title: Whole Genome Sequencing From Low Input Control Circulating Cell-Free DNA
design: Amplified sequencing libraries were prepared using a three step, library preparation protocol for sequencing plasma ccfDNA . Briefly, 10 uL of eluted ccfDNA at 0.1 ng/uL was used for template preparation, library synthesis and amplification were performed in a single tube with the SMARTer ThruPLEX Plasma Seq Library Preparation protocol according to the manufacturers instructions (Takara Bio USA, Mountain View, CA). NGS libraries were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, Brea, CA) then amplified by a round of PCR (14 cycles) and tagged with Illumina-compatible indexes for multiplex sequencing (SMARTer DNA HT Dual Index Kit, Takara Bio USA). Fragment analysis of the libraries for each sample showed a median sample size of 310 bp (170 bp ccfDNA plus 140 bp adapters) containing library products of the mononucleosomal DNA fragments. Libraries were sequenced on a NovaSeq 6000 (Illumina) S1 platform.