Amplicon Sequencing in Cancer Genomics: Uncovering Mutations

The Role of Amplicon Sequencing in Cancer Genomics

Cancer is driven by somatic mutations that can vary from patient to patient, and pinpointing these mutations is crucial for tailoring treatment. NGS sequencing has revolutionized the ability to profile tumors by uncovering key mutations. Specifically, amplicon-based targeted sequencing offers a powerful approach to identify these genetic changes efficiently.

Compared to hybrid capture sequencing methods, which may struggle with low DNA samples or low-frequency mutations, PCR amplification in amplicon sequencing allows for greater sensitivity in detecting mutations within tumor DNA. This method is also more cost-effective, making it a popular choice in routine cancer diagnostics and research.

Uncovering Mutations with Amplicon Sequencing

One of the most significant benefits of amplicon sequencing is its ability to uncover mutations in small quantities of DNA, such as in circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs). This is especially useful for liquid biopsies and monitoring cancer progression with minimal invasion.

Target sequences from specific regions of interest can be amplified and sequenced using PCR amplification, allowing for the identification of mutations at very low frequencies. In cases like small cell lung cancer or breast cancer, these rare somatic mutations can be subtle yet have a profound impact on treatment decisions. Amplicon sequencing shines here because of its high sensitivity, enabling it to detect mutations even when normal cells are mixed in the sample.

CleanPlex DNA and RNA Amplicon Sequencing: A Game-Changer in Cancer Research

At the forefront of amplicon sequencing technology is CleanPlex DNA and RNA Technology. Developed by Paragon Genomics, this multiplex PCR-based method offers a streamlined workflow that can process tumor DNA from a variety of sample types, including FFPE tissues and liquid biopsies. The entire process can be completed in just 3 hours, making it an ideal tool for cancer research and diagnostics.

CleanPlex Custom NGS Panels allow researchers to focus on specific cancer genes or create bespoke panels that suit their research needs. This flexibility has made CleanPlex popular in studies targeting small cell lung cancer, breast cancer, and other forms of cancer, allowing for the discovery of key mutations that guide personalized medicine.

In addition to DNA sequencing, CleanPlex RNA Technology adds a step to convert RNA into cDNA, opening doors to gene expression analysis and cancer fusion gene detection. These insights into the genetic architecture of cancers are essential for advancing both research and treatment.

Key Applications of CleanPlex Technology in Cancer Research

• Genomic Profiling of Circulating Tumor Cells (CTCs): Circulating tumor cells provide a non-invasive way to monitor cancer, and amplicon-based targeted sequencing has proven especially useful in analyzing the genetic material of these cells. In a collaboration with Mayo Clinic, CleanPlex OncoZoom Cancer Hotspot Panel was used to analyze circulating tumor DNA and CTCs, resulting in highly sensitive and accurate genomic profiles.
• Homologous Recombination Deficiency (HRD): HRD impairs a cell’s ability to repair DNA breaks, leading to genomic instability and cancer progression. At Paragon Genomics, we’ve developed custom HRD panels that assess genomic scarring and HRD status, crucial for guiding treatment choices. Comprehensive genomic profiling (CGP) with next-generation sequencing facilitates this evaluation, particularly relevant in ovarian, breast, prostate, and pancreatic cancers. This approach not only informs the use of PARP inhibitors but also aids in identifying candidates for clinical trials, enhancing personalized cancer treatment strategies.

Deep Sequencing and the Future of Cancer Precision Medicine

As cancer research advances, the need for deeper insights into tumor DNA becomes increasingly pressing. Deep sequencing through methods like massively parallel sequencing enables researchers to explore a patient’s genetic landscape more thoroughly, identifying rare mutations and other genetic alterations that may go undetected with less sensitive methods.

Explore Our Oncology Publications

Paragon Genomics actively contributes to advancing cancer research through a variety of groundbreaking studies. From exploring the synergistic antitumor effects of liposomal-based formulations to investigating genetic mutations in breast cancer and the molecular diversity of juvenile myelomonocytic leukemia, our publications reflect our dedication to precision medicine. Discover how our work is shaping the future of oncology research by exploring our Oncology Publications Here.

Paragon Genomics: Empowering Precision Medicine with CleanPlex Technology

In the rapidly evolving field of cancer genomics, the ability to identify and understand somatic mutations through techniques like amplicon sequencing is essential for driving innovation in personalized medicine. Paragon Genomics’ CleanPlex Technology provides researchers and clinicians with the tools they need to uncover the unique genetic makeup of cancers, ensuring that treatments can be tailored to each patient’s specific disease profile. As the future of cancer research continues to unfold, amplicon sequencing remains a cornerstone in uncovering mutations and advancing precision medicine.