sensitivity and absolute quantification capabilities — especially in applications like hematologic malignancies, treatment monitoring, and liquid biopsy testing."
Absolute quantification of rare targets, without the need to generate a standard curve, as is the case with qPCR, could be a game changer for applications like MRD or treatment monitoring.
Piyush Gupta, founder and chief science and technology officer of diagnostic developer Naveris, sees two other key trends amplifying dPCR's expansion — increasing multiplexing capabilities and the potential for integrated multiomic platforms that can measure both nucleic acids and proteins.
Multiplexing dPCR is "particularly exciting," Gupta said, because the ability to assess a vast number of biomarkers in a single run is seen as one of the main advantages of NGS.
Head and neck cancers are one area where dPCR is increasingly being adopted for diagnosis and treatment monitoring, particularly for cases caused by human papillomavirus infection. Overall, cases have been rising, and there were approximately 1.5 million cases of head and neck cancer and 500,000 deaths globally in 2020.
Naveris' NavDx HPV test for head and neck cancers uses Bio-Rad's Droplet Digital PCR, also called ddPCR, but Gupta said his team is also actively working on multiomics innovations as well as considering collaborations with other dPCR vendors.
At testing service provider Biodesix, meanwhile, Chief Development Officer Gary Pestano said that his team uses multiple platforms, with a focus on Bio-Rad's QX200. It also uses the Bio-Rad QX ONE for its multiplexing capabilities as well as quantitation, Pestano said, while its molecular residual disease application being developed with collaborators at Memorial Sloan Kettering Cancer Center uses the Bio-Rad QX600, which he said provides an even higher order of multiplexing and quantitation.
"Increasingly, we are also seeing quantitation become a strong driver for technology choice as molecular monitoring studies are being undertaken," Pestano said.
Multiplexing dPCR can be enabled by increasing the number of optical channels in instrumentation, and here Stilla Technologies, an oncology-focused instrument maker which is being acquired by Bio-Rad, currently leads the way with seven channels, while the QX600 is a six-channel system that enables higher multiplexing.
Novel chemistry approaches from providers like Pxlence and ChromaCode are also increasing the number of targets that can be detected per reaction, while a 31-plex liquid biopsy test using a drop-off probe method developed by Stilla collaborators in France is a good example of high multiplexing research.
"If digital PCR platforms can achieve an order of magnitude increase in biomarker multiplexing, their unmatched sensitivity and single-molecule detection could make them serious contenders to displace NGS for blood-based cancer detection, especially in low-abundance settings where performance is paramount," Gupta said.
Ghent University's Trypsteen also said that while dPCR's cost per sample compared to qPCR is often cited as an obstacle to adoption, "with the multiplexing of several targets, the resulting price per target is actually low."
Dx systems, IVD tests
Despite these potential advantages, dPCR has been making inroads into clinical oncology at a very measured pace. Prior to being acquired by Bio-Rad, digital PCR developer RainDance was working on a BCR-ABL assay to measure leukemia treatment response.
Bio-Rad subsequently advanced an unrelated test called QXDx BCR-ABL %IS Kit on a dedicated diagnostics-focused instrument, the QXDx. The assays and system were CE marked in 2017 and cleared by the US Food and Drug Administration in 2019, with the firm stating that obtaining regulatory clearances for liquid biopsy IVD tests was a high priority.
Bio-Rad's BCR-ABL remains commercially available in the US and Europe, Kulisch said, adding that last year the firm saw growing demand for it, particularly in Europe following its IVDR registration aligned with new European Union guidelines.
Qiagen joined the dPCR party with the launch of its QiAcuity system in 2020 and last year asserted customer interest in oncohematology and companion diagnostics when it debuted its dedicated diagnostics system, the QiAcuity-Dx. The system has both research-use and IVD modes, and Qiagen said at the time that it would be submitting a BCR-ABL test to the FDA in the second half of 2025.
Meanwhile, Roche launched its Digital Light Cycler in 2022 with a dedicated regulated bioanalysis mode, saying at the time it would target the oncology space.
"Roche continues to explore areas and use cases that utilize the strength of digital PCR to advance clinical diagnostic solutions," a spokesperson for Roche commented in an email. While the firm is continually evaluating high-value medical content for its molecular diagnostic technologies to improve clinical diagnostics, it does not comment on projects in development, the spokesperson said.
Perhaps indicative of the strategic shifts in the oncology dPCR space, Qiagen has since hit pause on its BCR-ABL assay FDA submission, according to Arnold. Rather, the firm is expanding its portfolio of RUO assays, he said, allowing it to "respond more quickly to market needs, accelerate customer adoption, and lay the groundwork for future IVD conversions based on real-world demand."
Schade noted that Qiagen continues to pursue FDA approval for a portfolio of diagnostics.
"This includes developing IVD-labeled systems and assays, building regulatory infrastructure, and pursuing key FDA and IVDR submissions to bring digital PCR into routine clinical care," she said, for mutation detection, gene fusions, and copy number variations, and targeting both hematologic and solid tumor indications such as breast cancer.
Kulisch, meanwhile, said that Bio-Rad is also developing novel RUOs, such as its recently launched suite of methylation detection assays.
Last year Bio-Rad launched its research-use ddPLEX ESR1 mutation detection assay that can discriminate and quantify seven gene variants with high sensitivity from formalin-fixed, paraffin-embedded tissue and plasma samples.
Developed with input from researchers at the UK's Institute of Cancer Research, the test can be used in advanced breast cancer clincal research. Detecting ESR1 mutations is key to treatment with the Menarini Group's selective estrogen receptor degrader Orserdu (elacestrant), Kulisch noted, while serial monitoring of ESR1 status using plasma circulating tumor DNA has been included in ongoing clinical trials. The National Comprehensive Cancer Network has also recently recommended the use of ctDNA as the preferred method for testing of ESR1 mutations.
Bio-Rad is also developing similar assays aimed at biomarker detection in non-small cell squamous cell lung cancer, breast cancer, and other tumor types, Kulisch said.
At Thermo Fisher, Eron said the goal is to provide customers with reliable, precise tools and to ensure solutions comply with regulatory requirements in respective jurisdictions. Its Absolute Q digital PCR system supports the firm's TaqMan assays as well as third-party dPCR kits, and many third-party assay developers already provide kits for Absolute Q, according to Eron.
Support and collaboration
Besides nurturing relationships with clinical researchers, Bio-Rad, Qiagen, and Thermo Fisher support molecular kit makers.
Kulisch noted that Bio-Rad is collaborating with Allegheny Health Network and the department of molecular medicine at Aarhus University Hospital in Denmark to generate clinical evidence for MRD monitoring post curative-intent treatment in patients with solid-tumor cancers.
Biodesix has "a strong working relationship with Bio-Rad," Pestano said, with the two firms collaborating on development of ddPCR-based MRD assays as well as clinical trials at MSKCC.
Bio-Rad also recently invested in Geneoscopy and its ddPCR-based ColoSense colorectal cancer test, which was cleared by the FDA last year and is now offered in commercial partnership by the Laboratory Corporation of America. An EGFR assay for non-small cell lung cancer from Gencurix, a member of Bio-Rad's licensed kit provider program, was recently adopted by Samsung Seoul Hospital, Kulisch said, and Gencurix continues assay development for NSCLC, CRC, melanoma, and thyroid and endometrial cancers.
Bio-Rad's pending acquisition of Stilla and its Nio family of automated digital PCR systems is expected to complement its existing portfolio and accelerate the development of digital PCR solutions, including for clinical oncology applications, according to Kulisch.
As part of Qiagen's strategic approach, Arnold said the firm also collaborates with select third-party developers to expand the ecosystem around digital PCR in clinical oncology.
"These partnerships, which include pharma, diagnostics, and clinical laboratory companies, allow us to complement our own assay pipeline and give customers broader access to clinically validated solutions," he said.
Examples of collaboration areas include companion diagnostics, laboratory-developed test content, and regional assay providers that align with the firm's regulatory and quality standards. A recent example, albeit in the infectious disease space, might be Qiagen's support of researchers at Brown University Health's Rhode Island Hospital who are developing a blood-based pathogen RNA test for pneumonia on the QiAcuity-Dx system.
Kit makers and service providers are also keeping an open approach to dPCR system partners.
GT Molecular's McKee said his firm has developed assays for a host of qPCR and dPCR systems using its proprietary chemistries for ultrasensitive, multitarget detection. Within dPCR, GT Molecular has assays for Bio-Rad's QX200 and QX600, Thermo Fisher's Absolute Q, Roche's Digital Light Cycler, and Qiagen's QiAcuity, and it often collaborates with platform manufacturers to ensure optimized performance and ease of use. This enables its assay development teams to be "especially responsive to market demands and custom requests from our commercial and government partners."
Toward the future
Ultimately, enabling clinicians to more effectively tailor cancer care in the future may necessitate marrying dPCR with other approaches.
For example, Eron said Thermo Fisher leverages its qPCR and NGS capabilities to offer combined solutions, "as these complementary technologies address different use cases in clinical oncology." The firm also offers custom assay design capabilities for clinical oncology and recently launched its Applied Biosystems dPCR Universal Master Mix to enable porting of any of 21 million qPCR TaqMan assays to the Absolute Q.
"By leveraging our comprehensive suite of solutions, including qPCR, NGS, and dPCR, we provide a complete ecosystem of solutions designed to streamline workflows," Eron said.
Similarly, Arnold said that dPCR enhances Qiagen's companion diagnostics offering for pharma, "where we provide a full suite of molecular testing technologies — qPCR, dPCR, multiplexing, and NGS — across all sample types, from FFPE to plasma."
At the DIGPCR labs, Trypsteen and colleagues are working with the Ghent University spinout Pxlence and contract research organization CellCarta on a dPCR workflow for mutation detection and MRD monitoring after treatment of adult and childhood cancers, which involves sequencing the tumor and developing patient-specific assays.
Naveris has also recently shown its blood-based fragmentomics assay for detecting gynecologic cancers, NavDx+Gyn, is sensitive and specific across 14 high-risk HPV strains associated with these cancers. Gupta said the firm is looking into Codetta Bio's multiomic biomarker measurement platform and is in dialogue with Qiagen about its fully integrated digital PCR platform.
Though the company may be open to different vendors and complementary analyses, Naveris is partial to dPCR for its current uses.
To Gupta, digital PCR (dPCR), particularly Droplet Digital PCR (ddPCR), plays a critical role in HPV-related cancer testing due to its exceptional sensitivity and specificity — especially in low-abundance samples where accurate detection of single viral DNA molecules is essential.
Compared to qPCR, ddPCR offers absolute quantification without reliance on standard curves, Gupta said.
Naveris also evaluated both dPCR and Illumina sequencing-based approaches when initially developing NavDx and determined that dPCR's single-molecule detection and absolute quantification offered "far superior performance" for detecting tumor-derived DNA, particularly in low-abundance blood samples.
"This is exactly the clinical context in which high sensitivity and specificity are critical: patients with low tumor burden, where the test must be both precise and reliable to provide meaningful clinical utility and patient benefit," he said.
At Biodesix, the GeneStrat ddPCR tests offered as a service have been major parts of the firm's portfolio for rare variant testing in lung oncology.
For its Nodify and IQ Lung tests, Biodesix uses Tecan's high-throughput ELISA and LC/MS/MS from Thermo and Agilent Technologies, Pestano said, while Bio-Rad's ddPCR, Thermo's amplicon-based NGS, and Bruker's MALDI-TOF underpin its GeneStrat targeted, GeneStrat NGS, and VeriStrat tests, respectively.
Importantly, its new assay development and clinical trial services also feature dPCR tests. "The regulatory framework we have built, and the molecular monitoring aspect of dPCR, are highly sought after qualities of our offering," Pestano said, adding that the firm expects to see its clinical trial services evolve into companion diagnostic tests in its GeneStrat portfolio.
The firm's goal is "to utilize the most robust technologies for the clinical question at hand," he added. As a result, in strategic relationships, Biodesix continues to evaluate technologies that may be used in all of its laboratory workflows, he said.
Meanwhile, Qiagen has a goal to triple its QiAcuity digital PCR business from $90 million in sales in 2023 to $250 million in 2028. As precision medicine advances, Qiagen expects routine adoption of dPCR to grow significantly, Arnold said.
"We see digital PCR as a vital component of the future of precision oncology, and we're committed to making that future a reality," he said.