Targeted Genomic Re-sequencing Technologies in 2025: Unleashing the Next Wave of Precision Genomics. Explore How Advanced Platforms and Market Forces Are Shaping the Future of Disease Research and Personalized Healthcare.

• Executive Summary: Key Trends and Market Drivers in 2025
• Technology Overview: Platforms, Methods, and Innovations
• Major Industry Players and Strategic Partnerships
• Market Size, Growth Projections, and Regional Analysis (2025–2030)
• Applications in Clinical Diagnostics and Precision Medicine
• Emerging Use Cases: Oncology, Rare Diseases, and Beyond
• Regulatory Landscape and Quality Standards
• Challenges: Data Management, Cost, and Accessibility
• Recent Breakthroughs and Pipeline Technologies
• Future Outlook: Opportunities, Investments, and Roadmap to 2030
• Sources & References

Executive Summary: Key Trends and Market Drivers in 2025

Targeted genomic re-sequencing technologies are poised for significant growth and transformation in 2025, driven by advances in sequencing chemistry, automation, and bioinformatics. These technologies, which focus on sequencing specific regions of the genome rather than the entire genome, are increasingly favored for their cost-effectiveness, scalability, and clinical utility. The market is witnessing robust demand from clinical diagnostics, oncology, rare disease research, and pharmacogenomics, as healthcare systems and research institutions seek more precise and actionable genomic insights.

Key industry leaders such as Illumina, Inc., Thermo Fisher Scientific, and Agilent Technologies continue to innovate in targeted sequencing platforms and reagent kits. Illumina’s sequencing-by-synthesis technology remains a cornerstone for high-throughput targeted applications, while Thermo Fisher Scientific’s Ion Torrent and AmpliSeq solutions are widely adopted for their flexibility and rapid turnaround. Agilent Technologies, with its SureSelect and HaloPlex target enrichment systems, is expanding its portfolio to address both research and clinical needs. These companies are investing in automation, streamlined workflows, and cloud-based data analysis to reduce hands-on time and improve reproducibility.

In 2025, the integration of artificial intelligence (AI) and machine learning into bioinformatics pipelines is accelerating the interpretation of targeted sequencing data, enabling faster and more accurate variant calling and annotation. This is particularly relevant for applications in oncology, where actionable mutations must be identified quickly to inform treatment decisions. The adoption of targeted re-sequencing in liquid biopsy and minimal residual disease (MRD) monitoring is also expanding, supported by advances in ultra-sensitive detection technologies and error-correction methods.

Regulatory trends are shaping the market as well. The U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) are providing clearer frameworks for the clinical validation and approval of targeted sequencing assays, fostering greater confidence among healthcare providers and payers. This regulatory clarity is expected to drive adoption in clinical laboratories and support reimbursement for genomic testing.

Looking ahead, the market outlook for targeted genomic re-sequencing technologies is robust. The convergence of lower sequencing costs, improved target enrichment methods, and enhanced data analytics is expected to broaden the accessibility of these technologies beyond major academic centers to regional hospitals and community clinics. Strategic partnerships between sequencing platform providers, reagent manufacturers, and healthcare networks are anticipated to further accelerate market penetration and innovation through 2025 and beyond.

Technology Overview: Platforms, Methods, and Innovations

Targeted genomic re-sequencing technologies have become central to precision genomics, enabling researchers and clinicians to focus sequencing efforts on specific genomic regions of interest, such as disease-associated genes, exomes, or regulatory elements. As of 2025, the field is characterized by rapid innovation in both platform hardware and enrichment methodologies, with a strong emphasis on scalability, accuracy, and cost-effectiveness.

The dominant platforms for targeted re-sequencing remain next-generation sequencing (NGS) systems, with Illumina maintaining a leading market position through its NovaSeq and NextSeq series. These platforms support a range of targeted approaches, including amplicon-based and hybrid capture-based enrichment. Amplicon-based methods, such as multiplex PCR, are favored for their simplicity and speed, while hybrid capture techniques offer greater flexibility and uniformity for larger panels or exome-scale targets. Illumina continues to expand its portfolio of enrichment kits, including the TruSight and Nextera lines, which are widely adopted in clinical and research settings.

Emerging competition comes from Thermo Fisher Scientific, whose Ion Torrent platforms and AmpliSeq technology are recognized for rapid, cost-effective targeted sequencing, particularly in oncology and inherited disease applications. Thermo Fisher Scientific has also advanced automation and sample-to-answer workflows, reducing turnaround times and increasing throughput for clinical laboratories.

Long-read sequencing is gaining traction in targeted applications, with Pacific Biosciences (PacBio) and Oxford Nanopore Technologies offering platforms capable of resolving complex genomic regions, structural variants, and phasing haplotypes. PacBio’s HiFi reads and Oxford Nanopore’s adaptive sampling technologies are being integrated into targeted workflows, enabling comprehensive analysis of challenging loci and repeat expansions that are difficult to resolve with short-read methods.

Innovations in probe design, automation, and informatics are further enhancing targeted re-sequencing. Companies such as Agilent Technologies and Integrated DNA Technologies (IDT) are advancing hybridization-based capture with customizable panels and improved probe chemistries, supporting high sensitivity and specificity even in low-input or degraded samples. Automation platforms from Beckman Coulter and PerkinElmer are streamlining library preparation, while cloud-based informatics solutions are reducing analysis bottlenecks.

Looking ahead, the next few years are expected to see further integration of targeted sequencing with single-cell and spatial genomics, as well as the adoption of AI-driven probe design and data interpretation. The convergence of these innovations is poised to expand the utility of targeted re-sequencing in diagnostics, population genomics, and translational research, with ongoing investments from major industry players ensuring continued technological advancement.

Major Industry Players and Strategic Partnerships

The landscape of targeted genomic re-sequencing technologies in 2025 is shaped by a dynamic interplay of established industry leaders, innovative startups, and strategic collaborations. These partnerships are driving advances in accuracy, throughput, and clinical utility, with a focus on applications in oncology, rare disease diagnostics, and population genomics.

Among the most influential players, Illumina, Inc. continues to dominate the market with its comprehensive suite of sequencing platforms and targeted enrichment solutions, such as the TruSight and AmpliSeq panels. Illumina’s ongoing collaborations with pharmaceutical companies and healthcare systems are expanding the clinical adoption of targeted sequencing, particularly in companion diagnostics and personalized medicine. In 2024, Illumina announced new partnerships with major hospital networks to integrate its sequencing workflows into routine cancer screening and hereditary disease testing.

Thermo Fisher Scientific remains a key competitor, leveraging its Ion Torrent and Oncomine platforms for targeted re-sequencing. The company’s strategic alliances with academic medical centers and biopharma firms have accelerated the development of custom gene panels and liquid biopsy assays. Thermo Fisher’s recent investments in automation and cloud-based data analysis are expected to further streamline targeted sequencing workflows through 2025 and beyond.

Agilent Technologies is another major player, recognized for its SureSelect target enrichment kits and NGS automation solutions. Agilent’s partnerships with clinical laboratories and research consortia have enabled the scaling of targeted re-sequencing for both translational research and clinical diagnostics. In 2025, Agilent is focusing on expanding its global reach, particularly in Asia-Pacific markets, through joint ventures and technology licensing agreements.

Emerging companies are also making significant contributions. Twist Bioscience has gained traction with its high-throughput, customizable DNA synthesis and target enrichment technologies, supporting large-scale population genomics projects and biobank initiatives. Twist’s collaborations with pharmaceutical companies and national genomics programs are expected to drive further innovation in panel design and sample multiplexing.

Strategic partnerships are increasingly central to the sector’s growth. For example, alliances between sequencing platform providers and bioinformatics firms are enabling seamless integration of data analysis pipelines, while collaborations with diagnostic laboratories are facilitating regulatory approvals and clinical implementation. As the demand for precision medicine accelerates, the next few years will likely see deeper integration of targeted re-sequencing technologies into healthcare systems, supported by ongoing industry consolidation and cross-sector partnerships.

Market Size, Growth Projections, and Regional Analysis (2025–2030)

The market for targeted genomic re-sequencing technologies is poised for robust growth between 2025 and 2030, driven by accelerating adoption in clinical diagnostics, oncology, rare disease research, and agricultural genomics. As of 2025, the global market is estimated to be valued in the multi-billion-dollar range, with North America and Europe leading in both revenue and installed base, followed by rapid expansion in Asia-Pacific due to increasing investments in healthcare infrastructure and genomics research.

Key industry players such as Illumina, Inc., Thermo Fisher Scientific, Agilent Technologies, and Pacific Biosciences continue to dominate the market, offering a range of targeted sequencing platforms and enrichment solutions. Illumina, Inc. maintains a significant market share with its sequencing-by-synthesis technology and targeted panels, while Thermo Fisher Scientific leverages its Ion Torrent and AmpliSeq platforms for both research and clinical applications. Agilent Technologies is recognized for its SureSelect target enrichment kits, and Pacific Biosciences is expanding its presence with long-read sequencing solutions that enable more comprehensive variant detection.

From 2025 to 2030, the market is projected to experience a compound annual growth rate (CAGR) in the high single digits to low double digits, reflecting increasing demand for precision medicine and companion diagnostics. The Asia-Pacific region, particularly China, Japan, and South Korea, is expected to witness the fastest growth, fueled by government genomics initiatives, rising healthcare expenditure, and the establishment of new sequencing centers. For example, national genomics projects and public-private partnerships in China are accelerating the adoption of targeted sequencing in both clinical and agricultural sectors.

In North America, the United States remains the largest market, supported by a mature regulatory environment, reimbursement frameworks, and a high concentration of academic and commercial genomics laboratories. Europe is also seeing steady growth, with the United Kingdom, Germany, and France investing in national genomics strategies and biobank initiatives. Meanwhile, emerging markets in Latin America and the Middle East are beginning to adopt targeted re-sequencing technologies, albeit at a slower pace due to infrastructure and funding constraints.

Looking ahead, the market outlook is shaped by ongoing technological innovation, such as the development of more cost-effective, high-throughput platforms and automated sample preparation workflows. Companies like Illumina, Inc. and Thermo Fisher Scientific are expected to introduce new targeted panels and integrated solutions tailored for specific disease areas, further expanding the addressable market. As regulatory approvals for clinical applications increase and sequencing costs continue to decline, targeted genomic re-sequencing is set to become a standard tool in both research and routine diagnostics worldwide.

Applications in Clinical Diagnostics and Precision Medicine

Targeted genomic re-sequencing technologies have become central to clinical diagnostics and precision medicine, offering high sensitivity and specificity for detecting clinically relevant genetic variants. As of 2025, these technologies are widely adopted in oncology, rare disease diagnosis, pharmacogenomics, and infectious disease management, driven by advances in panel design, sequencing chemistry, and bioinformatics.

In oncology, targeted re-sequencing panels enable the detection of actionable mutations in genes such as EGFR, KRAS, and BRCA1/2, guiding personalized therapy selection. Leading platforms, including the Illumina TruSight Oncology and Thermo Fisher Scientific Oncomine assays, are routinely used in clinical laboratories for tumor profiling and minimal residual disease monitoring. These panels are designed to cover hundreds of cancer-associated genes, allowing for rapid turnaround and cost-effective analysis compared to whole-genome sequencing.

Rare disease diagnostics have also benefited from targeted re-sequencing, with custom and pre-designed gene panels enabling the identification of pathogenic variants in hundreds of Mendelian disorders. Companies such as Agilent Technologies and Roche provide comprehensive solutions for clinical exome and disease-specific panels, supporting rapid diagnosis and improved patient management. The integration of these technologies into newborn screening and carrier testing is expected to expand further in the coming years, as regulatory frameworks and reimbursement policies evolve.

Pharmacogenomics is another area where targeted re-sequencing is making significant inroads. By interrogating variants in genes involved in drug metabolism (e.g., CYP2C19, TPMT), clinicians can tailor drug selection and dosing to individual genetic profiles, reducing adverse drug reactions and improving therapeutic outcomes. QIAGEN and Illumina offer targeted panels and workflow solutions for pharmacogenomic testing, which are increasingly being integrated into electronic health records and clinical decision support systems.

In infectious disease, targeted sequencing panels are used for pathogen identification, antimicrobial resistance profiling, and outbreak tracking. Thermo Fisher Scientific and Roche have developed panels for rapid detection of viral and bacterial pathogens, supporting hospital infection control and public health surveillance.

Looking ahead, the next few years are expected to see further miniaturization, automation, and integration of targeted re-sequencing workflows, with increasing adoption of long-read and single-molecule sequencing technologies from companies like Pacific Biosciences and Oxford Nanopore Technologies. These advances will enable more comprehensive variant detection, including structural variants and epigenetic modifications, further enhancing the clinical utility of targeted genomic re-sequencing in precision medicine.

Emerging Use Cases: Oncology, Rare Diseases, and Beyond

Targeted genomic re-sequencing technologies are rapidly transforming clinical and research paradigms in oncology, rare diseases, and a growing array of additional applications. As of 2025, these technologies—encompassing hybrid capture, amplicon-based, and CRISPR-based enrichment methods—are enabling high-resolution, cost-effective interrogation of specific genomic regions, driving precision medicine and translational research.

In oncology, targeted re-sequencing is now a mainstay for tumor profiling, minimal residual disease (MRD) detection, and therapy selection. Leading platforms from Illumina, Thermo Fisher Scientific, and Agilent Technologies offer customizable panels covering hundreds of cancer-associated genes, fusion events, and mutational hotspots. The adoption of liquid biopsy approaches, leveraging circulating tumor DNA (ctDNA), is accelerating, with targeted panels enabling non-invasive monitoring of tumor evolution and resistance mutations. For example, Illumina’s TruSight Oncology and Thermo Fisher Scientific’s Oncomine assays are widely used in clinical laboratories for both solid and hematologic malignancies. The integration of artificial intelligence for variant interpretation and reporting is expected to further streamline clinical workflows in the coming years.

Rare disease diagnostics are also benefiting from targeted re-sequencing, particularly for disorders with well-characterized genetic etiologies. Custom and pre-designed panels from Agilent Technologies, Illumina, and QIAGEN enable rapid, high-throughput screening of hundreds to thousands of genes implicated in Mendelian and ultra-rare conditions. This approach is reducing diagnostic odysseys and facilitating earlier intervention. In 2025, the trend is toward even more comprehensive panels, improved coverage of challenging genomic regions, and integration with copy number and structural variant detection.

Beyond oncology and rare diseases, targeted re-sequencing is expanding into pharmacogenomics, infectious disease surveillance, and population genomics. For instance, Illumina and Thermo Fisher Scientific are supporting large-scale screening for actionable pharmacogenetic variants, while QIAGEN’s solutions are being deployed for pathogen detection and antimicrobial resistance profiling. The scalability and flexibility of targeted approaches make them attractive for biobanking and longitudinal cohort studies, where cost and data management are critical.

Looking ahead, the next few years will likely see further miniaturization, automation, and integration of targeted re-sequencing workflows, with increasing adoption in decentralized and point-of-care settings. The convergence of sequencing chemistry innovations, microfluidics, and cloud-based analytics is poised to democratize access and accelerate the clinical impact of these technologies worldwide.

Regulatory Landscape and Quality Standards

The regulatory landscape for targeted genomic re-sequencing technologies is rapidly evolving as these platforms become increasingly integral to clinical diagnostics, precision medicine, and research. In 2025, regulatory agencies are intensifying their focus on ensuring the analytical validity, clinical utility, and data security of these technologies, while also fostering innovation and accessibility.

In the United States, the U.S. Food and Drug Administration (FDA) continues to refine its approach to next-generation sequencing (NGS) and targeted re-sequencing assays. The FDA’s 2023 guidance on the use of NGS-based tests for germline diseases set a precedent for risk-based regulatory frameworks, emphasizing the need for robust validation, quality control, and transparent bioinformatics pipelines. In 2025, the FDA is expected to further clarify requirements for companion diagnostics and laboratory-developed tests (LDTs) that utilize targeted re-sequencing, particularly as these tests expand into oncology, rare disease, and pharmacogenomics.

In Europe, the European Medicines Agency (EMA) and the European Commission are enforcing the In Vitro Diagnostic Regulation (IVDR), which became fully applicable in 2022. The IVDR imposes stricter requirements for clinical evidence, performance evaluation, and post-market surveillance of targeted sequencing assays. By 2025, most manufacturers are expected to have transitioned their products to IVDR compliance, with notified bodies playing a central role in conformity assessments. This regulatory shift is prompting leading sequencing technology providers such as Illumina, Thermo Fisher Scientific, and Pacific Biosciences to enhance their quality management systems and documentation to meet European standards.

Globally, harmonization efforts are underway through organizations like the International Organization for Standardization (ISO), which published ISO 20387 for biobanking and ISO 15189 for medical laboratories. These standards are increasingly referenced by regulatory bodies and accreditation agencies to ensure the reliability and reproducibility of targeted re-sequencing results. In Asia-Pacific, regulatory agencies in Japan and China are also updating their frameworks to align with international best practices, with a focus on data integrity and patient safety.

Looking ahead, the regulatory outlook for targeted genomic re-sequencing technologies will likely emphasize real-world evidence, interoperability, and cybersecurity. As sequencing moves closer to the point of care, regulators are expected to issue new guidance on the use of cloud-based analysis, artificial intelligence in variant interpretation, and the ethical management of genomic data. Industry leaders are actively engaging with regulators to shape these standards, ensuring that innovation in targeted re-sequencing is matched by rigorous quality and patient protection.

Challenges: Data Management, Cost, and Accessibility

Targeted genomic re-sequencing technologies have rapidly advanced, but their widespread adoption in 2025 and beyond is shaped by persistent challenges in data management, cost, and accessibility. As sequencing platforms become more sophisticated, the volume and complexity of data generated from targeted panels—ranging from a few genes to thousands—have increased exponentially. This surge necessitates robust data storage, transfer, and analysis solutions, which remain a bottleneck for many laboratories and clinical settings.

Major sequencing technology providers such as Illumina, Thermo Fisher Scientific, and Agilent Technologies have introduced integrated informatics platforms to streamline data handling. For example, Illumina’s cloud-based informatics solutions aim to facilitate secure data storage and scalable analysis, but the need for high-performance computing infrastructure and skilled bioinformaticians persists. Smaller labs and clinics, especially in low- and middle-income regions, often lack the resources to implement such systems, exacerbating disparities in access to advanced genomic diagnostics.

Cost remains a significant barrier despite ongoing reductions in sequencing reagent prices and instrument costs. While targeted re-sequencing is less expensive than whole-genome approaches, the total cost—including sample preparation, library construction, sequencing, and downstream analysis—can still be prohibitive for routine clinical use. Companies like Illumina and Thermo Fisher Scientific have introduced benchtop sequencers and streamlined workflows to lower per-sample costs, but the initial capital investment and recurring consumable expenses remain substantial. Additionally, the cost of maintaining compliance with regulatory standards for clinical diagnostics adds further financial pressure.

Accessibility is also influenced by intellectual property and licensing issues. Proprietary chemistries and software from leading manufacturers can limit interoperability and increase costs for end users. Efforts to develop open-source analysis tools and standardized data formats are ongoing, but adoption is uneven across the sector. Furthermore, the availability of targeted panels tailored to diverse populations is limited, potentially reducing the clinical utility of these technologies in underrepresented groups.

Looking ahead, the sector is expected to see incremental improvements in data management through enhanced cloud-based solutions and AI-driven analytics, as well as gradual cost reductions driven by competition and technological innovation. However, bridging the accessibility gap will require coordinated efforts among technology providers, healthcare systems, and policymakers to ensure equitable access to targeted genomic re-sequencing worldwide.

Recent Breakthroughs and Pipeline Technologies

Targeted genomic re-sequencing technologies have experienced significant advancements in recent years, with 2025 marking a period of rapid innovation and commercial deployment. These technologies, which focus on sequencing specific regions of the genome rather than the entire genome, are increasingly favored for their cost-effectiveness, scalability, and ability to deliver high-depth data for clinically relevant loci.

A major breakthrough has been the refinement of hybridization-based capture and amplicon-based enrichment methods. Companies such as Illumina, Inc. and Thermo Fisher Scientific have introduced updated panels and chemistries that enable more precise targeting of exons, regulatory regions, and disease-associated hotspots. Illumina’s latest enrichment kits, for example, now support ultra-high multiplexing, allowing hundreds of samples to be processed in a single run, which is particularly valuable for population-scale studies and clinical diagnostics.

Another notable development is the integration of CRISPR-based enrichment strategies. Pacific Biosciences (PacBio) and Agilent Technologies have both announced collaborations and product pipelines leveraging CRISPR/Cas systems to selectively enrich long genomic fragments. This approach enables the sequencing of complex regions, such as those with structural variants or repetitive elements, which are often missed by traditional short-read methods. PacBio’s long-read sequencing platforms, combined with targeted CRISPR enrichment, are now being piloted in translational research and rare disease diagnostics.

Automation and workflow simplification are also key trends. Roche has expanded its portfolio with automated library preparation systems that reduce hands-on time and variability, making targeted re-sequencing more accessible to clinical laboratories. Meanwhile, QIAGEN continues to develop integrated solutions that combine sample prep, target enrichment, and bioinformatics, streamlining the entire process from sample to report.

Looking ahead, the next few years are expected to see further convergence of targeted sequencing with real-time data analysis and AI-driven variant interpretation. Industry leaders are investing in cloud-based platforms and machine learning tools to accelerate the translation of sequencing data into actionable insights. As regulatory frameworks evolve and reimbursement pathways expand, targeted genomic re-sequencing is poised to become a mainstay in precision medicine, oncology, and inherited disease screening.

Future Outlook: Opportunities, Investments, and Roadmap to 2030

The future of targeted genomic re-sequencing technologies is poised for significant transformation as we approach 2025 and look toward 2030. The sector is experiencing robust investment, rapid technological innovation, and expanding applications across clinical diagnostics, pharmaceutical development, and agricultural genomics. Key industry players are intensifying their focus on improving accuracy, throughput, and cost-effectiveness, while also addressing the growing demand for personalized medicine and population-scale genomics.

Major sequencing platform providers such as Illumina, Inc. and Thermo Fisher Scientific are leading the charge in developing next-generation targeted sequencing solutions. Illumina’s continued investment in its sequencing-by-synthesis technology and the expansion of its NovaSeq and NextSeq platforms are expected to further reduce per-sample costs and increase scalability for targeted panels. Thermo Fisher Scientific, with its Ion Torrent technology, is focusing on rapid turnaround and flexible panel design, catering to both clinical and research markets. Both companies are also investing in automation and cloud-based bioinformatics to streamline workflows and data interpretation.

Emerging players such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies are pushing the boundaries of long-read sequencing, which is increasingly being integrated into targeted re-sequencing workflows to resolve complex genomic regions and structural variants. PacBio’s HiFi reads and Oxford Nanopore’s real-time, portable sequencing devices are expected to see broader adoption in clinical and field settings by 2025, especially as accuracy and affordability improve.

On the investment front, the sector is attracting substantial funding from both public and private sources. Governments in North America, Europe, and Asia-Pacific are supporting large-scale genomics initiatives, such as national biobanks and precision medicine programs, which rely heavily on targeted re-sequencing for variant detection and population health studies. Private investment is also flowing into start-ups developing novel target enrichment chemistries, automation solutions, and AI-driven data analysis platforms.

Looking ahead to 2030, the roadmap for targeted genomic re-sequencing technologies includes several key milestones:

• Widespread clinical adoption of targeted panels for oncology, rare disease, and pharmacogenomics, driven by regulatory approvals and reimbursement expansion.
• Integration of multi-omics data (genomics, transcriptomics, epigenomics) into targeted re-sequencing workflows for comprehensive biomarker discovery.
• Advancements in single-cell and spatial genomics, enabling high-resolution analysis of tissue heterogeneity and microenvironments.
• Continued reduction in sequencing costs, making population-scale screening feasible in both developed and emerging markets.
• Enhanced data security, privacy, and interoperability standards to support global data sharing and collaborative research.

As the technology matures, collaboration between sequencing platform providers, reagent manufacturers, and bioinformatics companies will be crucial to unlocking the full potential of targeted genomic re-sequencing. The next five years are expected to bring transformative opportunities for precision health, drug development, and sustainable agriculture, underpinned by ongoing innovation and strategic investment from industry leaders such as Illumina, Inc., Thermo Fisher Scientific, Pacific Biosciences, and Oxford Nanopore Technologies.

Sources & References

• Thermo Fisher Scientific
• Oxford Nanopore Technologies
• PerkinElmer
• Twist Bioscience
• Illumina, Inc.
• Thermo Fisher Scientific
• Roche
• QIAGEN
• European Medicines Agency
• European Commission
• International Organization for Standardization