Introduction to Amplicon Sequencing: A Quick Guide
Amplicon sequencing has become a cornerstone in next-generation sequencing (NGS), enabling researchers to focus on specific genomic regions and analyze genetic variation with high precision. This targeted sequencing method is widely used in various fields, from clinical diagnostics to environmental research. In this guide, we’ll break down the key components of amplicon sequencing and explain its role in modern research.
What is Amplicon Sequencing?
Amplicon sequencing is a targeted sequencing approach that uses polymerase chain reaction (PCR) to amplify specific genomic regions of interest. This method produces DNA fragments, called amplicons, which are then sequenced to detect genetic variants like single nucleotide polymorphisms (SNPs), insertions, deletions, and more. By focusing on targeted genomic regions, amplicon sequencing allows researchers to efficiently analyze genetic variation without the need for whole genome sequencing, making it an ideal solution for studies that require precise and cost-effective data.
Why Use Amplicon Sequencing?
Amplicon sequencing offers several advantages over other sequencing methods such as hybridization capture. It provides a faster, more affordable option for analyzing multiple samples while still maintaining high accuracy. By targeting specific genomic regions, this approach ensures that sequencing efforts are concentrated on areas of interest, which is particularly useful in applications like precision oncology, infectious disease detection, and environmental / applied genomics.
Paragon Genomics’ CleanPlex technology takes these advantages even further, offering a streamlined workflow and eliminating many of the challenges associated with traditional PCR amplification methods, such as background noise and scalability issues. This makes CleanPlex a go-to solution for researchers looking to efficiently sequence amplicon sequence variants across a wide range of studies.
The Amplicon Sequencing Workflow
Amplicon sequencing follows a straightforward workflow, which typically includes library preparation, sequencing, and data analysis.
1. Library Preparation
Library preparation is an integral part of the amplicon sequencing workflow, specifically during the multiplex PCR (mPCR) step. In this stage, targeted primers are used to amplify specific regions of interest from a sample. Following mPCR, our CleanPlex technology incorporates an innovative background cleaning process, eliminating unwanted byproducts such as primer dimers through steps like digestion and bead purification. This ensures that only high-quality, purified libraries proceed to sequencing, reducing background noise and improving data accuracy.
The mPCR process, central to amplicon sequencing, increases the number of copies of the targeted genomic regions, generating strong sequencing signals for accurate results. CleanPlex optimizes this process by minimizing background interference, allowing researchers to sequence a large number of genomic targets, even in challenging samples like formalin-fixed, paraffin-embedded (FFPE) tissues.
2. Sequencing
Once the library has been prepared the next step is sequencing. Amplicon sequencing is compatible with a variety of sequencing platforms from companies including Illumina, ThermoFisher (Ion Torrent), MGI, Oxford Nanopore Technologies, Element Biosciences, Singular Genomics, etc. These platforms read the nucleotide sequence of each amplicon, producing high-throughput sequencing data that can be used for further analysis. CleanPlex technology’s compatibility with major sequencing platforms ensures flexibility and adaptability, allowing researchers to choose the platform that best fits their study needs.
3. Data Analysis
The final step in the amplicon sequencing process is data analysis. After sequencing, researchers analyze the sequence data to detect genetic variants within the targeted genomic regions. CleanPlex technology not only generates high-quality sequence data but also improves the accuracy of data analysis by reducing background noise and enhancing signal quality. Statistical analysis tools are often used to interpret the data, comparing amplicon sequence variants and identifying significant genetic markers.
Applications of Amplicon Sequencing
Amplicon sequencing has a wide range of applications, from clinical diagnostics to evolutionary biology. Below are just a few examples of how this targeted sequencing method is used:
- Precision Oncology: Amplicon sequencing is crucial for identifying genetic mutations in cancer patients, helping doctors tailor treatments based on the patient’s specific genetic profile. Our CleanPlex technology has the ability to analyze genetic variation with high sensitivity which makes it ideal for detecting low-frequency mutations in tumor samples.
- Infectious Disease Detection: During the SARS-CoV-2 pandemic, amplicon sequencing played a key role in tracking viral mutations. Its ability to sequence multiple samples quickly and efficiently made it an invaluable tool for public health researchers.
- Environmental Genomics: In studies that involve marker gene sequencing, amplicon sequencing helps researchers identify microbial communities in various environments. By analyzing DNA fragments from specific genomic regions, they can determine the relative abundance of different species, offering insights into biodiversity and ecosystem health.
CleanPlex Technology: Pushing the Boundaries of Amplicon Sequencing
While traditional amplicon sequencing technologies have limitations, our CleanPlex technology addresses these challenges. By incorporating background cleaning, CleanPlex significantly reduces primer dimers and other unwanted artifacts, ensuring cleaner libraries and more reliable results. Additionally, CleanPlex is designed for scalability, enabling the amplification of thousands of targets in a single panel, which is a significant advantage for high-throughput sequencing projects.
This breakthrough technology allows researchers to sequence large panels with minimal hands-on time, making it a preferred choice for projects that require both speed and accuracy. With CleanPlex technology, our team is able to offer cutting-edge solutions that meet the evolving needs of genomic research.
The Future of Genomic Research with Amplicon Sequencing
Amplicon sequencing has transformed the landscape of targeted sequencing, offering researchers precise and cost-effective insights across various applications, from cancer research to pathogen detection. Our CleanPlex technology addresses common challenges in the amplicon sequencing process, ensuring clean, scalable results that lead to more confident data analysis.
As genomic research advances, our team continues to innovate, supporting discoveries in clinical diagnostics, environmental studies, and beyond. With CleanPlex technology, you can trust that your sequencing projects will deliver the reliable, high-quality data needed to fuel groundbreaking research and drive meaningful outcomes.
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