Technologies driving the furture of Precision Oncology Assays. - The Shift to Biomarker Driven Cancer Care - Core Technologies - Why qPCR became the frontline tool - Engineering scalable oncology diagnostics - The Future of Precision Oncology - Nature and Nurture - Move Beyond Genome
From Sample to Insight Technologies Driving the Future of Precision Oncology Assays
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From Sample to Insight Technologies Driving the Future of Precision Oncology Assays Contents
The Shift to Biomarker-Driven Cancer Care
5
Core Technologies in Precision Oncology
12
Why qPCR Became the Frontline Tool in Early Cancer Diagnostics
21
Engineering Scalable Oncology Diagnostics to Accelerate Patient-Centered Care
29
The Future of Precision Oncology
35
Nature, Nurture, and Diagnostics: Time to Move Beyond the Genome
41
© GEN Publishing • October 2025 Cover & TOC Images : TEK Image / Science Photo Library / Getty Images Cavan Images / iStock / Getty Images Plus
From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Introduction P recision oncology is reshaping cancer diagnosis and treatment, with molecular diagnostics at the core. These tools guide clinical decisions across the care continuum—from early detection and tumor profiling to treatment monitoring and recurrence detection. Emerging applications like minimal residual disease (MRD) tracking and real-time therapy adjustment are quickly becoming standard practice, supported by growing clinical evidence. The driver behind this transformation is a deeper understanding of tumors at the molecular level. Genomic profiling has become a powerful tool for identifying the mutations that drive cancer progression, enabling more targeted, personalized treatment strategies that go beyond traditional histology. At the same time, diagnostic technologies have advanced significantly in speed, scalability, and clinical utility. Key platforms include quantitative PCR (qPCR), targeted next-generation sequencing (tNGS), and whole-genome sequencing (WGS). Each brings distinct strengths: qPCR provides rapid, cost-effective detection of known mutations; tNGS enables broad multiplexed profiling; and WGS delivers a complete, unbiased view of the genome, ideal for complex cases and discovery efforts. As the global cancer burden continues to rise, especially in regions where advanced diagnostics have been limited, expanding the reach of precision testing is critical. The future of oncology depends on technologies that not only offer analytical power but also integrate seamlessly into varied healthcare environments. Scalable, workflow-optimized solutions will be essential to improving cancer care in emerging and previously underserved markets—bringing earlier detection, better treatment decisions, and improved outcomes to more patients worldwide.
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The Shift to Biomarker-Driven Cancer Care
enables earlier detection, better-aligned treatment decisions, and ongoing disease monitoring with unprecedented precision. This chapter will explore the shift to biomark- er-driven care, review key biomarker types, and discuss their role across the modern cancer care continuum. From Morphology to Molecular Precision The use of cancer biomarkers began decades ago with early tools such as alpha-fetoprotein (AFP) for liver cancer and prostate-specific antigen (PSA) for prostate cancer. These markers supported detection and disease monitoring but lacked the specificity needed for therapeutic guidance. 2 Over the past 20 years, however, genomic advances have dramatically expanded the scope and power of biomarker-based diagnostics. Landmark efforts like The Cancer Genome Atlas (TCGA) uncovered the immense molecular heterogeneity of cancer, revealing key driver mutations and signaling pathways across tumor types. 3 These discoveries laid the foundation for a new generation of diagnostics focused on molecular subtyping, mutation detection and therapy selection. By analyzing tumor DNA, clinicians can now identify oncogenic drivers and genetic alterations responsible for tumor growth—and match patients with targeted therapies that are more likely to be effective based on their tumor’s specific molecular profile.
C ancer care is undergoing a fundamental transformation. For decades, diagnosis and treatment were guided primarily by tumor type, anatomical location and histological features. While this framework provided a clinical foundation, it often failed to account for the biological complexity within tumors—leading to variable treatment responses and inconsistent outcomes. Today, precision oncology is redefining this approach. 1 Powered by biomarker-driven diag- nostics, clinicians can now characterize tumors at the molecular level, enabling more personalized, targeted interventions based on a cancer’s unique biology rather than its morphology alone. As molecular understanding deepens, biomarker testing has become a cornerstone of modern oncology—informing not only what therapies to use, but also how and when to intervene. This shift
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Understanding Cancer Biomarkers: Classification, Function, and Clinical Impact Oncology biomarkers are measurable biological indicators that offer critical insights into cancer development, progression, and response to treatment. Found in tumor tissue, blood, or other body fluids, these markers can guide clinical decision-making at nearly every stage of the cancer care continuum—from early detection and diagnosis to treatment selection, monitoring, and prognosits. 4
Biomarkers are commonly classified by their clinical purpose: Biomarker Type Function Diagnostic
Confirms the presence or type of cancer (e.g., PSA, CA-125)
Prognostic Predictive
Predicts disease course or aggressiveness (e.g., Ki-67 proliferation index) Indicates likely response to specific therapy (e.g., EGFR mutations) Reflects biological response to a therapy (e.g., BCR-ABL levels) Tracks disease status or recurrence (e.g., ctDNA for MRD testing)
Pharmacodynamic
Monitoring
Biomarkers can also be categorized by their molecular origin or mechanism: Molecular Class Examples Genetic Alterations Mutations, amplifications, translocations Protein-Based Markers
Enzymes, receptors, hormones, tumor-associated antigens
Epigenetic Changes
DNA methylation, histone modification RNA expression profiles, protein isoforms
Transcriptomic/Proteomic Immune-Related Markers
PD-L1 expression, tumor mutational burden (TMB)
Leukemia : Detection of the Philadelphia chromo- some in acute lymphoblastic leukemia (ALL) and chronic myelogenous leukemia (CML) supports treatment with tyrosine kinase inhibitors such as imatinib (Gleevec) or dasatinib (Sprycel), or later nilotinib (Tasigna). Colorectal cancer : RAS mutation testing helps identify patients likely to benefit from EGFR-tar- geted therapies like cetuximab (Erbitux) or panitu- mumab (Vectibix).
The first biomarker tests—such as those assessing estrogen receptor status in breast cancer—were intro- duced over 30 years ago to determine eligibility for targeted treatments. As a result of these early advances, routine biomarker testing has become a standard part of care for several common tumor types: 5 Breast cancer : Testing for estrogen and proges- terone receptors, as well as HER2 overexpression, guides the use of targeted therapies like trastu- zumab (Herceptin) or lapatinib (Tykerb).
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Non-small cell lung cancer (NSCLC) : EGFR mutation testing determines eligibility for anti-EGFR tyrosine kinase inhibitors (TKIs), such as the first-generation agents gefitinib (Iressa) or erlotinib (Tarceva). Metastatic melanoma : BRAF mutation testing identifies candidates for BRAF-targeted therapies like dabrafenib (Tafinlar), alone or in combination with MEK. More recently, treatments have been developed for KRAS G12C mutations and PIK3CA hotspot mutations (e.g., codons 542, 545, and 1047), further expanding mutation-specific therapeutic options. 6 The field has also progressed toward identi- fying more complex alterations, including gene fusions and germline mutations. For instance,
the PML-RARA fusion in acute myeloid leukemia defines a subgroup with exceptional sensitivity to retinoic acid and arsenic trioxide. Similarly, gene fusions involving ALK, RET, ROS1, FGFR2, NTRK, and NRG have become actionable biomarkers used to match patients to targeted therapies across multiple tumor types. 7 Collectively, the integration of biomarkers into oncology practice enables earlier and more accurate diagnosis, patient stratification based on risk or therapeutic response, personalized therapy selection to increase efficacy and reduce toxicity, real-time treatment monitoring, and long-term surveillance to detect recurrence earlier than traditional imaging.
Timeline of biomarker test approvals by the US Food and Drug Administration. Image adapted from: Zhou, L., Xu, N., Zhang, T., & Wang, Y. (2022). The role of biomarkers in personalized immunotherapy. Biomarker Research, 10, 32. https://doi. org/10.1186/s40364-022-00378-0
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
The Cancer Care Continuum: A Critical Framework for Modern Oncology The modern view of cancer care is no longer defined by a linear model. Instead, it embraces a continuum—a patient-centered, adaptive frame- work that spans from risk assessment to long-term survivorship. 7 This model recognizes that a patient’s needs, disease behavior, and treatment opportuni- ties shift over time, requiring ongoing, coordinated decision-making. By aligning care across this
continuum, healthcare providers can improve outcomes, reduce unnecessary interventions, and enhance the overall patient experience. Within this framework, biomarker testing and molecular diagnostics play a pivotal role at every stage. Below are key applications of precision tools across the continuum ( Figure 1 ).
PRECISION ONCOLOGY ACROSS THE CANCER CARE CONTINUUM
Figure 1. Precision oncology across the cancer care continuum
• Risk Assessment & Prevention Germline genetic testing and family history analysis help identify individuals at increased risk of cancer. Inherited mutations in genes like BRCA1/2, TP53, and APC can guide proactive strategies such as enhanced surveillance, prophy- lactic surgery, or chemoprevention. • Early Detection, Screening, & Risk Stratification Tools such as liquid biopsy and germline testing support early cancer detection and identify high-risk individuals before symptoms appear.
Circulating tumor DNA (ctDNA) and inherited mutations enable timely intervention that can significantly improve outcomes. • Diagnosis & Molecular Subtyping Once cancer is detected, biomarker testing enables precise molecular classification, revealing driver mutations, gene fusions, or expression signatures that inform both diagnosis and treatment planning. • Treatment Selection & Personalization Companion diagnostics and comprehensive genomic profiling help match patients to
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
targeted therapies based on actionable muta- tions, improving treatment effectiveness and minimizing unnecessary toxicity. • Monitoring Treatment Response Real-time tools like ctDNA assays provide early insights into how a patient is responding to treatment allowing clinicians to adjust therapies faster than traditional imaging would indicate. • Recurrence Surveillance & Long-Term Management Minimal residual disease (MRD) testing is reshaping post-treatment care by detecting recurrence at the molecular level, often before clinical symptoms emerge. This enables earlier intervention and supports personalized long- term management plans. While the cancer care continuum is a useful framework, it oversimplifies the complexity of clinical practice. 8 Advances in biology have shown that the stages of care are not always distinct— many tools serve multiple roles. For example, colonoscopy functions both as a screening test and a preventive intervention when polyps are removed. Germline testing may begin as a risk assessment tool but also informs treatment decisions and guides family screening. Similarly, ctDNA assays can support early detection, treatment monitoring, and recurrence surveillance, while BRCA1/2 mutations influence prevention, therapy selection, and eligibility for targeted therapies. Recognizing these overlaps is essential to designing more responsive and integrated care models. As diagnostics become increasingly multi-
faceted, they must be embedded seamlessly into clinical workflows—not as isolated checkpoints, but as interconnected tools that inform decisions throughout the patient’s journey. Rather than viewing each phase of care as a rigid category, the cancer care continuum should be seen as a dynamic, cyclical process. Patients may move between remission, recurrence, surveillance, and active treatment depending on disease progression. Diagnostic tools must be adapt- able, enabling clinicians to respond in real time to shifting patient needs, emerging molecular insights, and evolving therapeutic options. Improving this model means: • Embedding molecular testing earlier in the pathway, even before a cancer diagnosis, to identify risk and guide prevention 4 • Using biomarker testing to monitor changes over time and support personalized, ongoing decision-making 9
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Steps to biomarker-driven targeted cancer therapy to improve patient outcomes. Image adapted from: American Cancer Society Cancer Action Network. (2020, September 28). Improving access to biomarker testing: Advancing precision medicine in cancer care. Retrieved June 23, 2025, from https://www.fightcancer.org/policy-resources/improving-access-biomarker-testing
• Ensuring diagnostic insights are within electronic medical records and care team communications 10 • Building infrastructure for repeat testing, including reimbursement pathways and lab access, to support dynamic testing at multiple time points 11 Ultimately, a more fluid and connected approach to cancer care enables clinicians to anticipate, adapt, and personalize treatment continuously— rather than responding in isolated episodes. It also empowers patients by aligning clinical decisions with the evolving biology of their disease, ensuring that precision medicine delivers on its full promise. As biomarkers take on an increasingly central role in guiding cancer diagnosis and treatment, it’s the enabling technologies behind them that make true precision possible. Scientists at
Meridian have spent years working closely with assay developers to address the technical chal- lenges of implementing biomarker testing in real-world clinical settings. Through this collab- oration, they’ve developed inhibitor-tolerant qPCR mixes that help reduce turnaround times by minimizing sample prep and enabling direct amplification from complex clinical matrices. Meridian’s team has also pioneered stabilization technologies—supporting room-temperature storage and transport for reagents that would traditionally require cold-chain logistics. These innovations help ensure molecular tests remain robust, scalable, and accessible wherever and whenever they are needed most. View our catalog on Specimen-specific™ Inhib- itor Tolerant qPCR & LAMP Master Mixes for Ultra-Sensitive Detection to learn more about our solutions. n
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
References 1. Tsimberidou, A. M., et al. (2020). Review of precision cancer medicine: Evolution of the treatment paradigm. Cancer Treatment Reviews, 86 , 102019. https://doi.org/10.1016/j. ctrv.2020.102019 2. Diamandis, E. P. (2010). Cancer biomarkers: Can we turn recent failures into success? Journal of the National Cancer Institute, 102 (19), 1462-1467. https://doi.org/10.1093/jnci/ djq306 3. The Cancer Genome Atlas Research Network, et al . (2013). The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics, 45 (10), 1113-1120. https://doi. org/10.1038/ng.2764 4. Passaro, A., et al. (2024). Cancer biomarkers: Emerging trends and clinical implications for personalized treat- ment. Cell, 187 (7), 1617-1635. https://doi.org/10.1016/j. cell.2024.02.041 5. Smith, A. (2022, August 26). From then to now: How genomic testing for cancer has expanded. Targeted Ther- apies in Oncology, 11 (11), 83. https://www.targetedonc. com/view/from-then-to-now-how-genomic-testing-for- cancer-has-expanded 6. Chan, C.-H., et al. (2023). PAK and PI3K pathway activation confers resistance to KRAS G12C inhibitor sotorasib. British Journal of Cancer, 128 (1), 148-159. https://doi.org/10.1038/ s41416-022-02032-w
7. Cancer Australia. (n.d.). Cancer continuum . Retrieved June 23, 2025, from https://ncci.canceraustralia.gov.au/ continuum 8. National Cancer Institute, Division of Cancer Control and Population Sciences. (n.d.). Cancer control continuum . U.S. Department of Health and Human Services. Retrieved June 23, 2025, from https://cancercontrol.cancer.gov/ about-dccps/about-cc/cancer-control-continuum 9. Zhuang, L., et al. (2025). Advancing Precision Oncology Through Modeling of Longitudinal and Multimodal Data. IEEE Reviews in Biomedical Engineering (Early Access). https://doi.org/10.1109/RBME.2025.3577587 10. Committee on Improving the Quality of Cancer Care: Addressing the Challenges of an Aging Population; Board on Health Care Services; Institute of Medicine. (2013, December 27). Delivering high-quality cancer care: Charting a new course for a system in crisis (L. Levit, E. Balogh, S. Nass, & P. A. Ganz, Eds.). National Academies Press. https:// doi.org/10.17226/18359 11. Agarwal, A., Ressler, D., & Snyder, G. (2015). The current and future state of companion diagnostics. Pharmacog- enomics and Personalized Medicine, 8 , 99-110. https://doi. org/10.2147/PGPM.S49493
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Core Technologies in Precision Oncology
This transformation has been driven by breakthroughs in genomic technologies, automation, bioinformatics, and a deeper understanding of cancer biology. At the core of precision oncology’s evolution lie three founda- tional technologies that are driving today’s commer- cialized clinical applications: quantitative PCR (qPCR), targeted next-generation sequencing (tNGS), and whole-genome sequencing (WGS). Each offers distinct advantages for specific clinical needs, and increasingly, developers are combining them to maximize diag- nostic power. 1 While other traditional (digital PCR) and emerging technologies continue to shape research and discovery in academic settings, these three remain central to current diagnostic offerings. This article explores the unique strengths, applica- tions, and considerations of each platform and how they can be strategically combined to drive the future of cancer diagnostics.
M olecular diagnostics are reshaping cancer care far beyond detection—they are rede- fining how we diagnose, monitor, and treat malignancies across the care continuum. Over the past two decades, the field has evolved from early PCR-based assays used in infectious disease and hereditary testing to advanced sequencing platforms capable of decoding entire cancer genomes.
qPCR: Speed, Simplicity, and Sensitivity Quantitative PCR (qPCR), also known as real-time PCR, is a molecular technique that amplifies and quantifies specific DNA sequences in real time. It remains the most accessible tool in the precision oncology toolbox. Known for its speed, sensitivity, and ease of use, qPCR is ideal for applications requiring rapid detection of known genetic mutations, such as EGFR in non-small cell lung cancer, BRAF in melanoma, or KRAS in colorectal cancer. It is widely used in FDA-approved
companion diagnostics to guide targeted therapies 2 ( Table 1 ). However, its limitations lie in its targeted nature: qPCR requires prior knowledge of the mutation being tested and cannot detect unknown variants or structural changes, making it less suitable for compre- hensive mutation profiling or monitoring evolving resistance mechanisms. 3 As a result, qPCR is often used as a frontline tool, followed by sequencing when deeper insight is required.
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qPCR’s primary advantages include: • Rapid turnaround (results in hours) • High sensitivity for low-abundance targets (e.g., in liquid biopsy) • Cost-effectiveness and scalability for large screening efforts • Compatibility with automated systems and regulatory pathways Companion diagnostics (CDx) based on PCR have become a cornerstone of precision oncology, enabling the selection of targeted therapies based on the unique genetic profile of a patient’s tumor. These molecular tests are developed alongside specific drugs to identify patients most likely to benefit or, in some cases, those at risk of adverse effects. Regulatory bodies such as the U.S. FDA and EMA often require CDx approval in parallel with the associ- ated therapeutic, as biomarker identification is essential to treatment efficacy. PCR’s widespread adoption in companion diagnostics is largely
due to its proven speed, analytical reliability, and strong regulatory precedent. For example, in non-small cell lung cancer (NSCLC), EGFR mutation detection via qPCR guides eligibility for tyrosine kinase inhibitors (TKIs), while BRAF V600E testing informs BRAF inhibitor use in melanoma. These assays exemplify how CDx can improve outcomes by guiding therapy selection, streamlining clinical decisions, and avoiding ineffective treatments (U.S. FDA, 2024).
Table 1. Examples of FDA-cleared qPCR precision oncology assays used in clinical practice
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Targeted NGS (tNGS): Multiplex Power for Broader Profiling Targeted next-generation sequencing (tNGS) is a high-throughput sequencing method that focuses on specific genes or genomic regions of interest. While widely used in oncology, tNGS is also applied in areas such as inherited disease testing, pharma- cogenomics, and infectious disease surveillance. In cancer diagnostics, it enables the simultaneous analysis of dozens to hundreds of genes, offering
• Hybrid-capture sequencing relies on probe- based enrichment to capture longer stretches of DNA. This method provides greater uniformity of coverage and higher sensitivity for detecting complex genomic alterations, such as gene fusions, copy number variations, and rearrange- ments. It is preferred for broader panels or when comprehensive variant detection is required. tNGS is central to many commercial oncology panels ( Table 2 ) and liquid biopsy assays due to its flexibility, scalability, and ability to evolve alongside emerging biomarkers. Its broad multi- plexing capacity allows developers to consolidate dozens—or even hundreds—of targets into a single assay, improving efficiency and conserving precious sample material. This is especially important in oncology, where tumor biopsies are often small, degraded, or difficult to obtain. By enabling simultaneous detection of multiple mutation types from minimal input, tNGS supports comprehensive molecular profiling without the need for multiple tests or repeat procedures. However, tNGS also comes with challenges. It requires high-quality nucleic acid input, which can be difficult to obtain from formalin-fixed, paraffin-embedded (FFPE) tissue or low-yield liquid
broader mutation coverage than single-target assays while keeping data interpretation and cost manageable. tNGS can detect a wide range of variant types, including single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations, and gene fusions—and supports appli- cations such as tumor profiling, minimal residual disease (MRD) monitoring, and therapy selection. 3.4 There are two common approaches to tNGS, each offering distinct advantages depending on the assay’s goals and complexity ( Figure 1 ): • Amplicon-based sequencing uses PCR ampli- fication to target specific regions of interest. It is typically faster, requires less DNA input, and is more cost-effective, making it well-suited for focused panels with known hotspots. However, it may have limited sensitivity for detecting structural variants or alterations in regions with high GC content.
Figure 1 . Hybrid-capture and amplicon-based targeted next-generation sequencing (tNGS) workflows.
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Table 2. Examples of FDA-cleared targeted tNGS assays used in clinical practice
biopsy samples. The workflows are more complex than PCR-based methods, typically involving longer turnaround times, higher per-sample costs, and the need for specialized equipment and personnel. Additionally, the downstream
bioinformatics analysis can be resource-intensive, and variant interpretation, especially for less well-characterized mutations, remains a significant bottleneck in clinical reporting. 5
Whole Genome Sequencing (WGS): Unbiased Insight for Complex Cases
Whole-genome sequencing (WGS) is a high- throughput genomic technique that decodes the entire DNA sequence of an organism’s genome in a single assay. Unlike targeted methods that focus on specific genes or regions, WGS provides an unbiased, base-by-base view across all chro- mosomes. It captures a broad spectrum of variant types, including single-nucleotide variants (SNVs), insertions and deletions (indels), copy number alterations, structural rearrangements, and muta- tions in noncoding regions. 6 As sequencing tech- nologies have advanced, WGS has become faster, more accurate and increasingly cost-efficient—
enabling its integration into large-scale genomic research and increasingly, clinical exploration.
In oncology, this comprehensive scope makes WGS particularly valuable for translational research, rare cancer characterization, and biomarker discovery. Because it does not rely on prior assumptions about which regions are relevant, WGS is uniquely suited to detect novel driver mutations, charac- terize complex structural variants and uncover regulatory alterations in noncoding regions that may influence tumor behavior. Its ability to deliver a complete genomic snapshot provides deeper
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
insights into tumor heterogeneity, clonal evolu- tion, and mechanisms of drug resistance—critical factors in the development of next-generation diagnostics and therapeutics. Key advantages of WGS include: • Detection of all variant types across the entire genome • An unbiased, comprehensive view of both coding and noncoding regions • Utility in resistance mechanism studies, rare cancers, and discovery research Today, WGS is increasingly being implemented in specialized oncology settings, particularly for rare, refractory, or undiagnosed cancers where conven- tional panels fail to yield actionable insights 7 ( Table 3 ). It is also being applied in research-driven clinical trials and national precision medicine initia- tives to uncover novel biomarkers, track disease evolution, and guide the use of emerging targeted
therapies. In pediatric oncology and hematologic malignancies, WGS has shown promise in detecting cryptic rearrangements, and complex genomic alterations that inform prognosis and influence treatment selection. As sequencing costs continue to fall and data analysis tools become more acces- sible, WGS is expected to play an expanding role in comprehensive cancer aprofiling and personalized treatment planning. However, broader clinical adoption of WGS remains limited by several challenges. These include high sequencing costs, longer turnaround times, and the need for advanced bioinformatics infrastructure to manage and interpret the vast volume of data generated. In addition, many of the variants identified through WGS are of uncertain clinical significance, requiring expert curation, robust databases, and clinical correlation—factors that continue to complicate reporting and down- stream clinical decision-making. 8 ease of use make it ideal for detecting well-characterized, high-prevalence mutations that inform immediate treatment decisions— such as EGFR, KRAS, or BRAF status in frontline therapy selection. • tNGS follows when a broader molecular picture is required. It enables comprehensive mutation profiling, including less common variants, gene fusions and copy number alterations across dozens to hundreds of genes. This depth of information
The Power of Strategic Combinations and Integration As the complexity of cancer biology and treatment continues to grow, no single diagnostic technology can meet all clinical needs. Instead, forward-
looking oncology strategies increasingly rely on a layered, multi-platform approach—leveraging the unique strengths of qPCR, targeted NGS (tNGS), and whole-genome sequencing (WGS) at different stages of care 9 ( Table 4 ). • qPCR is typically used as a first-line tool for rapid eligibility screening. Its speed, low cost, and
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supports precision therapy selection, clinical trial enrollment, and monitoring of treatment response or minimal residual disease (MRD). • WGS plays a critical role in exploratory analysis, especially in complex, treatment-resistant, or rare cancer cases where other methods fail to reveal actionable findings. Its unbiased, whole-genome coverage helps uncover novel driver mutations, structural rearrangements and noncoding alter-
ations that may influence tumor behavior or drug resistance. While other traditional (digital PCR) and emerging technologies continue to shape research and discovery in academic settings, these three remain central to current diagnostic offerings. Together, these platforms form a complementary diagnostic continuum—where qPCR provides fast answers for established biomarkers, tNGS offers
Table 3. Overview of CLIA-approved EGS assays supporting precision oncology.
Highest
Table 4. Summary of key differences: qPCR vs tNGS vs. WGS in precision oncology diagnostics.
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
MERIDAN'S SOLUTIONS
qPCR
NGS
multi-target resolution for more nuanced clinical deci- sions and WGS enables deep discovery in challenging or ambiguous cases. This combination maximizes diagnostic yield, improves efficiency, and ensures that each patient receives the right level of analysis at the right time in their care pathway. As the field moves toward increasingly adaptive and personalized cancer care, the ability to strate- gically integrate molecular platforms will be key to optimizing outcomes, streamlining workflows and delivering precision medicine at scale. Translating Innovation into Impact in Precision Oncology Diagnostics From rapid mutation detection to deep tumor profiling, qPCR, tNGS, and WGS each serve a critical role in the evolving precision oncology landscape. However, the success of any platform also depends on what powers it. High-quality, stable, and scalable reagents are essential for achieving reliable perfor- mance, regulatory readiness, and global scalability. Assay developers must not only navigate platform
selection but also address challenges such as cold- chain logistics, reproducibility, and assay stability— especially in decentralized or resource-limited environments. Meridian supports this end-to-end journey with future-ready solutions, including glycerol-free enzymes, lyophilization-ready master mixes, customized enzyme formulation services, and technical expertise to optimize reagent performance for assay development, scalability, and long-term stability. As we move toward a future where diagnos- tics increasingly drive treatment adaptation, resistance prediction, and real-time moni- toring, developers must choose platforms and partners that align with long-term clinical and commercial goals. Strategic use of molecular technologies—combined with expert reagent support—enables developers to deliver diag- nostics that meet the highest standards of impact, scalability, and innovation.
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Meridian is committed to helping developers build assays that not only perform but also transform cancer care for patients everywhere. Learn more about our Solutions for Next-Generation Sequencing and our Custom Enzyme Stabilization Services
While advanced sequencing platforms are expanding the reach of molecular oncology, quantitative PCR remains the most trusted frontline tool for early detection—thanks to its proven strengths in sensitivity, speed, and accessibility. From rapid mutation detection to deep tumor profiling, qPCR, tNGS, and WGS each serve a critical role in the evolving precision oncology landscape. But the success of any platform depends on what powers it. As a partner to References 1. Roychowdhury, S. & Chinnaiyan, A. M. (2014). Translating genomics for precision cancer medicine. Annual Review of Genomics and Human Genetics , 15, 395-415. https://doi. org/10.1146/annurev-genom-090413-025552 2. U.S. Food and Drug Administration. (n.d.). List of cleared or approved companion diagnostic devices (in vitro and imaging tools). Retrieved June 5, 2025, from https://www.fda.gov/ medical-devices/in-vitro-diagnostics/list-cleared-or-approved- companion-diagnostic-devices-in-vitro-and-imaging-tools
leading assay developers, Meridian provides the technical expertise and reagent stability needed for diagnostic scale-up. Glycerol-free enzymes, lyophilization-ready master mixes, and customized formulation services are helping developers address common barriers—such as cold-chain logistics, inhibitor sensitivity, and long-term reagent stability. These innovations enable robust assay performance across diverse clinical settings, supporting the global delivery of high-impact diagnostic tools. n
3. Merker, J. D., et al. (2018). Circulating tumor DNA analysis in patients with cancer: American Society of Clinical Oncology and College of American Pathologists joint review. Journal of Clinical Oncology , 36(16), 1631-1641. https://doi.org/10.1200/JCO.2017.76.8671 4. Frampton, G. M., et al. (2013). Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nature Biotechnology, 31(11), 1023- 1031. https://doi.org/10.1038/nbt.2696
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5. Jennings, L. J., et al. (2017). Guidelines for validation of next-generation sequencing–based oncology panels: A joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists. Journal of Molecular Diagnostics , 19(3), 341-365. https://doi.org/10.1016/j.jmoldx.2017.01.011 6. Belkadi, A., et al. (2015). Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proceedings of the National Academy of Sciences of the United States of America , 112(17), 5473-5478. https://doi.org/10.1073/pnas.1418631112
7. Cuppen, E., et al. (2022). Implementation of whole- genome and transcriptome sequencing into clinical cancer care. JCO Precision Oncology , 6, e2200245. https:// doi.org/10.1200/PO.22.00245 8. Goodwin, S., McPherson, J. & McCombie, W. (2016). Coming of age: Ten years of next-generation sequencing technologies. Nature Reviews Genetics , 17(6), 333-351. https://doi.org/10.1038/nrg.2016.49 9. Malone, E. R., et al. (2020). Molecular profiling for precision cancer therapies. Genome Medicine , 12, 8. https://doi. org/10.1186/s13073-019-0703-1
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Why qPCR Became the Frontline Tool in Early Cancer Diagnostics
qPCR (RT-qPCR) to monitor minimal residual disease (MRD) in chronic myeloid leukemia (CML) by quantifying BCR-ABL fusion transcripts—a breakthrough that established a new gold standard for precision monitoring in hematologic malignan- cies.¹ This use case became a model for how qPCR could deliver precise, real-time insights into disease burden and treatment response. As cancer diagnostics evolved, qPCR found broader applications in solid tumors, guiding targeted therapies by detecting mutations such as EGFR in non-small cell lung cancer, KRAS in colorectal cancer, and BRAF in melanoma ( Figure 1 ). These advances laid the ground- work for qPCR’s integration into FDA-approved companion diagnostics, where it remains a gold standard for rapid, actionable mutation detection. By enabling precise, gene-level mutation detection, qPCR laid the groundwork for molecular stratifica- tion, targeted therapies and real-time monitoring
S ince its introduction in the early 1990s, and reliable method to detect and quantify nucleic acids. It reshaped clinical diagnostics—first enabling rapid infectious disease detection, then extending into oncology as one of the earliest tools to identify cancer-related genetic mutations. A significant early application of qPCR in oncology was the use of reverse transcription quantitative PCR (qPCR) transformed molec- ular biology by providing a fast, sensitive,
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Figure 1 . Key early oncology milestones.
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
in precision oncology. As the field continues to advance, qPCR is maintaining its position as a frontline diagnostic tool—particularly in early cancer detection. Its unique combination of speed, affordability, sensitivity, and broad accessibility
makes it indispensable in both centralized labs and decentralized screening programs. Its continued dominance in early cancer diagnostics is driven by these strengths, alongside ongoing innovations that are expanding its clinical utility.
The Advantages of qPCR in Cancer Diagnostics
High Sensitivity for Low-Abundance Targets qPCR’s greatest strength lies in its ability to detect low-abundance targets with high analyt- ical sensitivity. This makes it especially effective for identifying trace levels of tumor DNA in early- stage disease, residual disease post-treatment, or in circulating biomarkers such as cell-free DNA (cfDNA). In FDA-approved companion diagnos- tics, qPCR’s high sensitivity enables the detection of clinically actionable mutations such as EGFR, BRAF, or KRAS ( Table 1 ).
qPCR is the most established and widely adopted molecular diagnostic technology for oncology, particularly in applications requiring rapid, high-sen- sitivity detection of known mutations. While technol- ogies like NGS offer broader insights, qPCR excels in delivering rapid, targeted results, especially for early detection, treatment selection and routine screening. Its proven role in companion diagnostics, minimal infrastructure needs, and automation compatibility make it ideal for both centralized labs and decentral- ized settings, securing its place as a frontline tool in precision oncology.
Table 1. Examples of real-world sensitivity levels from FDA-approved qPCR-based companion diagnostics.
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
With more than 68 FDA-approved tests ( Table 2 ), qPCR-based companion diagnostics have become a cornerstone of precision oncology. Their ability to rapidly and sensitively detect clinically actionable mutations, often at levels matching or surpassing standard NGS (typically 0.5–2% VAF, unless using ultra-deep or error-corrected methods), makes them ideal for focused, mutation-specific applications. qPCR Sensitivity Overview: • Limit of detection (LOD): Reliably detects as few as 1–10 mutant copies among 10,000+ wild-type molecules • Variant allele frequency (VAF): Capable of identifying mutations at frequencies as low as 0.1% These same performance advantages, ultra-low detection limits, high specificity, and fast turn- around, make qPCR especially well-suited for longitudinal monitoring, such as minimal residual
disease (MRD) tracking and early recurrence detec- tion via liquid biopsy. As oncology moves toward more adaptive, biomarker-driven care models, qPCR will remain a vital tool for enabling timely, data-guided treatment decisions.
Rapid Turnaround Time & Compatibility with Automation
Unlike sequencing-based methods that can take days to deliver and interpret results, qPCR provides clinically actionable answers within hours. This speed is especially critical for time-sensitive deci- sions, such as determining eligibility for targeted therapies or enrolling patients in biomarker-driven trials. Just as importantly, qPCR workflows are automation-friendly and require minimal hands-on time—enabling high-throughput testing without sacrificing turnaround. Together, these attributes make qPCR an ideal choice for integrated care settings, where rapid, scalable diagnostics are essential for timely intervention.
Table 2. Examples of FDA-cleared qPCR precision oncology assays used in clinical practice.
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Cost-Effective and Scalable for Screening qPCR offers one of the most cost-effective solutions in early cancer diagnostics. While next-generation sequencing (NGS) can range from $300 to $3,000 per sample, qPCR tests typically cost between $50 and $200—making them far more accessible for large-scale screening and routine use. Its afford- ability extends beyond reagents to equipment, maintenance, data analysis, and labor. This cost advantage has enabled qPCR’s integration into national screening programs and low-resource settings. For example, in India, qPCR has been used to screen for HPV-driven cervical cancer since 2012, offering a faster, more scalable alternative to cytology. 2 Similarly, qPCR-based EGFR testing has been standard in many Chinese hospitals since
2016 due to its low cost and rapid turnaround, even in regional centers. 3 Scalability is another key strength. qPCR supports high-throughput formats (96- or 384-well plates), requires minimal input, and is easily automated— allowing labs to process hundreds or thousands of samples daily. During the COVID-19 pandemic, qPCR was used worldwide to test millions of samples, demonstrating its unmatched scalability under pressure. For early detection efforts and public health programs targeting high-incidence cancers like colorectal, cervical, and lung, qPCR provides a prac- tical balance of sensitivity, speed, and affordability, making it a powerful tool for both diagnosis and cancer prevention at scale.
Advances in qPCR Chemistry Driving Clinical Success While the core principles of qPCR have remained consistent since the 1990s, ongoing advances in qPCR chemistry have significantly enhanced its performance, robustness, and clinical applicability. These innovations have addressed early limitations around sensitivity, specificity, multiplexing, and sample compatibility, enabling qPCR to remain a frontline diagnostic tool even as molecular testing demands have grown more complex. Next-gener- ation DNA polymerases used in qPCR have been rationally designed or evolved through a combina- tion of site-directed mutagenesis, directed evolu- tion, and protein domain optimization to meet the demands of clinical diagnostics—particularly when
working with challenging sample types like FFPE tissue, blood, and plasma.
Key Areas of DNA Polymerase Enzyme Optimization for Modern Molecular Diagnostics
1. Inhibitor Resistance: ° Enzymes are engineered with mutations that reduce binding affinity to common PCR inhib- itors, such as heme (from blood), urea (from
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
urine), bile salts, and formalin-induced modifica- tions in FFPE samples. ° Buffers are optimized with additives and proprietary enhancers that further stabilize the enzyme and neutralize inhibitors—ensuring sensitive and robust performance across clinical sample types.
4. Lyophilization and Ambient Stability Compatibility:
° Certain polymerases have been reformulated with proprietary stabilizers or engineered for struc- tural resilience, allowing them to retain activity after lyophilization or exposure to room-tem- perature storage. This is especially valuable for automation, point-of-care, and cold-chain inde- pendent diagnostics, expanding access to molec- ular diagnostics in remote and resource-limited environments. Expanding qPCR Utility through Multiplexing Traditionally, comprehensive mutation screening required NGS due to its high multiplexing capacity. However, recent advances in qPCR chemistry and assay design are enabling broad, multi-target detection without the need for sequencing-based platforms. Innovations such as multiplexed hydrolysis probes, optimized super-mixes, and non-overlapping fluorophores now allow qPCR assays to detect 4 to 6 or more targets in a single reaction, dramatically expanding its utility in oncology and infectious disease diagnostics. In the context of syndromic panels, these high-plex qPCR assays can simultaneously test for multiple oncogenic mutations or actionable biomarkers, streamlining workflows for diseases with over- lapping clinical presentations. For example, in
2. Improved Processivity and Speed: ° Polymerases have been modified to increase processivity, enabling faster and more efficient amplification even in the presence of fragmented or low-input DNA. ° Fusion polymerases (e.g., those linked to thermo- stable DNA-binding proteins) improve template affinity and thermal stability, which is especially beneficial in high-GC regions common in many cancer-relevant genes. 3. Thermal Stability: ° Enzymes have been stabilized through amino acid substitutions that increase their half-life at high temperatures, making them suitable for fast-cycling protocols, and allow robust ampli- fication of difficult targets, including GC-rich oncogenic regions, which are prone to secondary structures that can inhibit less-optimized enzymes.
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From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
non-small cell lung cancer (NSCLC), multiplexed qPCR panels can assess EGFR, KRAS, BRAF, and ALK alterations in parallel, accelerating time to result and guiding targeted therapy decisions from a single run. 4 This expanded capacity enables broad mutation screening in tissue-limited samples, offering a
faster, more affordable, and simpler alternative to NGS—ideal for clinical labs and time-sensitive or resource-limited settings. As the technology evolves, it will continue to expand diagnostic coverage while preserving the speed, affordability, and regulatory familiarity that make it an attractive alternative to sequencing.
Performance Insight Meridian’s MDX092 Air-Dryable™ Direct DNA qPCR Blood mix successfully amplified target DNA down to 10 copies, even in the presence of 20% heparin- plasma. In contrast, comparator mixes did not detect the target at this low level. These findings underscore the importance of inhibitor-tolerant chemistry for enabling sensitive mutation detection in real-world clinical samples.
Reagent Solutions for Oncology qPCR Applications qPCR’s continued dominance in oncology depends on more than just platform design—it requires reagent systems that deliver consistency, sensi- tivity, and flexibility under real-world conditions. Meridian provides a portfolio of high-performance qPCR enzymes and master mixes engineered to meet the evolving demands. Their reagents are
Enzymes Optimized for Clinical Sample Types
To address common barriers like sample inhibi- tion and DNA degradation, Meridian’s next-gen- eration DNA polymerases are engineered to perform reliably with low-input inhibitor-rich clinical matrices, including formalin-fixed paraf- fin-embedded (FFPE) tissue, plasma, and other challenging sample types. In one evaluation using 20% heparin-plasma ( Figure 2 ), a common yet inhibitory matrix in blood-derived liquid
optimized for clinical sample types and diag- nostic workflows, supporting applications such as companion diagnostics, MRD monitoring, and high-throughput mutation screening.
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