Molecular Technologies Shaping Precision Oncology Diagnostics - A Comparison of qPCR, Targeted NGS, and Whole Genome Sequencing. Meridian is a primary manufacturer of specialized high-quality molecular reagents and offers solutions to a wide range of industries to diagnose and treat diseases, discover new therapeutics or develop tests for environmental, food and cosmetic safety.
From Single Mutations to Whole Genomes:
Molecular Technologies Shaping Precision Oncology Diagnostics
A Comparison of qPCR, Targeted NGS, and Whole Genome Sequencing
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Advances in molecular technologies have deepened our understanding of cancer, enabling earlier and more accurate diagnoses, more effective targeted therapies, and improved survival rates across many cancer types. Over the past two decades molecular diagnostics have moved into a central and increasingly critical role across the oncology care continuum. Tumor profiling, minimal residual disease (MRD) tracking, and real-time therapy adaptation are now widely integrated into clinical practice, enabling more personalized care while supporting the management of cancer as a chronic condition. 1, 2 The evolving clinical demands of precision oncology have driven advancements in technologies such as quantitative PCR (qPCR), targeted next-generation sequencing (tNGS), and whole-genome sequencing (WGS), enhancing their speed, sensitivity, and analytical depth. Each platform offers distinct strengths: qPCR provides rapid, cost-effective detection of known mutations; tNGS enables broader, multiplexed mutation profiling across dozens to hundreds of genes; and WGS delivers an unbiased, comprehensive view of the cancer genome, including rare or complex alterations. As these technologies mature, diagnostic assay developers must navigate complex decisions around platform selection, assay design, and reagent optimization—decisions that directly impact assay performance, regulatory approval, and how effectively they deliver accessible, cost-effective cancer diagnostics in both centralized and point-of-care settings. The rise of precision oncology is fundamentally reshaping how cancer is diagnosed and treated.
THE IMPACT OF PRECISION ONCOLOGY ACROSS CANCER CARE
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KIDNEY CANCER
OVARIAN CANCER
A TIMELINE OF PRECISION ONCOLOGY DIAGNOSTICS
2000
2010
2020
HISTOPATHOLOGY & IMAGING Broad cancer classification, limited molecular insight
SINGLE-GENE BIOMARKER TESTING (HER2)
PANEL-BASED TESTING & PCR/ISH ASSAYS More refined subtyping eligibility for multiple therapies
NGS & COMPREHENSIVE GENETIC PROFILING (CGP) Multi-biomarker detection pan- cancer testing, liquid biopsy
First targeted therapies enabled by diagnostics
Milestones in the Advancement of Oncology Diagnostics
generation sequencing (tNGS) expanded diagnostic capabilities by allowing the simultaneous analysis of dozens to hundreds of cancer-relevant genes, improving mutation profiling and therapy selection. More recent advances in sequencing technology, including improvements in short- and long-read platforms and library preparation, have made whole- genome sequencing (WGS) clinically feasible, enabling high-accuracy, full-genome coverage. Although not yet widely adopted in clinical practice, WGS continues to emerge as a powerful tool for comprehensive tumor characterization, capable of uncovering rare, novel, and complex genomic alterations. Overall, while many technologies have contributed to the advancement of cancer care, qPCR, tNGS, and WGS have been the primary drivers of clinical adoption—transforming molecular diagnostics from a research tool into a cornerstone of precision oncology. 5
Advances in cancer biology have exposed the limits of traditional diagnostics such as histology and immunohistochemistry, driving a shift toward molecularly guided decision-making that is redefining how clinicians classify and treat cancer. Large-scale genomic studies 3, 4 conducted over the past two decades have identified key driver mutations, signaling pathways, and molecular subtypes across diverse cancers, revealing the underlying heterogeneity of tumors once considered homogeneous. This paradigm shift in cancer understanding has underscored the need for precise, molecular-level diagnostics capable of detecting clinically relevant changes. Technologies such as quantitative PCR (qPCR) initially met this need by enabling high- sensitivity detection of specific, actionable mutations— laying the foundation for modern companion diagnostics (CDx). The advent of targeted next-
Quantitative PCR
Targeted Next-Generation Sequencing
Whole-Genome Sequencing
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FROM SINGLE MUTATIONS TO WHOLE GENOMES | MOLECULAR TECHNOLOGIES SHAPING PRECISION ONCOLOGY DIAGNOSTICS
BREAST CANCER
PRECISION ONCOLOGY AT EVERY STAGE GUIDING CANCER CARE FROM START TO FINISH
Molecular Diagnostics Across the Cancer Care Continuum
Today, molecular diagnostics span the entire spectrum of cancer care—from early screening to residual disease monitoring. Earlier and more accurate diagnoses are possible through techniques such as liquid biopsy, which detect circulating tumor DNA (ctDNA) and other cancer biomarkers from small biological samples like blood, saliva, or urine. Once cancer is identified, tumor profiling technologies such as qPCR and targeted NGS help define the molecular subtype of the disease, revealing actionable mutations that guide personalized treatment strategies. During therapy, molecular diagnostics support real-time monitoring of treatment response through blood- based biomarkers and dynamic genomic changes. After treatment, ongoing surveillance using ctDNA and minimal residual disease (MRD) testing enables early detection of recurrence—often before clinical symptoms appear. This ability to guide adaptive therapy, by escalating or de-escalating treatment,
supports long-term maintenance strategies and helps shift cancer management toward a chronic condition rather than a terminal diagnosis. 6 The widespread adoption of molecular diagnostics in cancer care is backed by strong evidence linking genomic-guided treatment to improved outcomes and extended survival. Trials such as BATTLE-2 in NSCLC 7 and studies in metastatic colorectal cancer 8 show that biomarker-driven therapies yield better clinical responses. A population-wide analysis by the AACR GENIE consortium 9 further confirmed longer median survival in patients receiving matched targeted therapies. These findings not only validate the impact of molecular diagnostics on patient outcomes today, but also underscore how continued advances in molecular technologies will further drive personalized treatment, extend survival, and support the management of cancer as a chronic disease.
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MOLECULAR TECHNIQUES GUIDING ASSAY DESIGN | qPCR
Choices in Molecular Techniques Guide Assay Design
MUTATION DETECTION & GENOMIC COVERAGE DIFFER BY SEQUENCING METHOD
For assay developers, meeting both clinical and operational requirements requires balancing analytical performance, cost-efficiency, and usability. Precision oncology depends on technologies that accurately detect genetic alterations, guide treatment decisions, and deliver results that can be effectively interpreted across diverse healthcare settings. In today’s commercial landscape, three techniques— qPCR , targeted next-generation sequencing ( tNGS ), and whole-genome sequencing ( WGS )—dominate. These techniques underpin most regulatory-approved oncology assays, owing to their clinical utility, scalability, and established regulatory pathways. 10, 11 Selecting the right technology requires careful alignment with the assay’s intended use, as each one presents trade-offs in turnaround time, assay breadth, infrastructure demands, and accessibility. These factors must be weighed during assay design and commercialization to maximize both clinical utility and market viability.
qPCR Precision with Speed and Simplicity Quantitative PCR (qPCR) is the most established and widely adopted molecular diagnostic technology for oncology. It forms the foundation of many FDA- approved companion diagnostics (CDx) (refer to Table 1 ), including therapies targeting EGFR mutations in non-small cell lung cancer (NSCLC), BRAF V600E in melanoma, 12 and KRAS wild-type status in colorectal cancer. 13 These assays typically use allele-specific amplification or probe-based detection methods to achieve precise, reproducible results with minimal input material.
qPCR’s primary strengths include fast turnaround time—often within hours—low cost per test, and high sensitivity for detecting single or limited mutations, making it ideal for cancers with well-characterized genetic drivers. However, its utility is limited to pre- defined targets and lacks the ability to detect novel or complex genomic alterations such as gene fusions or structural variants. While it remains a gold standard for detecting known driver mutations, qPCR’s narrower analytical range makes it less suitable for applications requiring broad genomic profiling or the detection of emerging biomarkers. 14
Table 1 . Examples of FDA-Cleared qPCR Precision Oncology Assays Used in Clinical Practice
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FROM SINGLE MUTATIONS TO WHOLE GENOMES | MOLECULAR TECHNOLOGIES SHAPING PRECISION ONCOLOGY DIAGNOSTICS
MOLECULAR TECHNIQUES GUIDING ASSAY DESIGN | tNGS
Hybrid-Capture tNGS Workflow
Amplicon-Based tNGS Workflow
Targeted NGS Breadth & Clinical Depth in One Assay Targeted next-generation sequencing (tNGS) is a technique that bridges the gap between qPCR single-target assays and genome-wide sequencing approaches, offering a high level of multiplexing while maintaining manageable data complexity. Panels typically span 20 to 500 genes and detect a broad range of variant types, including single nucleotide variants (SNVs), small insertions/deletions (indels), gene fusions, and copy number alterations. 15, 16 Many FDA-approved commercial assays, such as those used for solid tumors, hematologic malignancies, and liquid biopsy applications, are now based on tNGS ( Table 2 ). tNGS panels can either employ amplicon-based or hybrid-capture enrichment methods followed by sequencing. Amplicon-based methods rely on qPCR amplification and are typically faster, more cost- efficient, and better suited for small, focused panels, though they have reduced sensitivity for detecting
structural variants and low-complexity regions. 17 In contrast, hybrid-capture methods allow more uniform coverage and improved detection of complex genomic alterations, including gene fusions, copy number variations, and microsatellite instability (MSI), though they require longer workflows and higher DNA input. 18 From a development perspective, tNGS assays provide a scalable solution that can be updated as new biomarkers gain clinical relevance. This makes them well-suited for tumor profiling, therapy selection, and minimal residual disease (MRD) monitoring. However, implementation can be limited by factors such as the need for advanced bioinformatics support, low-quality samples, and longer turnaround times—especially in decentralized or low-resource clinical settings. 14, 19 Despite these challenges, tNGS strikes a valuable balance between genomic breadth, analytical depth, and clinical feasibility—making it a versatile platform for precision oncology applications.
Table 2 . Examples of FDA-Cleared Targeted NGS Assays Used in Clinical Practice
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MOLECULAR TECHNIQUES GUIDING ASSAY DESIGN | WGS
WGS Workflow
Whole-genome sequencing (WGS) provides the most comprehensive genomic view, enabling the detection of all mutation types—including rare and novel alterations—across the entire genome. This unbiased approach allows for simultaneous analysis of single nucleotide variants (SNVs), insertions/deletions, copy number alterations, structural rearrangements, and non-coding mutations, making it especially valuable for identifying new biomarkers, characterizing complex tumor subtypes, and uncovering resistance mechanisms. 20 Despite its scientific value, WGS remains rarely used in routine clinical diagnostics due to several key barriers: high sequencing and data processing costs, long turnaround times, and the requirement for WGS Comprehensive Insight, Limited Accessibility
advanced bioinformatics infrastructure and secure data storage. 21 Interpretation complexity further limits clinical adoption, as many detected variants are of uncertain significance and must be carefully reviewed by experts—using clinical databases and patient context—to determine their relevance and potential impact on diagnosis and treatment. 22 In oncology assay development, WGS is typically reserved for translational research, rare or undiagnosed cancers, or situations where targeted panels fail to yield actionable results ( Table 3 ). As sequencing technologies improve, costs decline, and AI-driven tools enhance variant interpretation, WGS may become more clinically accessible. For now, however, it remains a specialized and infrastructure- heavy option with limited scalability in commercial diagnostic workflows. 23, 24
Table 3 . Overview of CLIA-Approved WGS Assays Supporting Precision Oncology
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FROM SINGLE MUTATIONS TO WHOLE GENOMES | MOLECULAR TECHNOLOGIES SHAPING PRECISION ONCOLOGY DIAGNOSTICS
Table 4 . Summary of Key Differences: qPCR vs. tNGS vs. WGS in Precision Oncology Diagnostics
Expanding Precision Oncology Through Scalable, Accessible, and Future-Proof Diagnostic Design
sustainability. This includes modular workflows that can scale from RUO to IVD, and flexible architectures capable of incorporating updated gene panels and new bioinformatics software platforms. Finally, the choice of molecular technique—qPCR, tNGS, or WGS— should reflect not only the assay’s role in the clinical pathway, but also the cost, interpretive complexity, and bioinformatics infrastructure required to support effective market uptake. 14, 15 To succeed, assay developers must think holistically— from scalable, future-ready workflows to integration of user-friendly reporting systems. 17, 18 Strategic partnerships with experienced reagent suppliers and service providers can reduce development risk, accelerate R&D timelines, and ensure manufacturing readiness at a global scale. In a landscape where the value of a diagnostic lies not only in its performance but also in its ability to support care delivery, the next era of precision oncology will be defined by greater integration, accessibility, and intelligence across diagnostic, therapeutic, and monitoring strategies.
As precision oncology becomes a cornerstone of modern cancer care, the accessibility of molecular diagnostics is emerging as a defining challenge—and opportunity—for assay developers. While centralized genomic testing remains the norm in high-resource settings, this model often excludes patients in underserved regions, where logistical barriers, infrastructure limitations, and workforce shortages restrict access to novel molecular techniques. Bridging this gap requires a new generation of precision oncology diagnostics that are not only analytically robust but also point-of-care compatible, scalable, and globally deployable. 25, 26 Infrastructure-light solutions that eliminate cold- chain dependencies and minimize reliance on specialized personnel are well-suited to meet the growing demand for precision diagnostics in regional hospitals, community clinics, and emerging markets. 19, 27 Future-proofing assays—by designing them to adapt to evolving biomarkers, regulatory changes, and technological advances—is also essential for maintaining long-term clinical relevance and market
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MERIDIAN’S SOLUTIONS
qPCR
Ultra-Sensitive, Inhibitor-Tolerant Master Mixes
How Meridian Bioscience Empowers Assay Developers
Lyo-Ready Master Mixes
Meridian Bioscience provides end-to-end support for diagnostic developers aiming to bring high-performing oncology assays to market quickly and reliably. With decades of experience in enzyme manufacturing and molecular reagent formulation, Meridian supplies the critical raw materials and technical expertise needed to address challenges like stability, scalability, and performance consistency. A core strength lies in its custom enzyme stabilization services, which allow developers to create ambient-stable assays using their existing enzymes and workflows. By removing glycerol, enzymes can be lyophilized or air-dried—eliminating cold-chain requirements, extending shelf life, and simplifying distribution. This is especially valuable for future- proofing diagnostics, enabling point-of-care use, and expanding access to oncology testing worldwide.
Glycerol-Free Enzymes
NGS
Meridian also offers custom formulation, regulatory documentation, ISO 13485 production, and support across qPCR, isothermal amplification, and targeted NGS workflows. Whether improving sensitivity, stabilizing multiplex assays, or enabling decentralized deployment, Meridian delivers the infrastructure and expertise to accelerate assay development and global impact.
Glycerol-Free NGS Library Prep Components
To learn more about Meridian’s precision oncology reagent solutions, contact us :
The Power of Ambient-Temperature Stable Assays
Extend assay shelf life & eliminate cold- chain logistics
Improve the LOD for low-abundance targets
Gain operational efficiencies & reduce costs
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FROM SINGLE MUTATIONS TO WHOLE GENOMES MOLECULAR TECHNOLOGIES SHAPING PRECISION ONCOLOGY DIAGNOSTICS
Innovation continues to drive increased access to precision oncology—enabling broader, faster, and more decentralized testing.
Future Outlook: Advancing the Next Era of Precision Oncology
with programmable targeting; AI-driven molecular pathology, which streamlines data interpretation and integrates histological and genomic insights; and multi-omics approaches, which synthesize genomic, transcriptomic, proteomic, and metabolic data for a more complete view of tumor biology. These trends are converging toward a future where diagnostics not only detect mutations but predict response, guide therapy adaptation, and anticipate resistance—all within modular, scalable platforms. To fully realize this future, assay developers must align technology decisions with clinical need, regulatory readiness, and deployment realities. That includes investing in ambient-stable assay formats, building in bioinformatics scalability, and forging expert partnerships to support manufacturing, interpretation, and regulatory compliance. Future-proofing assay design—through modularity, flexibility, and robust validation—will be key to ensuring long-term clinical and commercial impact. By combining scientific precision with strategic foresight, the diagnostics industry is well-positioned to lead the next era of personalized cancer care— delivering the right test, for the right patient, at the right time, and in every corner of the world.
Precision oncology continues to redefine how we detect, characterize, and manage cancer—requiring diagnostic solutions that are not only analytically strong, but also scalable, accessible, and clinically actionable. Today, technologies such as qPCR, targeted NGS (tNGS), and whole-genome sequencing (WGS) form the foundation of most commercial oncology assays. Their regulatory acceptance, high sensitivity, and adaptability make them essential for applications including companion diagnostics, tumor profiling, and minimal residual disease (MRD) monitoring. 10, 26 Other well-established methods—like digital droplet PCR (ddPCR) and multiplex ligation-dependent probe amplification (MLPA)—also remain valuable, especially in workflows requiring ultra-sensitive detection or precise copy number analysis. 19, 27 However, their limited multiplexing capabilities and narrower scope often restrict broader use in commercial in vitro diagnostic (IVD) panels. Looking forward, translational research is introducing powerful innovations that are expected to shape the future of precision diagnostics. Technologies such as single-cell sequencing, RNA-based expression profiling, and spatial transcriptomics are delivering high-resolution insights into tumor heterogeneity, evolution, and microenvironmental interactions—critical dimensions of modern cancer care. 28, 29 Though not yet mainstream in clinical diagnostics due to cost and regulatory hurdles, these tools are likely to inform future iterations of companion assays and stratified care models. At the same time, the market is being transformed by disruptive technologies like CRISPR-based diagnostics, which enable ultra-specific mutation detection
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About Meridian
Meridian is a fully integrated life science company that develops, manufactures, markets, and distributes a broad range of innovative diagnostic products and critical raw materials. We are dedicated to developing and delivering better solutions that give answers with speed, accuracy, and simplicity that redefine the possibilities of life from discovery to diagnosis. As the Life Science Division of Meridian, our focus is on supporting immunological and molecular test manufacturers with original raw materials for human, animal, plant, and environmental applications. The large portfolio of antigens, antibodies, blockers, molecular enzymes, nucleotides, and optimized mixes for qPCR and isothermal amplification applications are designed to simplify assay design and enable accurate test results. We strive to provide our customers with solutions they need when they need them—from novel antigens and antibodies to major disease outbreaks such as Zika and SARS-CoV-2 to pioneering the market with our innovative air-dried qPCR/RT-qPCR mixes. We take pride in providing our customers with unparalleled support, customer service, and quality.
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