How Much Does a Next-Generation Sequencer Cost?

Next-generation sequencing (NGS) is a powerful, scalable technology that can sequence millions of DNA fragments simultaneously, offering far greater efficiency than traditional methods. This speed and precision make NGS a cornerstone in healthcare and genomics. It enables precision medicine by identifying genetic mutations for personalized treatments, informs targeted cancer therapies, and helps diagnose rare inherited diseases. NGS also plays a crucial role in microbial research, pathogen detection, and drug discovery by uncovering genetic factors that influence treatment responses.

In this post, we’ll break down the costs of NGS technology. We’ll cover the basics, explore popular manufacturers and models, and provide price ranges to guide your procurement decisions—helping you stay within budget while accessing the right equipment for your lab’s needs.

What is Next-Generation Sequencing (NGS) & How Does It Work?

Next-generation sequencing (NGS) is a transformative technology that allows the rapid, high-throughput sequencing of DNA and RNA. NGS can simultaneously sequence millions of DNA fragments, providing comprehensive genomic data far faster and more efficiently than traditional sequencing methods. It has revolutionized the field of genomics, offering unprecedented insights into genetic variation, gene expression, and disease mechanisms.

History of NGS

NGS emerged in the mid-2000s as a significant leap beyond earlier sequencing methods, particularly Sanger sequencing, which had been the standard for decades. Developed by Frederick Sanger in 1977, Sanger sequencing was a slower, labor-intensive process that could only sequence one DNA fragment at a time. While reliable and accurate, Sanger sequencing was costly and time-consuming for large-scale projects, such as sequencing an entire genome.

The introduction of NGS changed that landscape. NGS technologies allowed researchers to sequence massive amounts of DNA in parallel, drastically reducing the time and cost required for large-scale genomic studies. The Human Genome Project, completed in 2003, took over a decade and cost billions of dollars using Sanger sequencing. Today, thanks to NGS, a human genome can be sequenced in days for a fraction of the cost.

How NGS Works

NGS involves fragmenting DNA or RNA into smaller pieces, attaching adapters to the fragments, and loading them onto a sequencing platform. Once loaded, these fragments are sequenced in parallel, generating massive amounts of data. The sequencing process uses various chemistries and technologies—such as sequencing by synthesis, sequencing by ligation, or real-time sequencing—depending on the platform.

NGS platforms read the sequence of each fragment by detecting the incorporation of nucleotides (the building blocks of DNA or RNA) or by monitoring real-time biochemical reactions. The resulting data is then reconstructed using bioinformatics tools to piece together the entire sequence or transcriptome.

NGS as an Alternative to Traditional Methods

NGS is a powerful alternative to traditional methods like Sanger sequencing and microarrays. While Sanger sequencing is limited to reading single DNA fragments and requires cloning or PCR amplification, NGS can handle millions of fragments in parallel, providing higher throughput and efficiency. 

Microarrays, another older method, measure gene expression by hybridizing labeled nucleic acids to probes on a chip. Although useful, microarrays are limited to detecting only known sequences, whereas NGS can identify novel variants and perform more comprehensive analyses.

Applications of NGS

NGS has wide-ranging applications in both research and clinical settings:

  • Whole Genome Sequencing (WGS): WGS sequences an organism's entire genome, providing a complete view of its genetic makeup, including coding and non-coding regions. This enables the detection of single nucleotide polymorphisms (SNPs), structural variants, and other genomic changes linked to disease.
  • Whole Exome Sequencing (WES): WES focuses on sequencing the exome, or protein-coding regions of the genome, which are the most functionally relevant for understanding disease. It is a cost-effective alternative to WGS, often used for diagnosing genetic disorders.
  • RNA Sequencing (RNA-seq): RNA-seq analyzes RNA to measure gene expression levels and investigate alternative splicing events. This method provides insights into gene regulation, expression patterns in different tissues, and the molecular mechanisms of diseases.

NGS continues to advance the fields of precision medicine, cancer research, and genetic disease diagnostics, offering researchers and clinicians a powerful tool for comprehensive genomic analysis.

Key Components & Features

Several essential components drive the efficiency and accuracy of NGS, making it a versatile tool for genomic analysis:

  • Sequencing Technologies: NGS utilizes advanced technologies to decode DNA and RNA. Sequencing by Synthesis (SBS), a widely used method, incorporates fluorescently labeled nucleotides into DNA strands and captures fluorescence to determine the sequence. Sequencing by Ligation uses short DNA probes to identify sequences via ligation events. Single-Molecule Real-Time (SMRT) Sequencing observes DNA synthesis in real-time, offering long reads and reducing the need for amplification. Each of these technologies contributes to the overall speed, accuracy, and flexibility of NGS.
  • Sequencing Platforms: Different NGS platforms offer unique strengths for various applications. Illumina platforms are known for their high throughput and accuracy, making them the go-to choice for everything from whole genome sequencing to targeted panels. Oxford Nanopore excels in real-time sequencing of long DNA fragments, making it ideal for analyzing structural variations and fast sequencing needs. Pacific Biosciences (PacBio) specializes in long-read sequencing, enabling the resolution of complex regions in genomes and enhancing genome assembly. These platforms offer versatility and precision for a wide range of genomic studies.
  • Library Preparation & Flow Cells: Library preparation is crucial to NGS, as it readies DNA or RNA for sequencing. This process starts by fragmenting the samples, then ligating adapters to the ends to ensure they bind to the flow cell for amplification. PCR amplification is used to enrich the library for fragments of interest, ensuring sufficient quantities for sequencing. The flow cell, a specialized slide, captures these prepared DNA fragments, allowing for high-density sequencing that boosts efficiency and data quality.

This combination of cutting-edge technologies and robust platforms enables next-generation sequencing to deliver rapid, accurate, and scalable genetic analysis, supporting everything from basic research to clinical diagnostics.

NGS Platform Costs: Price Ranges, Features, & Capabilities

The cost of next-generation sequencing (NGS) platforms varies widely depending on their features, throughput, and intended applications. Below is a comparison of popular NGS models from leading manufacturers, highlighting their key capabilities along with price ranges to help you find the best fit for your lab’s needs:

  • Illumina: Offers a broad range of sequencers tailored to different project scales. For smaller studies, the MiSeq is ideal for targeted sequencing and microbiome research. The NextSeq 2000 provides a mid-range solution, suitable for clinical and research labs. For larger, high-throughput projects, the HiSeq offers extensive capabilities, while the NovaSeq X is a premium system designed for large-scale genomics. Price ranges: MiSeq ($90K to $150K), NextSeq 2000 (~$335K), HiSeq ($600K to $1M), NovaSeq X (starting at $985K)
  • Oxford Nanopore Technologies: Provides a unique and scalable approach to NGS. The portable MinION is a highly affordable option for small-scale, real-time sequencing projects. For larger-scale needs, the PromethION offers high throughput and long-read sequencing capabilities, suitable for comprehensive genomic analysis. Price ranges: MinION (~$1K), PromethION (over $200K)
  • PacBio: Specializes in long-read sequencing, ideal for resolving complex genomic regions with high accuracy. The Sequel IIe system is particularly suited for detailed genome assemblies, structural variation analysis, and variant detection, making it a go-to for precise genomic research. Price range: Sequel IIe ($350K to $500K)
  • Ion Torrent: Offers a more affordable option for targeted sequencing. The Ion S5 is designed for smaller labs focusing on targeted gene panels, while the Ion Proton offers greater sequencing capabilities for larger-scale projects without a substantial price increase. Price ranges: Ion S5 ($65K), Ion Proton ($150K)
  • BGI Genomics: A rising competitor, known for its cost-effective, high-throughput systems. The MGI DNBSEQ-T7 is designed to sequence entire genomes quickly, offering a competitive price-to-performance ratio for large-scale genomics. Price range: MGI DNBSEQ-T7 ($600K to $800K)

Cost Comparison of NGS Models by Features

The cost of next-generation sequencers depends on key factors like system size, throughput, and read length. These features not only impact pricing but also determine the suitability of a sequencer for different research needs:

  • Benchtop vs. Larger Systems: Benchtop models, such as the Illumina MiSeq or Ion Torrent S5, typically range from $90K to $150K. These smaller systems offer a cost-effective solution for labs with smaller-scale projects. In contrast, larger systems like the Illumina HiSeq and NovaSeq X, designed for high-throughput and large-scale genomic studies, can cost upwards of $1M. Larger systems are ideal for labs requiring extensive data output and more complex analyses.
  • High-Throughput Capabilities: Throughput plays a critical role in cost. High-throughput systems can process larger sample volumes and generate more data quickly, making them essential for large-scale projects such as population genomics. While these systems come at a higher cost, they save time and resources in high-demand labs.
  • Read Length vs. Throughput: Read length refers to how much DNA is sequenced in one go. Platforms offering long reads, like Pacific Biosciences (PacBio) and Oxford Nanopore, are ideal for resolving complex genomic regions but may have higher costs and lower throughput compared to short-read platforms like Illumina. Short-read systems are generally faster and more affordable, making them suitable for high-throughput projects.

Factors Influencing the Cost of Next-Generation Sequencing (NGS)

Several key factors impact the cost of next-generation sequencing (NGS), including the type of sequencing tasks, materials and construction, and additional features like automation and bioinformatics tools. Understanding these variables helps laboratories make informed decisions about which systems and setups best fit their research needs and budgets.

Material & Construction

The materials used in NGS workflows also influence costs, directly impacting efficiency, data accuracy, and the overall cost of running NGS workflows:

  • Reagents: Essential for DNA fragmentation, ligation, and amplification. Their quality and quantity affect both performance and price.
  • Library Preparation Kits: Vary in complexity and features, impacting the ease of sample prep and overall costs.
  • Flow Cells: Specialized components where sequencing reactions occur. Their design and capacity for high-density sequencing can significantly affect expenses.

Automation & Data Analysis

Additional features enhance NGS efficiency but also add to the cost:

  • Automation: Streamlines workflows, reduces manual labor, and increases throughput, leading to long-term cost savings by minimizing errors and speeding up processes.
  • Data Analysis Tools & Bioinformatics: Crucial for processing the vast amounts of data generated by NGS. Advanced bioinformatics platforms support comprehensive data interpretation, enabling accurate variant detection and genomic insights. Though essential, these tools come with added costs, especially for labs handling large datasets.

Sequencing Technologies & Their Costs

Different sequencing technologies affect both pricing and performance. However, they offer specific advantages depending on the research focus, with long-read methods offering precision in difficult genomic regions at a higher cost per base:

  • Sequencing by Synthesis (SBS): Offers high accuracy and throughput, commonly used in large-scale genomic studies. It’s a cost-efficient option for many labs.
  • Sequencing by Ligation & Single-Molecule Real-Time (SMRT): These alternatives offer longer read lengths, ideal for resolving complex genomic regions, though they often come with higher costs and lower throughput compared to SBS.

Costs of Sequencing Applications

The cost of sequencing has dropped significantly in recent years. The affordability of these methods continues to improve, driving more widespread adoption in both clinical and research settings:

  • Human Genome Sequencing: Initially costing billions during the Human Genome Project, today’s whole genome sequencing can be completed for around $1,000, making it accessible for a range of research and clinical applications.
  • Whole Exome Sequencing: Typically costs between $300 and $1,500, depending on platform and service options.
  • Targeted Sequencing & RNA-seq: Targeted gene panels cost between $100 and $1,000, while RNA-seq can range from $500 to $3,000, depending on the depth of sequencing.

Consumables & Reagents Costs

Consumables and reagents are ongoing costs that can quickly accumulate in NGS workflows. Efficient management of these resources is crucial for controlling costs in high-throughput environments:

  • Reagents: Include enzymes, buffers, and nucleotides necessary for sample prep and sequencing reactions. Prices can range from a few hundred to several thousand dollars, depending on the quantity and quality.
  • Flow Cells: Used in sequencing reactions, these consumables range from $500 to $1,500 depending on platform capacity.

Additional Considerations: High-Throughput, Data Management, & More

High-throughput sequencing allows labs to analyze multiple samples simultaneously, significantly reducing the cost per base. Platforms like Illumina’s NovaSeq and NextSeq handle large data volumes in a single run, making comprehensive genomic studies more feasible and cost-effective. 

This scalability, combined with advancements in automation and consumable pricing, continues to lower overall NGS costs, making the technology increasingly accessible for large-scale genomics and precision medicine applications.

Managing the vast datasets generated by high-throughput sequencing requires robust bioinformatics tools. These platforms enable sequence alignment, variant identification, and genomic annotation, helping researchers derive meaningful insights from NGS data. While bioinformatics tools add to the overall cost, they are essential for ensuring data accuracy and enabling key discoveries.

Beyond the core equipment, several additional factors influence the total cost of NGS:

  • Workflow Integration: Seamless integration of NGS platforms into existing lab processes can impact costs. Proper training, resource management, and workflow optimization help reduce expenses and enhance efficiency.
  • Maintenance & Replacement: Regular maintenance and timely replacement of components, such as flow cells and optics, are crucial for ensuring optimal system performance and preventing costly disruptions.
  • Operational Costs: Energy efficiency, consumable management, and service contracts significantly influence long-term expenses. Opting for energy-efficient platforms and managing consumables effectively can result in substantial cost savings over time.

By accounting for these additional considerations, labs can better maintain their budgets while maximizing the efficiency and output of their sequencing workflows.

How Leasing an NGS System Can Benefit Your Lab

Leasing an NGS system offers significant advantages for labs looking to optimize both financial resources and research capabilities. One of the most impactful benefits of leasing is the ability to extend your lab’s cash runway. Instead of tying up a large portion of your budget in the upfront costs of purchasing equipment, leasing allows you to allocate resources more strategically across R&D, operations, and other essential areas, providing financial flexibility.

Leasing can also accelerate your lab's progress toward critical R&D and commercial milestones. By accessing the latest NGS technology without the heavy capital investment, your lab can increase productivity, process more samples, and generate results faster, keeping you on track to achieve key objectives sooner. Faster progress in research and development often translates to earlier validation of your work, a crucial factor for both scientific advancement and commercial viability.

Moreover, by reaching milestones more quickly and demonstrating your lab's capacity to deliver, leasing can position you for a stronger next round of funding. Investors are more likely to support labs that show efficient use of resources and a clear trajectory toward commercialization. With the right equipment in place, you can demonstrate tangible progress and secure funding at a more favorable valuation, enhancing the long-term growth and success of your lab.

Choosing the Right Equipment for Your Research

When selecting a next-generation sequencer, key factors like sequencing technology, system size, and operational costs must align with your research needs and budget. Platforms such as Illumina, Oxford Nanopore, and PacBio offer different capabilities, from throughput to read length and accuracy, impacting both the initial investment and long-term costs.

The choice between benchtop systems and high-throughput models depends on your project’s scale and funding. Additionally, the cost of consumables like library preparation kits and flow cells, along with maintenance and service contracts, plays a significant role in ongoing expenses. Efficient workflow integration further enhances productivity and reduces turnaround times, optimizing overall performance. Understanding your research objectives and financial constraints is essential for making the right decision. By selecting a sequencer that meets both scientific and budgetary needs, your lab can remain competitive and capable of delivering impactful research outcomes.

Leasing a next-generation sequencer through Excedr offers an alternative solution, enabling your lab to acquire essential equipment while extending your cash runway and accelerating research milestones.

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