Lossless and Contamination-Free Digital PCR

The realization of the vast potential of digital PCR (dPCR), to provide extremely accurate and sensitive measurements in the clinical setting, has thus far been hindered by challenges such as assay robustness and high costs. Existing popular dPCR platforms that target the clinic have not reached wide-spread adoption, due to problems with sample loss and risk of contamination during sample preparation, compartmentalization, and transfers; limitations of dynamic range and signal-to-noise in the result readout also restricts broad applications. Here we introduce a lossless and contamination-free dPCR technology termed CLEAR-dPCR, which addresses these challenges by completing the dPCR sample preparation, PCR reaction, and readout all in one tube. We achieve this by adjusting the refractive index of the aqueous PCR mix to make the emulsion optically transparent, and devised a light-sheet microscope to capture 3D images of the cleared emulsion for results readout. This approach demonstrates improved accuracy over existing dPCR platforms, and enables a greatly increased dynamic range to be comparable to that of real-time quantitative PCR (qPCR). CLEAR-dPCR is an easy to operate, sensitive and accurate dPCR platform that we envision will fulfill the potential of dPCR for routine use clinical diagnosis.