Table 2.

Relative power of each method to detect common alterations

Gene	Gene type*	Alteration type	# Samples altered	WES	WGS	SNP array	RNA-Seq
KRAS	OG	Mut	7	7 (100 %)	7 (100 %)	0 (0 %)	7 (100 %)
TP53	TSG	Mut	7	7 (100 %)	7 (100 %)	0 (0 %)	7 (100 %)
		HD	0	na	na	na	na
CDKN2A/p16	TSG	Mut	3	3 (100 %)	3 (100 %)	0 (0 %)	3 (100 %)
		HD	4	4 (100 %)	4** (100 %)	4 (100 %)	4 (100 %)
SMAD4/DPC4	TSG	Mut	2	2 (100 %)	2 (100 %)	0 (0 %)	2 (100 %)
		HD	4	4 (100 %)	4 (100 %)	4 (100 %)	4 (100 %)

^*OG oncogene, TSG tumor suppressor gene, MUT mutation (includes frameshifting indels and point mutations), HD homozygous deletion, WES whole exome sequencing, WGS whole genome sequencing

^**1 p16 mutation was not reported as an alteration by the standard Illumina pipeline, but visualization of the bam file clearly showed a homozygous deletion