Target enrichment panels have become indispensable tools in high-resolution molecular profiling. They are widely used across applications such as oncology, prenatal diagnostics, and pathogen surveillance. A recent study validated a targeted sequencing panel covering 61 cancer-related genes across 43 clinical samples. The panel detected 794 mutations, including all 92 known variants confirmed by orthogonal methods, achieving 99.99% repeatability and 99.98% reproducibility. What set this apart was its ability to deliver highly consistent results across different sample types, something many previous panels struggled with, especially when working with low-quality or limited samples. This breakthrough provides clinicians with a more reliable and sensitive tool for genomic profiling, enabling better-informed treatment decisions in precision oncology.

These workflows rely on isolating and amplifying specific regions of interest from samples that are often limited and complex. The accuracy and consistency of these assays depend critically on proper PCR clean-ups.

Image credit: https://www.researchgate.net/figure/Overview-of-the-main-steps-in-Next-Generation-Sequencing-workflow_fig1_282061980 

PCR amplification, alongside the target amplicons, often contains by-products such as primer dimers, nonspecific fragments, and residual enzymes, all of which can complicate downstream analysis. Adding to this, high molecular weight genomic DNA (gDNA) can enter the sample during collection, storage, or cell lysis. Even when present in trace amounts, gDNA poses a disproportionate risk to assays that rely on detecting low-frequency variants or subtle biological signals.

In oncology, where circulating tumor DNA (ctDNA) may represent less than one percent of total cfDNA, this contamination can mask or distort variant allele frequencies to the point of generating false negatives or spurious calls. Similarly, in non-invasive prenatal testing, the fetal fraction’s subtle signals are easily diluted by maternal gDNA, compromising sensitivity and accuracy. These are not theoretical concerns; they are challenges encountered daily in labs striving for precision and reproducibility.

Fragment size selection is critical for PCR cleanup. By selectively enriching for amplicons within a defined size range, laboratories can reduce amplification bias introduced by preferential polymerase activity on shorter fragments, thereby maintaining uniform representation across all target loci. This control over fragment distribution enhances library complexity and improves cluster density during sequencing, which is particularly critical in high-depth NGS panels designed to detect low-frequency variants. Moreover, precise exclusion of high molecular weight genomic DNA minimizes stochastic noise, stabilizes variant allele frequency measurements, and prevents confounding signals in sensitive applications such as liquid biopsy or non-invasive prenatal testing. Size selection also preserves the structural integrity of diagnostically relevant fragments, facilitating secondary analyses including nucleosome footprinting, chromatin accessibility mapping, and methylation profiling. 

Tools like CamSelect NGS provide programmable control over fragment thresholds, offering reproducible, high-resolution enrichment that aligns precisely with assay-specific requirements. CamSelect NGS is optimized for precise PCR clean-up and size selection of fragments below 1 kb. It works through a suspension of magnetic beads in a specialized polymer and inorganic salt solution, which imparts a size-dependent affinity for nucleic acids: fragments above a defined threshold preferentially bind to the beads, while smaller or unwanted components remain in solution. This reversible binding allows laboratories to selectively retain or remove DNA or RNA sequences based on their size, effectively eliminating primers, adapters, short fragments, and residual enzymes while preserving diagnostically relevant molecules. The overall workflow involves combining the sample with the CamSelect reagent, allowing the desired fragments to interact with the beads, performing magnetic separation and washes to remove contaminants, and finally eluting the purified, size-selected nucleic acids for downstream applications such as next-generation sequencing. 

For a more detailed protocol, go here.

For laboratories implementing target enrichment workflows, the future of PCR clean-up is moving toward highly precise, reproducible, and automation-ready strategies that directly impact assay performance. Tools like CamSelect simplify this process by efficiently removing unwanted fragments and preserving the DNA that matters most, helping labs generate cleaner libraries and more reliable results. See how CamSelect can make PCR clean-up faster, easier, and more consistent in your workflows. Learn more here.