Alvarado John, Jacky Lucien, Yurk Dominic, Aguiar Aaron, Belitz Paul, Schwartz Jerrod J
ChromaCode Inc, Carlsbad, CA, USA.
Asari AI, Pasadena, CA, USA.
Sci Rep. 2025 Jul 4;15(1):23947. doi: 10.1038/s41598-025-08814-5.
Polymerase chain reaction (PCR) is an essential tool in research and diagnostics but is limited by the number of resolvable targets, reliance on target-specific probes, and assay-specific data interpretation. To overcome these challenges, we introduce Universal Signal Encoding PCR (USE-PCR), a novel approach combining universal hydrolysis probes, amplitude modulation, multispectral encoding, and standardized analysis for robust, scalable target detection. Using 32 synthetic templates, USE-PCR demonstrates a mean target identification accuracy of 92.6% ± 10.7% at high template copy and 97.6% ± 4.4% at low template copy, with linear correlation coefficients of 0.99 across four dPCR platforms and a dynamic range spanning four orders of magnitude. Integrating USE-PCR with RNase H-based detection chemistry enables 32 single nucleotide variants to be called simultaneously with up to 86.5% accuracy in cancer cell lines. Together, these results position USE-PCR as a transformative platform for high throughput, multiplexed analyte detection with applications in research and clinical settings.
聚合酶链反应（PCR）是研究和诊断中的一项重要工具，但受可分辨靶标的数量、对靶标特异性探针的依赖以及检测方法特定的数据解读的限制。为克服这些挑战，我们引入了通用信号编码PCR（USE-PCR），这是一种结合通用水解探针、幅度调制、多光谱编码以及标准化分析的新方法，用于进行强大、可扩展的靶标检测。使用32种合成模板，USE-PCR在高模板拷贝数时显示出平均靶标识别准确率为92.6%±10.7%，在低模板拷贝数时为�7.6%±4.4%，在四个数字PCR平台上的线性相关系数为0.99，动态范围跨越四个数量级。将USE-PCR与基于核糖核酸酶H的检测化学方法相结合，能够在癌细胞系中同时检测32个单核苷酸变异，准确率高达86.5%。这些结果共同表明，USE-PCR是一个变革性平台，可用于高通量、多重分析物检测，在研究和临床环境中均有应用。
