Hybridization and wash reagents kit

Libraries were constructed using the KAPA Hyper Prep Kit (KAPA Biosystem) with an optimized manufacturer's protocol for different types of samples. In brief, an appropriate amount of cfDNA or fragmented FFPE-derived DNA underwent end-repair, 3′A-tailing, and indexed adapter ligation sequentially, followed by size selection using Agencourt AMPure XP beads (Beckman Coulter). Finally, libraries were amplified by PCR and purified using Agencourt AMPure XP beads.
Hybridization-based target enrichment was carried out with Geneseeq One pan- cancer gene panel (14 cancer-relevant genes) using a Hybridization and Wash Reagents Kit (Integrated DNA Technologies). After hybridization was complete, the captured targets were selected by pulling-down the biotinylated probe/target hybrids using Dynabeads M-270 (Life Technologies). Then, the off-target libraries were washed out. Captured libraries were amplified in KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems) for sequencing.

Genomic DNAs from FFPE sections were extracted with a QIAamp DNA FFPE Tissue Kit and quantified by Qubit 3.0 using the dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, USA). Library preparations were performed with a KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, USA). Target enrichment was performed using the xGen Exome Research Panel v1.0 and Hybridization and Wash Reagents Kit (Integrated DNA Technology, Coralville, USA) according to the manufacturer’s protocol. Sequencing was performed on an Illumina HiSeq 4000 platform using PE150 sequencing chemistry (Illumina, San Diego, USA) to a mean coverage depth of 150× for tumor samples and 50× for matched normal control samples.