Table 2.

Most frequently altered GBM CAN-genes. All CAN-genes are listed in table S7.

Point mutations * Amplifications Homozygous deletions
GeneNo. of tumorsFraction of tumors (%)No. of tumorsFraction of tumors (%)No. of tumorsFraction of tumors (%)Fraction of tumors with any alteration (%)Passenger probability
CDKN2A 0/22 0 0/22 0 11/22 50 50 <0.01
TP53 37/105 35 0/22 0 1/22 5 40 <0.01
EGFR 15/105 14 5/22 23 0/22 0 37 <0.01
PTEN 27/105 26 0/22 0 1/22 5 30 <0.01
NF1 16/105 15 0/22 0 0/22 0 15 0.04
CDK4 0/22 0 3/22 14 0/22 0 14 <0.01
RB1 8/105 8 0/22 0 1/22 5 12 0.02
IDH1 12/105 11 0/22 0 0/22 0 11 <0.01
PIK3CA 10/105 10 0/22 0 0/22 0 10 0.10
PIK3R1 8/105 8 0/22 0 0/22 0 8 0.10
  • * Fraction of tumors with point mutations indicates the fraction of mutated GBMs out of the 105 samples in the Discovery and Prevalence Screens. CDKN2A and CDK4 were not analyzed for point mutations in the Prevalence Screen because no sequence alterations were detected in these genes in the Discovery Screen.

  • Fraction of tumors with amplifications and deletions indicates the number of tumors with these types of alterations in the 22 Discovery Screen samples.

  • Passenger probability indicates the probability obtained using the average of the lower and upper bound background mutation rates (12).