title: WES of head and neck cancer patients
design: Isolated DNA extraction from FFPE samples was performed Mag-Bind FFPE DNA/RNA (OMEGA Bio-Tec, Georgia, USA) per the manufacturers recommendation.Extracted genomic DNA was then quantified with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA)and quality assessed by Tapestation genomic DNA Assay (Agilent Technologies, California, USA). Library preparation was performed using KAPA Hyper Prep kit (Roche, Basel, Switzerland) per manufacturers recommendations. Exome capture was performed with IDT xGen Exome Research Panel v2.0. Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, CA, USA), and QuantStudio  5 System (Applied Biosystems, USA). Illumina 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina Novaseq S4 (Illumina, California, USA) with a read length configuration of 150 PE. Tumor FFPE samples were targeted for 156M PE reads (78M in each direction) and samples originating from buffy coat were targeted 52M PE reads (26M in each direction)