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The putative cancer-associated GESPs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).

Summary of the G-score of the putative cancer-causing GESPs driven by SCNAs in each cancer type

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				ACC		BLCA		BRCA		CESC		CHOL		COAD		DLBC		ESCA		GBM		HNSC		KICH		KIRC		KIRP		LAML		LGG		LIHC		LUAD		LUSC		MESO		OV		PAAD		PCPG		PRAD		READ		SARC		SKCM		STAD		TGCT		THCA		THYM		UCEC		UCS		UVM
HGNC Name	Ensembl Gene ID	HGNC Symbol	Genomic Location	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del	Amp	Del
erb-b2 receptor tyrosine kinase 2	ENSG00000141736	ERBB2	chr17:39687914-39730426:+			0.4		0.99						0.25				1.1				0.19														0.19								0.15						0.32						1.06								0.48		0.73
growth factor receptor bound protein 7	ENSG00000141738	GRB7	chr17:39737927-39747291:+			0.38		0.97						0.25				1.1				0.17														0.18								0.15												1.04								0.45		0.66
anoctamin 1	ENSG00000131620	ANO1	chr11:70078302-70189528:+							0.32								2.82																				1.14
Fas associated via death domain	ENSG00000168040	FADD	chr11:70203163-70207390:+							0.32								2.82																				1.13																													0.11
fibroblast growth factor receptor substrate 2	ENSG00000166225	FRS2	chr12:69470349-69579789:+			0.61												0.47				0.26																0.27				0.33		0.11												0.46		0.26								0.57
epidermal growth factor receptor	ENSG00000146648	EGFR	chr7:55019021-55256620:+			0.36				0.19								0.72				0.71														0.24		0.5																		0.33
CDC42 small effector 1	ENSG00000197622	CDC42SE1	chr1:151050971-151070325:-	0.23						0.22		0.43						0.23																		0.44		0.31												0.17		0.45		0.22		0.22		0.13
histocompatibility minor 13	ENSG00000101294	HM13	chr20:31514428-31577923:+			0.33								0.18																						0.13		0.28				0.34								0.23								0.23								1.28
zinc finger DHHC-type containing 11	ENSG00000188818	ZDHHC11	chr5:795606-850986:-	0.81		0.27		0.13		0.22												0.16																0.39				0.48														0.18								0.16
tetraspanin 31	ENSG00000135452	TSPAN31	chr12:57738013-57750211:+	0.44																1.24												0.38				0.33																		0.26
ceramide synthase 2	ENSG00000143418	CERS2	chr1:150960583-150975004:-	0.23						0.22								0.24																		0.44		0.31												0.17		0.44		0.22		0.22		0.13
phosphatidylinositol-4-phosphate 5-kinase type 1 alpha	ENSG00000143398	PIP5K1A	chr1:151197949-151249536:+	0.23						0.22		0.43						0.26																				0.3														0.47		0.22		0.22		0.11
solute carrier family 12 member 7	ENSG00000113504	SLC12A7	chr5:1050376-1112035:-			0.27		0.13														0.16												0.28				0.38				0.48										0.34	0.13			0.18								0.16
CLPTM1 like	ENSG00000049656	CLPTM1L	chr5:1317744-1345099:-			0.26		0.13		0.2								0.38				0.17																0.37				0.48											0.13			0.17								0.15
solute carrier family 39 member 1	ENSG00000143570	SLC39A1	chr1:153959099-153968184:-	0.21						0.19		0.53						0.22																																0.15		0.43		0.21
TM2 domain containing 3	ENSG00000184277	TM2D3	chr15:101621444-101652391:-							0.17								0.21				0.11												0.14				0.27				0.44										0.29		0.2
insulin like growth factor 1 receptor	ENSG00000140443	IGF1R	chr15:98648971-98964530:+					0.27		0.18												0.12																0.26				0.47										0.25		0.21
transmembrane 9 superfamily member 4	ENSG00000101337	TM9SF4	chr20:32109506-32167258:+																																															0.23																1.49
lysosomal associated membrane protein 1	ENSG00000185896	LAMP1	chr13:113297241-113323672:+					0.16		0.23												0.15												0.29		0.12		0.24														0.45
transmembrane and coiled-coil domains 3	ENSG00000150403	TMCO3	chr13:113490995-113554590:+					0.16		0.23												0.15												0.29		0.1		0.23														0.46

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