WXS of human HNSCC PDXs: Unknown HPV positive
Whole exome sequencing of PDXs was performed from snap-frozen tissue using the Illumina HiSeq (2x150bp) platform. Genomic DNA extraction was performed with Qiagen QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) per the manufacturers recommendation. DNA was quantified with Qubit 2.0 DNA HS Assay (Thermo) and quality-assessed by Tapestation genomic DNA assay (Agilent Technologies, Santa Clara, CA). Library preparation was performed using KAPA Hyper Prep kit (KAPA Biosystems, Wilmington, MA) per manufacturers instructions. Exome capture was performed with IDT xGen Exome Research Panel v1.0 (IDT, Skokie, IL). Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (Thermo), Tapestation High Sensitivity D1000 Assay (Agilent), and QuantStudio 5 System (Applied Biosystems, Foster City, CA).