WGS of blood plasma cfDNA: LuCaP 136 PDX
The collected PDX mouse-derived blood plasma was fractionated using serial and controlled centrifugation steps (2500g for 10 minutes followed by a 16000g spin for another 10 minutes). The QIAamp Circulating Nucleic Acid Kit was used to isolate cfDNA from PDX mouse-derived plasma using standard protocol. NGS libraries were prepared with 50ng input cfDNA into the KAPA hyperprep kit (Roche, Basel, Switzerland), adopting nine cycles of amplification and using the KAPA UDI dual indexed library adapters. Libraries were sequenced using either Illumina HiSeq 2500 (200 cycles) or Illumina NovaSeq 6000 (300 cycles). To match with Illumina HiSeq 2500 data, truncated 200 cycles FASTQ files were generated (100 bp paired end reads). Aligned data from multiple replicates were merged.