Post-Treatment Mouse 2
Human patient cell line implanted intracranially into mouse and treated with temozolomide and radiation. After tumor recurrence tumor is sampled and sequenced. Whole exome DNA was extracted following standard protocols. The sequencing libraries were prepared using the KAPA library prep protocol (catalog number KK8234, KAPA Biosystems, Wilmington, MA). The exomes were captured using the SureSelect XT Human All Exon V5 kit (Agilent Technologies, Santa Clara, CA). Samples were then sequenced 2100 bp to about 340 depth on the Illumina HiSeq 2000. The segmented copy number ratios (tumor versus normal) were inferred by applying Sequenza (version 2.1.1) [PMID: 25319062] to whole-exome sequencing data with the default parameters. Log2-transformed copy number segments were plotted over genome wide with copy number amplification as red and copy number loss as blue.