Table 1.

Fixed effect formulas used for each MEM model and their corresponding figures or data file

Fixed effects	Figures
IDH_mutation	Fig. 2c, d, Supplementary Fig. 3a–e
EGFR_cnv+EGFR_mut+CDKN2A_cnv+NF1_cnv+NF1_mut+TP53_cnv+TP53_mut+PTEN_cnv+PTEN_mut	Supplementary Fig. 5a
EGFR_cnv	Supplementary Fig. 5b, c
NF1_cnv*EGFR_cnv	Supplementary data 2
CDKN2A_cnv*EGFR_cnv	Fig. 5c, d, Supplementary Fig. 5d, e
TP53_cnv*EGFR_cnv	Supplementary data 2
Pathway-based classification	Supplementary data 2

* denotes both terms as single effects and an interacting term (ex. IDH_mut*EGFR_cnv= IDH_mut+ EGFR_cnv + IDH_mut:EGFR_cnv. “Mut” indicates mutation status (mutated versus wild type) and “cnv” indicates copy number variation.