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Copy Number

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).

Pan-cancer level overall G-score of GESPs that recurrently gained or lost copy number in at least one cancer types

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				Overall_Gscore		No. of Cancer Types
HGNC Name	Ensembl Gene ID	HGNC Symbol	Genomic Location	Amplification	Deletion	Amplification	Deletion
Rho related BTB domain containing 2	ENSG00000008853	RHOBTB2	chr8:22987417-23020199:+	0	1.16	0	7
TYRO3 protein tyrosine kinase	ENSG00000092445	TYRO3	chr15:41557675-41583586:+	0	1.16	0	5
TNF receptor superfamily member 10a	ENSG00000104689	TNFRSF10A	chr8:23190452-23225126:-	0	1.15	0	7
solute carrier family 39 member 14	ENSG00000104635	SLC39A14	chr8:22367249-22434129:+	0	1.14	0	7
ATPase Na+/K+ transporting subunit beta 2	ENSG00000129244	ATP1B2	chr17:7646627-7657768:+	0	1.12	0	3
ras homolog family member A	ENSG00000067560	RHOA	chr3:49359145-49412998:-	0	1.1	0	6
transmembrane protein 259	ENSG00000182087	TMEM259	chr19:1009648-1021179:-	0	1.09	0	3
enolase 1	ENSG00000074800	ENO1	chr1:8861002-8879249:-	0	1.09	0	6
ADP ribosylation factor like GTPase 4C	ENSG00000188042	ARL4C	chr2:234493041-234497053:-	0	1.07	0	4
chromosome 6 open reading frame 120	ENSG00000185127	C6orf120	chr6:169702190-169704856:+	0	1.06	0	4
radixin	ENSG00000137710	RDX	chr11:110174880-110296722:-	0	1.05	0	6
SID1 transmembrane family member 2	ENSG00000149577	SIDT2	chr11:117178733-117197445:+	0	1.05	0	5
insulin receptor substrate 1	ENSG00000169047	IRS1	chr2:226731317-226799759:-	0	1.04	0	4
toll like receptor 3	ENSG00000164342	TLR3	chr4:186069152-186088069:+	0	1.04	0	6
integral membrane protein 2C	ENSG00000135916	ITM2C	chr2:230864639-230879248:+	0	1.02	0	4
ring finger protein 26	ENSG00000173456	RNF26	chr11:119334527-119337313:+	0	1	0	5
suppression of tumorigenicity 14	ENSG00000149418	ST14	chr11:130159562-130210376:+	0	1	0	5
angio associated migratory cell protein	ENSG00000127837	AAMP	chr2:218264123-218270257:-	0	0.95	0	5
MARVEL domain containing 2	ENSG00000152939	MARVELD2	chr5:69415112-69444330:+	0	0.94	0	2
solute carrier family 39 member 9	ENSG00000029364	SLC39A9	chr14:69398015-69462388:+	0	0.94	0	5

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