FFPE DNA Extraction and Characterization

DNA was isolated from formalin fixed, paraffin-embedded (FFPE) samples following the manufacturer’s protocol for AllPrep DNA/RNA FFPE kit (Qiagen, Hilden, Germany) as previously described [23 (link), 24 (link)]. Tumor and adjacent normal regions were identified on H&E stained slides and aligned to tissue paraffin blocks. An 18-gauge sterile needle was used to core 2–4 samples from each region. Deparaffinization was performed using the xylene/ethanol method with the only modification being that samples were digested using proteinase K at 56 °C for 20–24 min. DNA isolation was then completed using the Allprep Isolation kit (Qiagen, Hilden, DE) following manufacturer protocol. Each sample was analyzed using a Nanodrop spectrophotometer for purity (260:230 and 260:280 ratios) and concentration was determined using 1uL of sample with the Qubit 2.0 Fluorometer and measured with a bioanalyzer as described [25 (link)]. DNA extraction for MDA8788–6 cell line was performed using Wizard® Genomic DNA Purification Kit (Promega, Madison, WI).