The landscape of advanced breast cancer diagnostics is rapidly evolving, driven by the emergence of targeted therapies for ESR1-mutation-positive disease and the need for accessible, accurate monitoring solutions. As new oral selective estrogen receptor degrader (SERD) therapies gain regulatory approval, laboratories face critical decisions about using testing platforms that can best serve patients while remaining economically sustainable.
In this interview, Gary Pestano, Chief Development Officer at Biodesix, and Prithwish Pal, Director of Global Product Marketing (Oncology) at Bio-Rad, discuss diagnostic challenges in ESR1 testing – from sensitivity and quantification in liquid biopsy to workflow integration and reimbursement strategies.
What are the most pressing challenges in precision diagnostics for breast cancer, and how is the diagnostics industry tackling them?
Prithwish Pal: One of the most exciting developments right now involves advanced breast cancer cases where patients are estrogen receptor-positive, HER2-negative, and have been on hormone therapy for several years but are developing resistance. Researchers have found that a mutation called ESR1 drives this resistance pathway.
In response, several pharmaceutical companies have developed a new class of drugs called SERDs that target patients with the ESR1 mutation. Menarini introduced the first of these drugs in 2023, receiving FDA and EMA approval the next year. Eli Lilly recently had their similar drug approved and launched it commercially in 2025. Other biotechs are also developing drugs in this class.
Currently, the approved companion diagnostic for both the Menarini and Eli Lilly drugs is a liquid biopsy test. However, the supplier operates as a centralized testing facility using next-generation sequencing (NGS), which raises some concerns about broad patient accessibility. The centralized model, combined with the relatively high cost of NGS, creates accessibility barriers.
When you consider the need for multiple serial tests for disease monitoring purposes – as demonstrated in the SERENA-6 trial – the costs escalate further. There are also reimbursement challenges, particularly in countries like the United States, where payers may not reimburse each monitoring test.
This is the current landscape driving change: pharmaceutical companies and others are actively seeking alternative tests that are more decentralized and cost-effective. That's where our collaboration with Biodesix comes into play.
Gary Pestano: There are essentially two pathways to get new tests to patients. One requires IVD approval, which involves significant investment, cost, and time. The other is laboratory-developed tests (LDTs), developed either in-house at hospitals or through centralized laboratories.
Between Biodesix and Bio-Rad, we bring years of experience with droplet digital PCR (ddPCR) technology and a highly qualified and certified centralized laboratory. Bio-Rad has introduced a multiplexed ddPCR ESR1 test, for research use only, as a distributed solution. Labs can use it for translational research purposes without a great deal of additional validation, but if they're offering it as a clinical test, they must validate it themselves.
Our partnership allows the clinical use of the ddPCR ESR1 test – which is highly complex, monitoring 11 variants with deep sensitivity – into a validated lab, so physicians can access it sooner than they would through a distributed format.
The synergy here is clear: Bio-Rad's technology and kits, combined with our certified laboratory, allow us to get this test to physicians and their patients faster.
What are the pros and cons of digital PCR assays for ESR1 mutations compared with other molecular assays?
PP: The advantages are clear: the digital PCR workflow is significantly less costly than NGS, with faster turnaround times. A ddPCR ESR1 test can be performed on plasma liquid biopsy samples, and is extremely sensitive for detection of circulating tumor DNA in those samples.
The main limitation is that digital PCR assays are very focused – typically examining 10 to 20 variants at a time. For broader discovery work, NGS is obviously the better method. But in a clinical case, where we know exactly which gene we're targeting, digital PCR offers significant advantages.
GP: Essentially, there are four approaches available for estrogen receptor testing: immunohistochemistry (IHC), NGS, and then the quantitative (q)PCR, and ddPCR technologies.
To build on Prithwish's point about NGS being broad versus digital PCR being targeted – this distinction is especially important here because we know exactly what we're looking for in a clinical setting: mutations in the ESR1 ligand-binding domain. It's a very specific target.
In this setting, NGS could actually complicate matters by providing too much information in the form of confounding mutations. We've heard this feedback directly: that an NGS panel, even if reimbursed in this setting, could actually complicate clinical decision-making.
What does the oncologist want to know from the diagnostic test? Are these mutations present – yes or no? It's that simple. That's the readout that ddPCR technology provides: present or absent for one of these 11 mutations. Sometimes they can co-occur, so you might see two or three mutations in the ligand-binding domain of the ESR1 gene from one specimen, but not much more than that.
Why is IHC not recommended for estrogen receptor mutation testing?
GP: IHC is excellent for the initial diagnosis at the estrogen receptor protein level in the tissue. It can confirm whether the patient is ER-positive and could start on endocrine therapy, which often includes aromatase inhibitors. However, ER status is not appropriate for resistance monitoring based on the mutations that arise in the ligand-binding domain of the ESR1 gene. The IHC test is not sensitive to the resistance mutations in the ligand-binding domain that indicate resistance to aromatase inhibitors.
Could qPCR gain traction in this setting, in your opinion?
GP: There are several kits available for qPCR testing but, from my perspective, we haven't embraced qPCR in this space for two key reasons. First, it doesn't provide a quantitative readout, which is really the power of ddPCR technology. Second, its sensitivity may be inferior to that of ddPCR.
How do high-complexity assays address the needs for sensitivity and quantification in liquid biopsy tests?
PP: As we discussed, ddPCR technology has a distinct advantage in its ability to perform absolute quantification, with extremely low levels of detection possible. You can perform quantification with NGS as well, but that's more of a relative quantification and may not be as sensitive.
While you can do quantification with qPCR, it requires standard curves, making the process more complicated. With ddPCR, you're literally counting molecules.
GP: We want assays to be as sensitive as possible, but we're not yet at the point where we know what the clinically relevant threshold for ESR1 mutations in blood should be. In lieu of that we've established thresholds at what we call the lower limit of detection.
Work needs to be done to make this clinically relevant in determining the decision-making threshold where an oncologist can confidently tell a patient they may need to switch therapy. Is two molecules sufficient? Or should it be four, or ten? These are the studies we'll be conducting going forward: to finalize the assay parameters, make them available, and then begin to establish what the clinical cutoff should be.
The key advantage is that we now have an assay we can tune. We know how to differentiate quantitatively between two molecules, four molecules, and ten molecules detected in blood. With a semi-quantitative or qualitative assay, you would probably never be able to accomplish this except by approximation. But we can do this now very confidently.
With the increasing complexity of molecular diagnostics, what changes to pathology workflows would most help labs to keep pace?
GP: From a laboratory perspective, I think reimbursement is critical, especially for high-complexity tests like those we have in precision medicine.
We're investing in instruments, people, assets, and partnerships with companies like Bio-Rad. At the end of it, we need to know we're going to be paid. It's a very practical consideration because why would you make those investments otherwise?
PP: While ddPCR is classed as a high-complexity test, the workflow is relatively much more straightforward than for many other applications.
In my opinion, the critical unmet need for ESR1 mutation testing is clear guidelines that explicitly state which tests should be done. Generally, guidelines recommend liquid biopsy without calling out particular technologies. I would like to see them explicitly state when to use liquid biopsy, and when to employ either digital PCR or NGS.
Education is also very important – for both oncologists and patients. We want to ensure that the treatment decision – made either by the oncologist or the patient – is the best one. Ultimately, that's what matters.
GP: Companies like AstraZeneca have really been leaning into that, organizing physician-to-physician peer teaching at conferences to share the ESR1 story and discuss appropriate tools. They're not endorsing specific products, but laying out the strengths and limitations of NGS, qPCR, and ddPCR technology – for us as labs and lab directors to make more appropriate decisions on whether to build or send out requests for this important testing.
There are things you can pick up off the shelf to do blood-based monitoring, but how should labs choose between them? What will work best with the existing workflow, technical competencies, and automated systems we already have in place? Pharma has a role in this education.
What needs to be done to democratize access to personalized medicine for breast cancer, particularly in low-resource settings?
PP: I think this is where technologies like ddPCR or qPCR really come into play. The lower complexity and lower cost are what make these tests accessible locally.
NGS is a great technology, but it's difficult to implement in a decentralized way, especially in emerging economies and other places where resources may not be available for NGS testing. That's where ddPCR technology and qPCR provide crucial alternatives.
GP: As noted, centralized laboratories provide another key solution. That might be hub labs in Europe that can serve large geographic areas, or US labs that focus on the community setting – where the vast majority of cancers are actually diagnosed.
The major academic centers on the US coasts serve a valuable need as tertiary referral centers for treatment, but diagnosis is mostly happening in the community. We serve that community through send-out tests to our centralized labs, making advanced diagnostics accessible regardless of local infrastructure.
How can industry partnerships help to democratize access to high-complexity tests?
GP: We've been collaborating with Bio-Rad on different activities for some time, including building awareness of ddPCR technology in clinical oncology, and supporting nucleic acid testing for COVID during the pandemic. It's been a long and fruitful series of engagements building toward where we are now – a commitment to bringing high-complexity tests to market together.
I think the unique aspect of our partnership with Bio-Rad is not necessarily just the technology or the test itself, but the market awareness and reimbursement strategy. I can't think of any other partnerships that have all these aspects built into them.
We're looking forward to leveraging our partnership to globalize access to molecular residual disease (MRD) testing around the world. MRD testing requires high-complexity tests and very expensive technology that exists only in limited geographies. Using ddPCR technology, we can actually bring this test to the world. That's the goal.
What are you excited about in the precision oncology space?
PP: It is a really exciting time to be working in the molecular diagnostics space. There has been so much happening in precision oncology. Being able to provide the patient with the right therapy at the right time has been game-changing in the last several years. Various genomics technologies, including ddPCR, have made that happen. As someone who has worked in the oncology space for over a decade, I’m very optimistic about the future directions of this field.
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