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Chunk #41 — Materials and methods — Microdroplet PCR — Universal PCR

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Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.
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Four microliters of amplicons (2.5 ng/μl), as determined by Agilent BioAnalyzer quantification from the initial droplet PCR, were combined with 2.5 μl 10× High-Fidelity Buffer (Invitrogen, 11304-029), 1.0 μl of MgSO4 50 mM (Invitrogen, 11304-029), 1.13 μl of 10 mM dNTP (New England Biolabs, NO447S/L), 2.5 μl of 4 M Betaine (Sigma, B2629-50G), 2.5 μl of RDT Droplet Stabilizer (RainDance Technologies, 30-00826), 1.25 μl dimethyl sulfoxide (Sigma, D8418-50 ml), 5.0 μl of a 0.5 μl 5 units/μl of Platinum High-Fidelity Taq (Invitrogen, 11304-029), 4.62 μl of Nuclease Free Water (Teknova-Fisher, 50843418) and 1 μM final of each universal primer, incorporating the remaining sequence to the Illumina adapter for cluster generation and sequencing. Samples were amplified in a Bio-Rad PTC-225 thermal cycler as follows: initial denaturation at 94°C for 2 minutes; 8 cycles at 94°C for 15 seconds, 56°C for 15 seconds and 68°C for 30 seconds; final extension at 68°C for 10 minutes, followed by a 4°C hold. Each sample was purified over a MinElute column (Qiagen, 28004) following the manufacturer's recommended protocol. The sample was eluted from the column