From Sample to Insight: Technologies Driving the Future of Precision Oncology Assays
Targeted NGS (tNGS): Multiplex Power for Broader Profiling Targeted next-generation sequencing (tNGS) is a high-throughput sequencing method that focuses on specific genes or genomic regions of interest. While widely used in oncology, tNGS is also applied in areas such as inherited disease testing, pharma- cogenomics, and infectious disease surveillance. In cancer diagnostics, it enables the simultaneous analysis of dozens to hundreds of genes, offering
• Hybrid-capture sequencing relies on probe- based enrichment to capture longer stretches of DNA. This method provides greater uniformity of coverage and higher sensitivity for detecting complex genomic alterations, such as gene fusions, copy number variations, and rearrange- ments. It is preferred for broader panels or when comprehensive variant detection is required. tNGS is central to many commercial oncology panels ( Table 2 ) and liquid biopsy assays due to its flexibility, scalability, and ability to evolve alongside emerging biomarkers. Its broad multi- plexing capacity allows developers to consolidate dozens—or even hundreds—of targets into a single assay, improving efficiency and conserving precious sample material. This is especially important in oncology, where tumor biopsies are often small, degraded, or difficult to obtain. By enabling simultaneous detection of multiple mutation types from minimal input, tNGS supports comprehensive molecular profiling without the need for multiple tests or repeat procedures. However, tNGS also comes with challenges. It requires high-quality nucleic acid input, which can be difficult to obtain from formalin-fixed, paraffin-embedded (FFPE) tissue or low-yield liquid
broader mutation coverage than single-target assays while keeping data interpretation and cost manageable. tNGS can detect a wide range of variant types, including single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations, and gene fusions—and supports appli- cations such as tumor profiling, minimal residual disease (MRD) monitoring, and therapy selection. 3.4 There are two common approaches to tNGS, each offering distinct advantages depending on the assay’s goals and complexity ( Figure 1 ): • Amplicon-based sequencing uses PCR ampli- fication to target specific regions of interest. It is typically faster, requires less DNA input, and is more cost-effective, making it well-suited for focused panels with known hotspots. However, it may have limited sensitivity for detecting structural variants or alterations in regions with high GC content.
Figure 1 . Hybrid-capture and amplicon-based targeted next-generation sequencing (tNGS) workflows.
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