Targeted NGS of FFPE and Liquid Biopsies

For targeted NGS, DNA extraction and sequencing libraries were prepared according to protocols described previously^{47 (link)}. Briefly, genomic DNA was extracted from FFPE tumor and liquid biopsies using a QIAamp DNA FFPE Tissue Kit and a QIAamp Circulating Nucleic Acid kit (Qiagen), respectively. Library preparations were performed using the KAPA Hyper Prep Kit (KAPA Biosystems). Target enrichment was performed using the xGen lockdown probes targeting 425 cancer-related genes (Geneseeq Prime). The target-enriched libraries were quantified by qPCR using the KAPA Library Quantification kit (KAPA Biosystems) and sequenced on HiSeq NGS platforms (Illumina) to generate 2 × 150-bp reads following the manufacturer’s instructions.