Whole genome sequencing of sample collected from patient MEA254 at time of diagnosis timepoint.
WGS libraries from FFPE-derived genomic DNA (10-250 ng input) were prepared in-house using the NEBNext UltraShear FFPE DNA Library Prep Kit (E6655S). FFPE DNA was first repaired using the NEBNext FFPE Repair Mix v2 following the default protocol to address the fragmentation and chemical modifications characteristic of FFPE-extracted material. A 15-minute enzymatic fragmentation step and limited PCR amplification were performed per manufacturer recommendations to maximize library preparation efficiency. NEBNext Multiplex Oligos for Illumina Unique Dual Index UMI Adaptors DNA Set 1 (E7395S) were used for dual-indexed library preparation. Library size was assessed using an Agilent 4200 TapeStation System with High Sensitivity D1000 ScreenTape; concentration was measured with KAPA Library Quantification Kits (KK4824) on a QuantStudio 5 instrument.