Frozen tumor tissue was homogenized with bead-beating using the Qiagen TissueLyser II in Qiagen DNeasy Blood and Tissue Kit Buffer ATL with proteinase K added. DNA was isolated with UltraPure phenol:chloroform:isoamyl alcohol isolation. TruSeq PCR-free library preparation was performed prior to Illumina paired-end sequencing to 60x genome coverage for tumor samples and 30x genome coverage for forebrain normal controls.