Exome sequencing of UT-SCC-42B
Genomic DNA was extracted from early-passage cells using a QIAamp DNA Blood Mini Kit (Qiagen; Hilden, Germany) and assessed electrophoretically and by Qubit high-sensitivity double-stranded DNA assay (Thermo Fisher Scientific). Exome libraries were prepared from 1 g DNA using the SureSelectXT2 system (Agilent Technologies) with v4 chemistry following the manufacturers protocol and sequenced on a NextSeq500 (Illumina; San Diego, CA) using high-output, 2150 bp flow cells. Reads were aligned to hg19 using BWA-MEM with default parameters and variants called using VarScan-2 mpileup2snp/indel specifying maximum depth 500, mapping quality 15, base quality 10, coverage 20, reads2 4 and variant frequency 0.1.