Targeted Sequencing and Resequencing Market By Technology (Amplicon-Based, Hybridization-Based, CRISPR-Based); By Workflow Step (Sample Preparation, Library Preparation, Target Enrichment, Sequencing, Data Analysis); By Application (Oncology, Rare Disease, Pharmacogenomics, Reproductive Health); By End User (Clinical Laboratories, Academic & Research Institutions, Hospitals, Biopharma & CROs); By Geography, Segment Revenue Estimation, Forecast, 2024–2030

Introduction And Strategic Context

The Global Targeted Sequencing And Resequencing Market will witness a steady CAGR of 10.6%, valued at around USD 6.1 billion in 2024, expected to grow to nearly USD 11.3 billion by 2030, according to Strategic Market Research.

 

Targeted sequencing and resequencing represent a high-precision, high-impact subset of next-generation sequencing (NGS). Rather than scanning the entire genome, this approach hones in on specific genes or regions of interest—reducing cost, increasing speed, and delivering deeper coverage. Between 2024 and 2030, its role is becoming critical across oncology, rare disease diagnosis, reproductive health, and pharmacogenomics.

 

Several converging forces are driving its strategic value. First, the clinical need for actionable genetic insights is expanding rapidly—oncologists, for example, now rely on gene panels to guide personalized treatment. Second, payers and providers are pushing back on the cost and complexity of whole genome sequencing. That’s made targeted panels a preferred tool, especially for inherited disorder testing and tumor profiling.

 

Third, from a regulatory and policy standpoint, guidelines are maturing. The FDA has clarified pathways for NGS-based diagnostics, while Europe’s IVDR is creating both challenges and demand for validated panels. Meanwhile, the CAP and ACMG are recommending gene-specific testing as part of newborn screening and carrier screening workflows.

 

Technology is moving fast, too. Panel designs are becoming more modular. Capture chemistries are improving. And AI is now being used to filter variants based on clinical significance—dramatically reducing the manual review burden.

 

The strategic stakeholder map here is diverse. Diagnostic labs are building proprietary gene panels. Biopharma companies are embedding sequencing into drug discovery. Hospital systems are investing in in-house sequencing cores. And startups are targeting ultra-rapid sequencing for prenatal and NICU use cases.

 

This is no longer just a tool for academic labs. It's becoming a clinical mainstay—one that balances precision with practicality.

 

Market Segmentation And Forecast Scope

The targeted sequencing and resequencing market is structured around how precisely healthcare providers, researchers, and drug developers seek to interrogate specific genomic regions. The segmentation reflects both the technical configurations and the end-user demand across diagnostics and therapeutics. Here’s how the market breaks down:

By Technology

This segment typically includes hybridization-based capture, amplicon-based sequencing, and CRISPR-based enrichment methods. Amplicon-based sequencing dominates current usage due to its speed, lower sample input requirements, and compatibility with small panel designs. However, hybrid capture techniques are gaining traction for larger panels and difficult-to-amplify regions—particularly in oncology.

Hybrid capture is expected to grow the fastest between 2024 and 2030, especially as comprehensive cancer profiling becomes mainstream in clinical settings.

 

By Workflow Step

The market can be divided into sample preparation, library preparation, target enrichment, sequencing, and data analysis. While sequencing and enrichment draw the most investment, the post-sequencing analytics segment is expanding rapidly due to rising demand for automation and variant interpretation.

Many labs now seek end-to-end solutions that integrate wet-lab kits with AI-enhanced bioinformatics, simplifying workflows for pathologists and clinical geneticists.

 

By Application

Key application areas include cancer diagnostics, rare disease detection, pharmacogenomics, and reproductive health. Among these, cancer diagnostics holds the largest share, accounting for an estimated 41% of total market revenue in 2024. This is due to the proliferation of tumor -specific gene panels being used for treatment selection, monitoring minimal residual disease, and resistance mutation profiling.

Rare disease diagnostics is the fastest-growing segment, driven by earlier pediatric screening mandates and growing awareness among neurologists and genetic counselors .

 

By End User

The primary end users are hospitals and clinical labs, academic and research institutions, pharmaceutical and biotechnology companies, and contract research organizations (CROs). Clinical laboratories lead the market in volume, as more of them incorporate NGS panels into standard diagnostic offerings.

That said, pharmaceutical companies are accelerating their use of targeted sequencing for biomarker discovery and companion diagnostic development—especially in immuno-oncology.

 

By Region

Geographically, the market is divided into North America, Europe, Asia Pacific, and Latin America, Middle East & Africa (LAMEA). North America holds the largest market share due to favorable reimbursement, a high concentration of CLIA-certified labs, and early integration of NGS in clinical workflows. Asia Pacific, however, is expanding fastest, led by China’s aggressive investments in genomics infrastructure and India's push for affordable molecular diagnostics.

 

Scope-wise, the market is no longer limited to academic centers. Panel-based sequencing is being bundled into point-of-care workflows, telehealth models, and even population screening pilots. Vendors are offering customizable kits for specific clinical questions—from BRCA testing to pharmacogenetic dosing guides—reshaping the way precision medicine is practiced.

 

Market Trends And Innovation Landscape

Targeted sequencing and resequencing aren’t riding the coattails of broader genomic trends—they’re setting their own trajectory. What used to be a cost-saving compromise compared to whole genome sequencing is now seen as a deliberate, precision-first strategy across diagnostics and drug development. The innovation pipeline is dense, competitive, and moving fast. Here’s where the momentum is building.

AI-Powered Variant Interpretation Is Becoming Standard

Variant filtering and classification have long been the bottleneck in clinical sequencing. Labs used to rely on manual reviews, legacy databases, and inconsistent annotation pipelines. That’s changing. AI tools are now automating not just annotation, but also prioritization of variants by clinical actionability.

Several platforms now use machine learning to flag likely pathogenic variants and suggest tiered clinical interpretations—especially in oncology and neurogenetics. This not only reduces turnaround time but also minimizes human error. One pathology lead in London noted that their diagnostic review time dropped by nearly 50% after integrating an AI-assisted pipeline.

 

CRISPR-Based Enrichment Methods Are on the Rise

Amplicon- and hybridization-based techniques still dominate, but CRISPR-based enrichment is gaining momentum for ultra-targeted panels. These platforms allow for higher specificity and minimal off-target reads—especially important in liquid biopsy and single-cell sequencing.

Researchers are using Cas-mediated capture to enrich challenging regions like GC-rich promoters and structural variants that other methods often miss. It’s still early-stage, but several startups are now designing CRISPR-driven kits aimed at difficult-to-sequence loci linked to pediatric neurological disorders.

 

Modular, Custom Panel Design Is the New Normal

Vendors are increasingly offering “build-your-own” sequencing panels where labs can combine genes relevant to specific clinical workflows. This is especially useful in oncology, where institutions want to test both common mutations (e.g., KRAS, EGFR) and rare fusion genes without overpaying for unused content.

This modular approach also helps regional labs meet reimbursement and regulatory requirements. In the EU, for example, IVDR mandates validated panels—so labs prefer smaller, focused designs that are easier to get approved.

 

Integration With Digital Pathology and Imaging

An emerging trend is the correlation of targeted genomic findings with histopathological images or radiomic data. Several platforms now offer dashboards that combine sequencing results with digital pathology annotations—creating a “multi-modal” patient profile.

This is particularly powerful in cancer, where genomic variants can now be visualized alongside biopsy slide interpretations. The goal isn’t just diagnostic clarity—it’s decision support for multi-disciplinary care teams.

 

Partnerships and Ecosystems Over Standalone Tools

Innovation isn’t just happening in silos. We’re seeing a wave of partnerships between sequencing platform providers, bioinformatics companies, and EMR vendors. These integrations allow for seamless ordering, automated data pushback, and better clinical decision-making.

Recent collaborations between sequencing vendors and AI-driven clinical decision support systems are aimed at embedding results into physician workflows—especially in large hospital networks.

 

Turnaround Time Is the Competitive Edge

Speed is no longer optional. Labs are now being asked to deliver results in under 48 hours for critical oncology or NICU cases. As a result, there's a push toward “sample-to-answer” solutions that compress prep, sequencing, and analysis into a single streamlined workflow.

One U.S. hospital recently piloted a system that combined same-day enrichment and overnight sequencing for neonatal metabolic panels. The total turnaround? 26 hours. That’s redefining what’s possible.

 

Bottom line: this isn’t about just shrinking cost or panel size. It’s about making targeted sequencing more intelligent, modular, and actionable—so clinicians don’t just get data, they get decisions.

 

Competitive Intelligence And Benchmarking

The targeted sequencing and resequencing market is marked by a tight race between legacy sequencing giants, clinical diagnostics innovators, and a growing band of specialized startups. While many of the same players dominate the broader genomics ecosystem, what separates them here is their ability to deliver highly customizable, clinically validated panels—and the infrastructure to interpret those results at scale.

Illumina

Illumina remains the foundational player in this space, especially with its dominance in sequencing platforms and capture-based enrichment kits. Its portfolio includes a wide range of fixed and custom panel solutions, often integrated with proprietary informatics tools. The company’s ability to bundle sequencers, kits, and cloud-based analytics remains unmatched.

What gives Illumina an edge in targeted sequencing is its vertical integration—customers can run from panel prep to interpretation without leaving their ecosystem. However, as reimbursement and regional regulations tighten, the pressure is on to prove clinical utility and cost-effectiveness for each panel design.

 

Thermo Fisher Scientific

Thermo Fisher's Ion Torrent platform has long positioned itself as a clinical sequencing workhorse. Its amplicon-based AmpliSeq technology is widely used for oncology panels and hereditary disorder testing. The company’s strength lies in rapid turnaround workflows and user-friendly kits for hospital and lab networks.

Thermo Fisher also invests heavily in companion diagnostics partnerships, particularly in oncology. These collaborations are key to expanding their installed base in pharmaceutical research and clinical trial applications.

 

Roche Sequencing Solutions

Roche has been building out its targeted sequencing capabilities through both in-house development and acquisitions. The AVENIO and KAPA HyperCap portfolios cater to both oncology diagnostics and broader research applications. Roche also benefits from its diagnostic heritage, which makes it easier to integrate sequencing tools into regulated lab environments.

The company is leveraging its clinical relationships to push into liquid biopsy and tumor profiling workflows, where precision and minimal sample use are paramount.

 

Agilent Technologies

Agilent plays a key role in the capture-based enrichment landscape. Its SureSelect and HaloPlex product lines are widely used in academic and clinical settings for custom panel development. Agilent’s differentiation lies in its robust hybridization chemistries and automation-friendly workflows.

It’s also investing in informatics platforms to pair sequencing prep with interpretation software—something that mid-sized labs increasingly need as they scale NGS services.

 

Twist Bioscience

Twist is emerging as a disruptive force thanks to its high-density DNA synthesis technology. This allows for ultra-flexible, scalable panel design at lower cost. Twist’s panels are popular among labs that want to test uncommon genes or frequently reconfigure panel content without high overhead.

The company also partners aggressively with bioinformatics firms to deliver end-to-end sequencing workflows. It’s particularly strong in oncology, rare disease, and emerging infectious disease sequencing.

 

Integrated DNA Technologies (IDT)

A subsidiary of Danaher, IDT offers highly customizable target enrichment tools and oligo pools that cater to both clinical and academic labs. Its xGen product line is respected for its high specificity and compatibility with multiple sequencing platforms.

While it doesn’t operate sequencing instruments, IDT's focus on high-performance reagents and flexible designs makes it a key supplier in the targeted sequencing supply chain.

 

Competitive Dynamics Snapshot

• Illumina and Thermo Fisher lead in installed systems and bundled workflows— favored by larger labs and hospital networks.

• Roche and Agilent are strong in regulated diagnostic environments, where robustness and compliance matter more than speed.

• Twist and IDT excel in flexibility and cost-efficiency, making them preferred by research-heavy institutions and early adopters.

• Strategic partnerships—especially in AI-enabled interpretation and oncology diagnostics—are shaping vendor choice more than sequencing throughput.

This market doesn’t reward the biggest toolset—it rewards the smartest fit. Companies that offer customizable, validated, and interpretable solutions are the ones gaining share in both high-throughput research centers and decentralized clinical labs.

 

Regional Landscape And Adoption Outlook

Adoption of targeted sequencing and resequencing varies sharply across geographies—not just in terms of volume, but in clinical strategy, reimbursement, and infrastructure readiness. While North America leads in maturity, other regions are catching up fast, often leapfrogging traditional barriers through public-private partnerships, regulatory reform, and technology localization.

North America

North America—particularly the United States—remains the anchor of this market. Adoption here is driven by a combination of clinical innovation, regulatory clarity, and payer experimentation. Many labs in the U.S. are CLIA-certified and CAP-accredited, enabling them to develop their own lab-developed tests (LDTs) using custom panels.

Targeted sequencing has become standard practice in cancer centers, pediatric hospitals, and transplant programs. From BRCA testing to comprehensive somatic mutation panels, clinicians are routinely ordering panel-based diagnostics over whole genome sequencing due to better cost-to-value ratios.

Canada, while slower to reimburse, is accelerating its adoption through provincial genomics initiatives and hospital-led research programs focused on rare disease and pharmacogenomics.

 

Europe

Europe is a mixed picture. Western Europe is sophisticated and policy-driven—Germany, France, and the UK are leading in adoption due to national genomics strategies and integrated health systems. For example, the UK's Genomic Medicine Service supports gene panel testing for conditions like epilepsy and inherited cardiac diseases.

However, the new In Vitro Diagnostic Regulation (IVDR) is reshaping the market. Labs now require validated, CE-marked kits for diagnostic use, pushing vendors to supply ready-to-go panels with full documentation. This has slowed LDTs but increased demand for compliant commercial products.

Eastern Europe is still catching up, with limited in-house sequencing infrastructure. Many labs rely on outsourced panels and cross-border partnerships for analysis, especially in oncology.

 

Asia Pacific

Asia Pacific is the fastest-growing region. China, in particular, has made targeted sequencing a national priority, especially through its cancer control plan and rare disease registry initiatives. Local players are developing panel kits that comply with China’s NMPA regulations, and large hospitals are investing in sequencing centers capable of high throughput.

India is emerging as a value-focused market. Targeted panels are now common in urban diagnostic chains for hereditary cancer and prenatal screening. Regulatory clarity remains a work in progress, but government programs are beginning to subsidize rare disease testing.

Japan and South Korea are highly specialized, with advanced clinical research driving innovation in pharmacogenetics and pediatric neurology. Reimbursement in Japan is relatively conservative, but adoption in academic and hospital settings remains high.

 

Latin America, Middle East, and Africa (LAMEA)

This region presents both challenges and opportunities. In Latin America, countries like Brazil and Mexico are leading with hospital-led initiatives in oncology and rare disease diagnostics. However, funding inconsistency and lack of local manufacturing still limit access.

The Middle East—especially Saudi Arabia and the UAE—is investing heavily in genomic infrastructure. National genome programs are being linked with personalized medicine pilots, and targeted sequencing is being introduced into both private and public health systems.

Africa remains in early-stage adoption. Most sequencing is outsourced or done through international collaborations. However, a few centers in Nigeria, South Africa, and Kenya are piloting targeted sequencing for sickle cell disease and infectious disease genomics. Cloud-based analysis platforms and portable sequencers are starting to close the infrastructure gap.

 

Key Regional Takeaways

• North America leads on infrastructure and clinical maturity.

• Europe is balancing innovation with compliance under new IVDR rules.

• Asia Pacific is setting the growth pace through scale and localization.

• LAMEA is the wildcard—low base, but huge upside if funding, training, and partnerships align.

In short, the regional map for this market isn’t just about demand—it’s about readiness. The right panel in the wrong regulatory or reimbursement context will fail. That’s why vendors are increasingly tailoring not just the science, but the business model, to the local environment.

 

End-User Dynamics And Use Case

End users in the targeted sequencing and resequencing market aren’t just purchasing technology—they’re navigating a balance of precision, cost, workflow compatibility, and clinical urgency. Each segment has a distinct role in driving market evolution, from high-throughput academic centers to regional hospitals trying to integrate genomics into everyday care.

Clinical Laboratories

Clinical labs—both independent and hospital-affiliated—are the backbone of market adoption. These labs typically deploy panel-based sequencing for oncology, inherited disorders, carrier screening, and pharmacogenomics. What sets them apart is their push for validated, cost-efficient workflows with fast turnaround times.

Many have moved beyond fixed panels to semi-custom or modular configurations, allowing them to adjust test menus based on referral volume or regional disease prevalence. These labs increasingly favor platforms with automation-ready kits and integrated bioinformatics, reducing manual handling and variant review workload.

In the U.S., for example, mid-sized reference labs are now offering 100–500 gene oncology panels with 5-day reporting cycles—blending clinical relevance with operational efficiency.

 

Academic and Research Institutions

Academic centers remain the innovation drivers. Here, the need is less about reimbursement and more about flexibility. These institutions develop novel panels for biomarker discovery, disease stratification, and therapy response prediction.

Research labs often run both commercial and in-house panels side by side. They value platforms that allow high customization, deeper coverage, and open-source analysis pipelines. Many also serve as contract service providers to pharma or biotech companies looking to validate biomarkers or develop companion diagnostics.

In Europe and Asia, large university hospitals double as both clinical service providers and national reference centers —accelerating the translation of research panels into clinical protocols.

 

Hospitals and Integrated Health Systems

Hospitals are steadily moving from send-out models to in-house targeted sequencing. Oncology departments lead the charge, especially where tumor boards require genomic input to guide treatment. Prenatal care, neurology, and transplant medicine are also emerging users.

That said, hospital adoption depends heavily on staffing. Many lack the bioinformatics infrastructure or trained molecular pathologists to interpret results internally. As a result, hospitals prefer sequencing platforms that offer plug-and-play panels, automated data pipelines, and integration with EMRs.

Some U.S. health systems have adopted targeted sequencing panels into their clinical pathways—for example, triggering pharmacogenetic testing for all cardiac patients or reflex BRCA testing in breast cancer cases.

 

Biopharmaceutical and Biotechnology Companies

Pharma companies are less focused on diagnostics than on discovery. Targeted sequencing is widely used in biomarker stratification, clinical trial enrollment, and drug response correlation studies.

These companies often partner with CROs or sequencing providers to run custom panels across thousands of trial samples. The goal is to link genetic variants to therapeutic outcomes—especially in immuno-oncology, rare diseases, and neurodegenerative drug pipelines.

One leading biotech firm recently adopted a targeted sequencing approach to filter Alzheimer’s clinical trial participants by APOE genotype and rare mutation status, improving trial efficiency and post-hoc analysis power.

 

Contract Research Organizations (CROs)

CROs serve as execution engines. They don’t typically design panels themselves but operate large-scale sequencing services for pharma sponsors, using validated workflows that comply with regulatory and GCP guidelines. CRO demand is increasing as more biopharma companies outsource genomic testing for trial sites across multiple geographies.

CROs prioritize speed, compliance, and global scale—pushing vendors to standardize and streamline panel-based workflows for global multicenter trials.

 

Use Case Highlight

A regional hospital network in Japan was struggling to implement NGS in routine oncology care due to high send-out costs and long delays. The oncology department piloted a targeted 52-gene solid tumor panel with in-house sequencing and cloud-based variant interpretation.

Within three months, average turnaround time dropped from 12 days to 4. Therapy-matched treatment rates rose by 28%, and patient satisfaction improved due to quicker decisions and fewer follow-up visits. The success led to hospital-wide expansion into hematology and inherited cancer testing—paving the way for broader precision medicine integration.

This example shows how targeted sequencing can become the foundation for more scalable and responsive genomic care—if it’s designed to fit real-world clinical workflows.

 

Recent Developments + Opportunities & Restraints

The targeted sequencing and resequencing space is in a rapid evolution cycle, shaped by breakthroughs in chemistry, AI, regulatory clarity, and partnerships across diagnostics and therapeutics. The last two years have brought several pivotal shifts that are redefining both the clinical and commercial landscape.

Recent Developments (Last 2 Years)

• Twist Bioscience expanded its custom panel offering in 2024 by launching an ultra-fast synthesis platform, reducing panel development time by 40% for research and diagnostic labs.

• Illumina announced a strategic integration of its DRAGEN Bio-IT platform with leading EMR systems in early 2023, aiming to automate variant-to-treatment workflows in clinical settings.

• Agilent Technologies rolled out a cloud-based panel design tool in 2023 that allows clinical labs to simulate coverage performance for custom panels before synthesis—accelerating validation timelines.

• Thermo Fisher Scientific launched a new AmpliSeq pharmacogenomics panel in 2024, covering over 200 markers linked to drug metabolism and adverse reactions, targeting hospital networks in the U.S. and Asia.

• Roche announced CE-IVD approval for its AVENIO ctDNA Targeted Kit in 2024, enabling broader adoption of liquid biopsy-based tumor profiling across European cancer centers .

 

Opportunities

• Clinical Mainstreaming of Pharmacogenomics : As more hospitals embed genotype-based prescribing into cardiology, psychiatry, and oncology workflows, there’s a growing opportunity for compact, cost-effective pharmacogenomic panels tailored to real-time care decisions.

• Emergence of Population Health Genomics : National genome initiatives and insurer-funded screening programs (especially in China, the Middle East, and Scandinavia) are increasingly relying on pre-configured panels that focus on common pathogenic variants, carrier status, and polygenic risk scoring.

• AI-Enabled Variant Curation at Scale : Mid-sized labs and hospital systems need automated solutions to handle variant classification. Vendors offering integrated AI curation and clinical report generation have a major opportunity to reduce labor intensity and improve turnaround.

 

Restraints

• Regulatory Complexity and Compliance Burden : With the introduction of IVDR in Europe and variable regulatory frameworks in Asia-Pacific, clinical labs are facing increasing pressure to use validated kits and submit detailed technical documentation—delaying panel deployment.

• Bioinformatics Infrastructure Gaps : Many hospitals and regional labs lack in-house bioinformatics teams or tools, which limits their ability to adopt sequencing panels—even when the hardware and reagents are available. This is especially challenging in underfunded systems across LAMEA and parts of Asia.

 

To be candid, the ceiling for growth in this market isn’t scientific—it’s operational. The platforms and panels exist. What holds back adoption is integration: into workflows, into budgets, into compliance frameworks. The vendors that solve for that—not just for sequencing accuracy—are the ones that will define the next chapter.

 

7.1. Report Coverage Table

Report Attribute	Details
Forecast Period	2024 – 2030
Market Size Value in 2024	USD 6.1 Billion
Revenue Forecast in 2030	USD 11.3 Billion
Overall Growth Rate	CAGR of 10.6% (2024 – 2030)
Base Year for Estimation	2024
Historical Data	2019 – 2023
Unit	USD Million, CAGR (2024 – 2030)
Segmentation	By Technology, Workflow Step, Application, End User, Geography
By Technology	Amplicon-Based, Hybridization-Based, CRISPR-Based
By Workflow Step	Sample Prep, Library Prep, Enrichment, Sequencing, Data Analysis
By Application	Oncology, Rare Disease, Pharmacogenomics, Reproductive Health
By End User	Clinical Laboratories, Academic & Research Institutions, Hospitals, Biopharma & CROs
By Region	North America, Europe, Asia-Pacific, Latin America, Middle East & Africa
Country Scope	U.S., Canada, Germany, U.K., France, China, India, Japan, Brazil, UAE
Market Drivers	- Growing demand for personalized cancer diagnostics - Cost-efficiency of panel-based sequencing vs. whole genome - Rise in AI-powered genomic interpretation
Customization Option	Available upon request