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Megapixel digital PCR

Abstract

We present a microfluidic 'megapixel' digital PCR device that uses surface tension–based sample partitioning and dehydration control to enable high-fidelity single DNA molecule amplification in 1,000,000 reactors of picoliter volume with densities up to 440,000 reactors cm−2. This device achieves a dynamic range of 107, single-nucleotide-variant detection below one copy per 100,000 wild-type sequences and the discrimination of a 1% difference in chromosome copy number.

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Figure 1: Megapixel digital PCR using planar emulsion arrays.
Figure 2: Dynamic range, sensitivity and precision of megapixel digital PCR.

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Acknowledgements

This research was funded by the Canadian Institute for Health Research (Catalyst NHG-91401), Terry Fox Foundation and the Natural Science and Engineering Research Council. Salary support was provided by the Michael Smith Foundation for Health Research (A.S. and C.L.H.), Natural Science and Engineering Research Council Collaborative Research and Training Experience Genome Science and Technology graduate program (M.V.), the Department of Foreign Affairs and International Trade of Canada (K.A.H.) and the Canadian Institute for Health Research Young Investigator program (C.L.H.). Infrastructure support was provided by Genome British Columbia, Genome Canada and Western Economic Diversification Fund.

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Authors

Contributions

K.A.H., C.T., M.V., C.D., A.S., K.L. and C.L.H. developed and optimized the device design. K.A.H. and C.D. developed fabrication protocols and fabricated devices. K.A.H., C.T. and C.D. performed the on-chip digital PCR experiments. K.A.H., O.I.P. and C.B.H. performed the off-chip qPCR experiments. M.V. and C.D. developed image analysis software. K.A.H., C.T., M.V. and C.D. performed data analysis. C.L.H. designed research. K.A.H., C.T., M.V. and C.L.H. wrote the manuscript.

Corresponding author

Correspondence to Carl L Hansen.

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Competing interests

C.L.H. has a financial interest in Fluidigm Corporation, which has products related to the subject matter of this study.

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Supplementary Figures 1–9, Supplementary Tables 1–2 and Supplementary Notes 1–9 (PDF 2853 kb)

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Heyries, K., Tropini, C., VanInsberghe, M. et al. Megapixel digital PCR. Nat Methods 8, 649–651 (2011). https://doi.org/10.1038/nmeth.1640

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