Amplicon Sequencing: Unlocking Precision in Genomic Analysis

Amplicon Sequencing: Unlocking Precision in Genomic Analysis

Amplicon sequencing has become a cornerstone of next-generation sequencing (NGS), enabling researchers to analyze specific genomic regions with high precision. This targeted approach is widely used across various fields, including clinical diagnostics, genetic research, and environmental studies. By providing accurate and efficient genetic analysis, amplicon sequencing plays a crucial role in detecting variants, studying microbial diversity, and advancing biomedical research.

Key Applications of Amplicon Sequencing

Genetic Variant Detection

Amplicon sequencing is widely used for identifying single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and somatic mutations with high sensitivity. It is particularly useful in cancer research, inherited disease screening, and population genetics, where detecting low-frequency variants is crucial. This method enables precise mutation profiling, making it ideal for liquid biopsy applications and tumor genetic analysis.

CRISPR Mutation Analysis

Genome editing technologies like CRISPR-Cas9 require thorough validation to ensure successful modifications and minimize unintended genetic changes. Amplicon sequencing allows researchers to assess editing efficiency by quantifying intended mutations while detecting potential off-target effects. This application is critical in gene therapy, functional genomics research, and engineered cell line development, ensuring precise and reliable genome modifications.

Infectious Disease Testing

Amplicon sequencing helps detect and monitor pathogens in clinical samples, making it a valuable tool for infectious disease research and outbreak tracking. With its ability to target specific genetic regions, it can support the rapid identification of viruses, bacteria, and other infectious agents.

Water Surveillance

Researchers use amplicon sequencing to monitor water sources for harmful microbes and pathogens. This approach provides accurate, high-throughput analysis to help maintain water safety and prevent the spread of waterborne diseases.

Conservation

Amplicon sequencing supports wildlife conservation by helping researchers study genetic diversity in endangered species. These insights guide breeding programs, track population health, and contribute to efforts that protect biodiversity.

Agrigenomics

Amplicon sequencing plays a key role in agrigenomics by supporting the genetic analysis of plants and animals. Researchers use this targeted approach to identify beneficial traits, track genetic variation, and advance breeding programs. From improving crop resilience and yield to supporting healthier livestock, amplicon sequencing helps drive innovation in agriculture. Whether studying disease resistance, growth patterns, or quality traits, this technology provides the reliable data needed to optimize plant and animal genetics for a wide range of applications.

Amplicon Sequencing Solutions at Paragon Genomics

At Paragon Genomics, we provide advanced amplicon sequencing solutions powered by our proprietary CleanPlex® technology. Designed to overcome the limitations of traditional methods, CleanPlex enhances sequencing accuracy by eliminating background noise, reducing primer dimers, and ensuring cleaner libraries. Our scalable approach enables the amplification of thousands of targets in a single panel, making sequencing workflows faster, more efficient, and highly reproducible.

1. CleanPlex® Custom Amplicon Panels

Our CleanPlex® technology delivers high-specificity, ultra-sensitive amplicon sequencing panels, ideal for applications such as cancer research, infectious disease monitoring, and inherited disease screening. By minimizing unwanted artifacts, CleanPlex ensures more reliable results with minimal hands-on time. View Custom Panels Here.

2. ​​CleanPlex® Ready-to-Use NGS Panels

Our CleanPlex® Ready-to-Use NGS panels are expertly designed to deliver high-performance target enrichment with minimal effort. Powered by our proprietary CleanPlex® technology, these panels use advanced multiplex PCR chemistry to remove non-specific PCR products and maximize sequencing efficiency. With a range of expertly optimized panels for applications like oncology, infectious diseases, and genetic research, CleanPlex Ready-to-Use Panels provide reliable, high-quality data straight out of the box. View Ready-to-Use NGS Panels Here.

Amplicon Sequencing: PCR-Based Enrichment for High Sensitivity and Speed

Amplicon sequencing, in contrast, uses PCR primers to amplify specific DNA fragments before sequencing. Instead of using hybridization probes, this method relies on short, custom-designed primers that flank the genomic regions of interest. These primers initiate polymerase chain reaction (PCR), a process that exponentially amplifies the target regions, producing highly concentrated amplicons ready for sequencing.

Advantages of Amplicon Sequencing

• Fast and Cost-Effective – Eliminates the need for expensive capture probes and reduces the number of sample preparation steps, making it cheaper and faster than hybridization capture.
• Highly Sensitive for Low-Frequency Variants – Can detect rare mutations present in as little as 1% of a DNA sample, making it particularly useful for liquid biopsies and tumor profiling.
• Low DNA Input Requirements – Requires significantly less starting material than hybridization-based methods, making it ideal for FFPE (formalin-fixed, paraffin-embedded) samples or degraded DNA.
• Multiplexing Capabilities – Allows researchers to sequence multiple genomic regions simultaneously, increasing throughput while reducing costs. 

Accelerate Your Research with Paragon Genomics

Whether you are studying genetic diseases, monitoring microbial communities, or validating CRISPR edits, Paragon Genomics provides high-performance amplicon sequencing solutions to support your research. Our cutting-edge technology ensures accurate, reliable, and scalable results to help you achieve your scientific goals with confidence.

Ready to begin your sequencing project? Contact us today to discuss your research needs and explore how our solutions can accelerate your discoveries.