Table 2. Genes that are either enriched or depleted in the NCI-60), and are cancer-driver genes^a.

			Variant identification and effect
Gene nameb	Functional categoryc	AA impactd	Unique identifierd	dbSNP IDe	NCI-60/ESP5400 frequencyf
TP53	Tumor suppressor, DDR, Apoptosis	R116Q	chr17:7577538_C_T	rs11540652	538
PIK3CA	Oncogene, Protein kinase		chr3:178928178_C_T		472
TET2	Tumor suppressor	S460F	chr4:106156478_C_T		358
NCOR1		R121C	chr17:16075191_G_A	rs140151735	358
GATA2	Oncogene	V211V	chr3:128204808_G_C		358
SETBP1		V81V	chr18:42281554_G_A		179
ASXL1	Tumor suppressor	A611T	chr20:31022346_G_A		179
APC	Tumor suppressor, Apoptosis	S140G	chr5:112103053_A_G	rs150973053	179
ARID1A	Tumor suppressor	R1053H	chr1:27094450_G_A		179
ARID1B		A1922A	chr6:157528080_G_T		179
PRDM1	Tumor suppressor	A385V	chr6:106553591_C_T		179
ACVR1B		D502D	chr12:52387882_C_T		179
ASXL1	Tumor suppressor	T557T	chr20:31021672_C_T		179
SMARCB1	Tumor suppressor	E201D	chr22:24158958_G_T	rs142218902	179
BAP1	Tumor suppressor		chr3:52439102_C_A	rs186001194	179
BRCA2	Tumor suppressor, DDR, Apoptosis	R2784Q	chr13:32944558_G_A	rs80359076	179
MSH2	Tumor suppressor, DDR	E198E	chr2:47637460_A_G		179
CDH1	Tumor suppressor	V391V	chr16:68847251_C_T	rs148080550	179
RUNX1	Tumor suppressor	V137V	chr21:36252870_G_A		179
MLH1	Tumor suppressor, DDR	E219A	chr3:37067468_A_C		179
TSC1	Tumor suppressor, Protein kinase, Apoptosis		chr9:135782112_C_T		179
BRCA2	Tumor suppressor, DDR, Apoptosis	R2896C	chr13:32950860_C_T		179
NCOR1		S1867S	chr17:15961885_G_A		179
ARID1B		D1713D	chr6:157527453_C_T	rs189662115	179
NF1	Tumor suppressor	L1954L	chr17:29661968_T_C		179
TP53	Tumor suppressor, DDR, Apoptosis	G113S	chr17:7577548_C_T	rs28934575	179
DNMT1		S809S	chr19:10260240_C_T		179
ABL1	Oncogene, Protein kinase, Apoptosis	P986P	chr9:133760635_A_G	rs35445683	179
ATM	Tumor suppressor, DDR, Apoptosis	R32C	chr11:108098524_C_T	rs148061139	179
PTCH1	Tumor suppressor		chr9:98241268_G_A		179
NOTCH2	Tumor suppressor, Apoptosis	H1160R	chr1:120479948_T_C	rs142876168	179
SETBP1		Q1244R	chr18:42533036_A_G		179
SETBP1		P256P	chr18:42530073_C_T	rs141858699	179
NF1	Tumor suppressor	A2596V	chr17:29684089_C_T		179
APC	Tumor suppressor, Apoptosis		chr5:112154629_C_T		179
CDC73	Tumor suppressor		chr1:193091510_G_A		179
MSH2	Tumor suppressor, DDR	D487E	chr2:47690244_C_G	rs35107951	179
ARID1A	Tumor suppressor	A1136A	chr1:27098992_G_A	rs146598030	179
ATM	Tumor suppressor, DDR, Apoptosis	R337C	chr11:108117798_C_T	rs138398778	179
ALK	Oncogene	L9L	chr2:30143499_G_C	rs4358080	0.092
KDM6A	Tumor suppressor		chrX:44913052_T_A	rs5952285	0.066
SMARCA4	Tumor suppressor	D1599D	chr19:11170839_T_C	rs7275	0.063

^aGenes selected from the boxed fractions from Figure 3A. Cancer-driver genes are as described previosly [58].

^bOfficial gene names as defined by the HUGO Gene Nomenclature Committee (http://www.genenames.org/).

^cDDR is DNA damage response, and SLC is solute carrier.

^dAmino acid impact. Example, R116Q indicates a change from R (Arg, arginine) to Q (Gln, glutamine).

^dDenotes the chromosome number, start location, and the nucleotide change. _* indicates that either an addition (+) or a deletion (−) of nucleotides.

^eSingle nucleotide polymorphisms identifiers as defined at dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/).

^fFrequency calculated as described in Materials and Methods.