Amplicon Sequencing Market Size, Share and Trends Analysis, By Product and Service (Instruments and Platforms, Kits and Reagents, and Service), By Target Type (DNA Amplicon Sequencing, RNA Amplicon Sequencing, and 16S/18S/ITS rRNA Amplicon Sequencing), By Application, By End-Use, and By Region, Forecast 2025-2032

Amplicon Sequencing Market Overview and Key Insights:

Amplicon sequencing market size reached USD 1,667.2 million in 2024 and is expected to register a revenue CAGR of 16.4% during the forecast period. It is a type of targeted next generation sequencing that employs PCR to generate DNA sequences known as amplicons. In comparison to hybrid-capture sequencing, amplicon sequencing is a quick and easy focused sequencing technology with a simple methodology and a short turnaround time. Amplicon sequencing has higher on-target rates than other targeted sequencing approaches due to the precision of primer design.

Market Drivers:

Growing prevalence of chronic disorders is a key driver of revenue growth in amplicon sequencing market. Beta-thalassemia is most prevalent in South Asia, the Middle East, North Africa, and Southern Europe. Beta-thalassemia carriers account for around 1.5% of the global population (80-90 million persons). Each year, 60,000 symptomatic individuals are born. The child has a 25% probability of getting beta-thalassemia and a 50% chance of being an asymptomatic carrier like their parents.

NGS and Third-Generation Sequencing (TGS) offer a significant advantage over traditional DNA analysis by simultaneously genotyping α- and β-thalassemia. This allows for a comprehensive diagnosis of the thalassemia and its genetic modifiers, which is essential for genetic counseling. Furthermore, sequencing data banking enables re-analysis when necessary. Instruments such as computational infrastructure for data analysis, a skilled bioinformatics technician, properly documented TS, and bioinformatics pipeline development and optimization in accordance with recommended guidelines are costly for any new laboratory, but will become less expensive as sample throughput grows.

On November 2024, Complete Genomics, a genomic sequencer manufacturer based in San Jose, California, has announced the launch of their mpox (MPXV) virus amplicon sequencing panel, which is part of the company’s pathogenic microorganism sequencing product range. The new mpox viral amplicon sequencing panel is a targeted sequencing product based on ATOPlex multiplex PCR technology and created using proprietary reagents, apparatus, and software. It encompasses the virus’s whole genome, allowing for quick identification and traceability, as well as relative quantification.

Market Opportunity:

Expanding microbiome & metagenomics research acts as opportunities for amplicon sequencing market. The typical method for analyzing the composition and diversity of microbiota in human and environmental samples is to profile bacterial communities using 16S rRNA gene amplicon sequencing. Several marker/target genes have been found for bacteria, archaea, fungus, and mycobacteria, and they are widely employed in amplicon sequencing. The highly conserved 16S rRNA gene suggests that it plays an important role in cellular function and survival, and hence serves as the foundation for precise genomic classification of known and unknown microbial species. The modest size of 16S rRNA genes (~1542 bp) makes them easier to sequence, even for huge sample quantities.

On September 2025, Oxford Nanopore Technologies, the firm behind a new generation of molecular sensing technology based on nanopores, has announced the release of the Microbial Amplicon Barcoding Kit 24 V14, which allows for faster and more flexible microbial investigation in a single workflow. Oxford Nanopore’s new kit has been optimized to deliver an information-rich, fast, and accessible full-length amplicon procedure that streamlines the approach for identifying bacteria, archaea, and fungi and allows for improved microbial community characterization.

Recent Trends:

Emerging trends include long-read/full-length amplicons, molecular barcoding & error correction, high multiplexing & throughput, and improved bioinformatics, simulators, and QC tools.

Long-read amplicon sequencing can produce accurate, efficient, and high-throughput sequences from single molecules, but PCR read lengths are limited. The data is straightforward to analyze; phased variations and breakpoints are present in high fidelity individual reads. Pacific Biosciences (PacBio) and Oxford Nanopore have recently developed new technology capable of producing lengthy sequencing reads of tens of thousands of nucleotides. Nanopore sequencing can give precise variant calling as well as extensive coverage of larger targeted regions, allowing for better study of repetitive regions and taxonomic assignment.

On November 2022, Element Biosciences, Inc., the developer of an innovative DNA sequencing platform that is disrupting the genomics industry, has announced the availability of its Element LoopSeq long-read sequencing technology kits for AVITI, allowing the Element AVITI System to perform both short- and long-read sequencing on the same instrument. Element LoopSeq is an exceptional long-read sequencing chemical that adds synthetic long-read capabilities to AVITI. Element LoopSeq generates highly precise continuous long reads, which are identical to the output of traditional long-read technologies but do not require an additional dedicated equipment.

Restraints & Challenges:

Amplicon sequencing has significant drawbacks, including limited taxonomic precision, copy number variations in rRNA genes, and taxonomic biases due to PCR amplification. Furthermore, the idea that amplicon-based approaches can only detect known alterations like SNPs and insertions/deletions (InDels) is unduly simplistic. While amplicon-based approaches are effective for finding hotspots, they are not limited to this use.

Random sampling errors can overestimate the β-diversity of microbial communities. These biases exist in all sequencing systems. Furthermore, resolution is limited to the genus or species level, and abundance estimations are imprecise due to 16S/18S copy number changes and PCR biases, which limits market expansion.

Product and Service Segment Insights and Analysis:

Based on the product and service, amplicon sequencing market is segmented into instruments & platforms, kits & reagents, and services.

Instruments and platforms segment contributed the largest market share in 2024. It is further sub segmented into Next-Generation Sequencing (NGS) platforms and PCR & qPCR systems. Amplicon sequencing is especially useful for genome targeting and detecting hotspot mutations, copy number variations, gene fusions, InDels, and single-nucleotide polymorphisms (SNPs). Because of its versatility, amplicon sequencing can be successfully employed in a wide range of areas, including nutrition, bacterial metagenomics, gene editing, and clinical research. Amplicon sequencing use either Sanger sequencing or NGS technologies. NGS techniques to targeted sequencing enable the simultaneous sequencing of thousands of amplicons. For research goals that require addressing hundreds of genes at once, next-generation amplicon sequencing offers high throughput per run at a low cost.

On July 2024, Paragon Genomics announced a distribution agreement with Biosecure ID for its CleanPlex products and technology in the United Kingdom and Republic of Ireland. CleanPlex from Paragon Genomics is an ultra-scalable and ultra-sensitive NGS target enrichment amplicon sequencing technology that delivers direct amplification sensitivity at the single cell level and allows for the inclusion of many genomic targets in a single test.

Target Type Segment Insights and Analysis:

Based on the target type, amplicon sequencing market is segmented into DNA amplicon sequencing, RNA amplicon sequencing, and 16S/18S/ITS rRNA amplicon sequencing.

16S/18S/ITS rRNA amplicon sequencing segment contributed the largest market share in 2024. It is further sub segmented into microbiome analysis and metagenomics and microbial diversity studies. Targeted DNA amplification with PCR is an essential aspect of daily work in laboratories around the world. Its applications include research, diagnostics, forensics, and even food analysis. Amplicon sequencing is frequently used to validate the generated DNA amplicons, particularly when they are employed for molecular cloning.

Amplicon sequencing is commonly used to analyze microbial communities, aid in taxonomic classification of microorganisms, and assess the functional capacities of microbiomes. Another fascinating application of amplicon sequencing is environmental DNA (eDNA) analysis. Organisms shed genetic material into the environment, known as eDNA. eDNA can be detected in tissue fragments and bodily excretions such as urine. Thus, amplicon sequencing can help with the investigation and monitoring of biodiversity, including the presence and abundance of organisms in terrestrial and aquatic habitats.

On March 2025, Zymo Research Corp., a biotechnology and microbiome research solutions provider, has announced the availability of their new Quick-16S Full-Length Library Prep Kit. This kit provides the quickest, most efficient full-length 16S library preparation methodology, producing high-quality libraries in as little as 30 minutes of hands-on time for 96 samples. The Quick-16S Full-Length Library Prep Kit aims to simplify and improve 16S amplicon sequencing by making full-length library preparation more accessible. This addition to the Quick-16S product line demonstrates Zymo Research’s dedication to provide simple solutions to complicated molecular research methodologies.

Application Segment Insights and Analysis:

Based on the application, amplicon sequencing market is segmented into oncology, inherited disease and rare disorder research, infectious diseases & pathogen detection, microbiome & metagenomics, drug discovery & development, and others.

Oncology segment contributed the largest market share in 2024. According to International Agency for Research on Cancer, lung cancer is the main cause of cancer deaths worldwide. One in every sixteen people will develop lung cancer during their lifetime. Smoking causes 80% of lung cancer fatalities, making it the main risk factor. People who have never smoked account for 20% of lung cancer deaths. Moreover, incidence and fatality rates rise as the Human Development Index (HDI) increases. If incidence and mortality rates remain the same as in 2022, lung cancer will impose a greater burden by 2050, with 4.62 million new cases and 3.55 million deaths.

On March 2025, the LuNGS Alliance, sponsored by the Cancer Research and Statistics Foundation (CRSF), has announced free Lung NGS (Next Generation Sequencing) biomarker testing for lung cancer patients in India. This program is supported by AstraZeneca, Pfizer, and Roche, with 4baseCare serving as the official laboratory partner. The effort intends to raise awareness of precision oncology as an important, accessible, and cost-effective therapy option for lung cancer.

Geographical Outlook:

Amplicon sequencing market is strategically segmented by geography to provide a comprehensive understanding of regional market dynamic. Discover demand analysis, emerging trends, and growth opportunities shaping market performance across different region and countries.

North America Amplicon Sequencing Market:

North America is registered to have highest market share in amplicon sequencing market in 2024. This is mainly driven by rising adoption of precision medicine and advancements in NGS platforms. Amplicon sequencing has become a key component of next-generation sequencing (NGS), allowing researchers to investigate specific genomic areas with great precision. Amplicon sequencing is a faster, cheaper, and more accurate technique to genetic investigation than methods such as hybridization capture. By focusing on specific genetic regions, it improves sequencing efficiency while lowering costs, making it excellent for precision oncology, infectious disease diagnosis, and environmental genomics. Unlike whole-genome sequencing, which examines entire genomes, amplicon sequencing focuses on pre-selected targets, allowing for exact variation discovery and detailed analysis of complicated materials.

On November 2024, Biotia, a pioneer in genomic-based infectious disease diagnostics, has achieved a significant milestone with the New York State Department of Health Clinical Laboratory Evaluation Program (CLEP) approval of their BIOTIA-ID Urine NGS Assay as a Laboratory Developed Test. NY has approved BIOTIA-ID, the first genomics-based urine diagnostic based on artificial intelligence (AI). BIOTIA-ID employs AI and genomics for comprehensive pathogen detection, decreasing false positives and overcoming the constraints of culture, PCR, and targeted 16S amplicon NGS testing, which frequently produce partial, ambiguous, or inconsistent results.

Asia Pacific Amplicon Sequencing Market:

Asia Pacific is expected to register the fastest growth rate during the forecasted period, driven by growing prevalence of chronic disorders, rising healthcare expenditure, and growing awareness towards cancer. Next Generation Sequencing (NGS) has emerged as a possible game changer in cancer care, as the Asia-Pacific (APAC) region continues to experience an increasing cancer burden, imposing clinical, societal, and economic costs. NGS enables the delivery of personalised cancer care through tumour profiling, and multiple studies in APAC have shown that it improves patient outcomes by shortening time to results, identifying more patients for matched therapies and clinical trials, and lowering diagnosis costs when compared to current practice.

On May 2025, Illumina, a global leader in DNA sequencing and array-based technologies, and the Okinawa Institute of Science and Technology (OIST), an international graduate university in Okinawa, Japan, have signed a Memorandum of Understanding (MOU) to accelerate genomics innovation in accordance with the One World, One Health framework, which acknowledges the interconnectedness of human, animal, and environmental health. This cooperation will bring together Illumina’s Next-Generation Sequencing (NGS) technologies with OIST’s competence in multidisciplinary science, including engineering, physics, biology, ecology, and marine sciences.

Competition Analysis:

Amplicon sequencing market is characterized by a fragmented structure, with several players competing across various segments and regions. List of major players included in amplicon sequencing market report are:

• Illumina, Inc.
• Eurofins Genomics
• Integrated DNA Technologies, Inc
• GENEWIZ from Azenta Life Sciences
• Paragon Genomics, Inc.
• CD Genomics
• Psomagen, Inc.
• Novogene Co., Ltd. 
• Massive Bioinformatics
• Thermo Fisher Scientific Inc.
• Zymo Research
• Charles River Laboratories
• Quintara Biosciences 
• QIAGEN 
• MtoZ-Biolabs Inc.

Strategic Developments in Amplicon Sequencing Market:

• In March 2024, seqWell, a global provider of genomic library workflow solutions, has announced the release of the new ExpressPlex HT Library Preparation Kit (ExpressPlex HT), the first commercially available next-generation sequencing (NGS) library preparation kit that includes all the necessary reagents and indices for multiplexing up to 6,144 samples in a pre-plated 384-well format. ExpressPlex HT employs a 90-minute procedure in a single mastermix reaction to simplify NGS library preparation by massive multiplexing, allowing for lower cost, high throughput sequencing of plasmids, amplicons, and other synthetic constructs used in synthetic biology.
• In July 2023, Integrated DNA Technologies (IDT) has announced the xGen Respiratory Virus Amplicon Panel, a new next-generation sequencing (NGS) option. The IDT xGen Respiratory Virus Amplicon Panel’s single-tube method generates overlapping amplicons and takes 2.5 hours from sample to sequencer, utilizing up to 1,536 unique dual indexing primers (UDIs) for multiplexed sequencing. With 98.7% total genome coverage of viral respiratory variants Respiratory Syncytial Virus (RSV) A, RSV B, Influenza A H1N1, Influenza A H3N2, Influenza B, and SARS-CoV-2, this specially built single panel is designed to monitor the evolution and spread of these six viruses.

Key Advantages for Stakeholders:

Navistrat Analytics’ industry report provides an in-depth quantitative analysis of various market segments, historical and current trends, market forecasts, and dynamics within the global market. The historical years covered in this report are 2022 to 2023, with 2024 serving as the base year for market size calculations. The forecast period extends from 2025 to 2032.

The report includes an executive summary and a comprehensive overview of market drivers, restraints, opportunities, and challenges (DROC), along with insights into regulatory standards. It features detailed analyses such as PORTER’s Five Forces, SWOT, and PESTLE, as well as assessments of technological trends and the competitive landscape.

PORTER’s Five Forces analysis helps stakeholders evaluate the impact of new entrants, competitive rivalry, supplier power, buyer power, and substitution threats, enabling them to assess the level of competition and the attractiveness of the global market. The competitive landscape provides stakeholders with a clear understanding of the current market positions of key players, offering valuable insights into their competitive environment.

Scope And Key Highlights Of Amplicon Sequencing Market Report:

 Amplicon Sequencing market report offers a detailed analysis of market size, including historical revenue (in USD Million) data for 2022-2023 and revenue forecasts for 2025-2032 across the following segments:

• Product and Service Outlook (Revenue, USD Million; 2022-2032)
  • Instruments and Platforms
    • Next-Generation Sequencing (NGS) platforms
    • PCR & qPCR systems
  • Accessories and Consumables
    • Library preparation kits
    • Amplification enzymes & primers
    • Sample preparation reagents
  • Services
    • Data analysis & bioinformatics services
    • Custom sequencing services

• Target Type Outlook (Revenue, USD Million; 2022-2032)
  • DNA Amplicon Sequencing
    • Targeted DNA regions
    • SNPs and structural variants
  • RNA Amplicon Sequencing
    • Transcriptome profiling
    • RNA editing & alternative splicing
    • Fusion gene detection
  • 16S/18S/ITS rRNA Amplicon Sequencing
    • Microbiome analysis
    • Metagenomics and microbial diversity studies

• Application Outlook (Revenue, USD Million; 2022-2032)
  • Oncology
  • Inherited Disease and Rare Disorder Research
  • Infectious Diseases & Pathogen Detection
  • Microbiome & Metagenomics
  • Drug Discovery & Development
  • Others

• End-Use Outlook (Revenue, USD Million; 2022-2032)
  • Pharmaceutical & Biotechnology Companies
  • Clinical Diagnostics Laboratories
  • Academic & Research Institutes
  • Contract Research Organizations (CROs)

• Regional Outlook (Revenue, USD Million; 2022-2032)
  • North America
    • U.S.
    • Canada
    • Mexico
  • Europe
    • Germany
    • France
    • U.K.
    • Italy
    • Spain
    • Benelux
    • Nordic Countries
    • Rest of Europe
  • Asia Pacific
    • China
    • India
    • Japan
    • South Korea
    • Oceania
    • ASEAN Countries
    • Rest of APAC
  • Latin America
    • Brazil
    • Rest of LATAM
  • Middle East & Africa
    • GCC Countries
    • South Africa
    • Israel
    • Turkey
    • Rest of MEA

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