Isolating Genomic and Cell-Free DNA from FFPE and Plasma

Genomic DNA (gDNA) was isolated from FFPEs using the QIAamp^® DNA FFPE Tissue Kit 50 (QIAGEN^®, Hilden, Germany), according to manufacturer instructions. For the plasma, 2 × 5 mL peripheral blood samples were collected in EDTA tubes at the time point of diagnosis, before tumor surgery and before the application of therapeutic substances with an S-Monovette. Blood was centrifuged at 1500× g for 10 min, and the plasma was stored at −80 °C until further analysis. Additionally, cfDNA was extracted from plasma (2 mL) using the QIAamp^® Circulating Nucleic Acid kit 50 (QIAGEN^®, Hilden, Germany), according to the manufacturer’s instructions. The DNA concentration was determined in the Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc., Waltham, MA, USA), as previously described [35 (link)].