Table 2. Variants unknown by both COSMIC and dbSNP and candidates to be new GBM-related functional somatic mutations.

Gene	Sample	AA change	FATHMM score	SIFT score	COSMIC	AF (Tumor)	Coverage (Tumor)
EGFR	SD01 RNA-seq-only	S229fs	93% (pathogenic)	85.8% (Dam)	No (S229C)	0.045	169
EGFR	SD01 RNA-seq-only	W477fs	51% (neutral)	85.8% (Dam)	No (W477*)	0.046	447
PIK3C2	SD01 WES-only	I255N	−3.49 (CANCER)	0 (Del)	No	0.433	64
CDKN2C	GBM02 RNA-seq-only	V130A	−0.21 (PASSENGER)	0.03 (Del)	No	0.027	470
PDGFRB	GBM02 RNA-seq-only	V840A	−2.34 (CANCER)	0.23 (Tol)	No	0.021	262
RB1	GBM03 RNA-seq-only	L872fs	77% (pathogenic)	85.8% (Dam)	No	0.035	355
EGFR	GBM05 RNA-seq-only	M600T	−1.69 (CANCER)	0.38 (Tol)	No (M600V)	8.1E-03	6,240
EGFR	GBM05 RNA-seq-only	L718R	−2.85 (CANCER)	0 (Del)	No (L718M)	4.5E-03	4,792
PDGFRB	GBM06 RNA-seq-only	Q1075R	−1.25 (CANCER)	0.52 (Tol)	No	0.058	90

Notes:

Variants included in the set of 29 GBM-related genes and not included in COSMIC or dbSNP are shown, although COSMIC contained alternative variants at the same positions for four mutations that were found by RNA-seq-only. For SIFTindel and FATHMM indels, the score is given as a confidence score. AF (tumor) shows the proportion of altered reads in tumor samples, with Coverage (tumor) being the total number of reads at the variant position. Allele Fraction and Coverage was used to further exclude potential artifacts, which are not listed here.

^*Indicates a nonsense mutation.