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Nat Biomed Eng. 2017;1:714-723. doi: 10.1038/s41551-017-0126-5. Epub 2017 Sep 4.

Multiplexed enrichment of rare DNA variants via sequence-selective and temperature-robust amplification.

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Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
Thermo Fisher, San Francisco, CA, 94080, USA.
Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06510, USA.
Department of Bioengineering, Rice University, Houston, TX, 77030, USA.


Rare DNA-sequence variants hold important clinical and biological information, but existing detection techniques are expensive, complex, allele-specific, or don't allow for significant multiplexing. Here, we report a temperature-robust polymerase-chain-reaction method, which we term blocker displacement amplification (BDA), that selectively amplifies all sequence variants, including single-nucleotide variants (SNVs), within a roughly 20-nucleotide window by 1,000-fold over wild-type sequences. This allows for easy detection and quantitation of hundreds of potential variants originally at ≤0.1% in allele frequency. BDA is compatible with inexpensive thermocycler instrumentation and employs a rationally designed competitive hybridization reaction to achieve comparable enrichment performance across annealing temperatures ranging from 56 °C to 64 °C. To show the sequence generality of BDA, we demonstrate enrichment of 156 SNVs and the reliable detection of single-digit copies. We also show that the BDA detection of rare driver mutations in cell-free DNA samples extracted from the blood plasma of lung-cancer patients is highly consistent with deep sequencing using molecular lineage tags, with a receiver operator characteristic accuracy of 95%.

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