Traditional PCR workflows require users to predefine the number of amplification cycles based on input quantity and assay type. This rigid framework is particularly problematic for formalin-fixed, paraffin-embedded (FFPE) samples, where nucleic acid degradation leads to highly variable input quality and unpredictable amplification efficiency. As a result, accurate quantification becomes difficult, often necessitating multiple thermocycler runs, grouped by input amount and integrity, along with labor-intensive pre- and post-PCR quality control steps. iconPCR, developed by n6, introduces a paradigm shift in PCR amplification through its AutoNorm technology. By monitoring fluorescence in real-time, iconPCR automatically terminates each individual reaction once a predefined amplification threshold is reached. This per-sample, real-time control eliminates the need for fixed-cycle settings and standardizes output across samples, regardless of input variability or degradation level. For FFPE and other challenging inputs, iconPCR dramatically simplifies workflows, reduces batch effects, and enhances the consistency and quality of sequencing libraries — enabling more efficient and accurate downstream analysis in both research and clinical settings.

Here we present two studies showcasing workflow and data quality improvements for FFPE NGS preparations:

Study 1: Optimized whole genome sequencing of FFPE samples
Study 2: Effect of overamplification during RNAseq of FFPE samples

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