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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
transmembrane 9 superfamily member 2	ENSG00000125304	TM9SF2	chr13:99501417-99564006:+	0.69	0	4	0
CD72 molecule	ENSG00000137101	CD72	chr9:35609533-35646810:-	0.69	0	2	0
protein kinase C alpha	ENSG00000154229	PRKCA	chr17:66302636-66810743:+	0.68	0	4	0
notch receptor 2	ENSG00000134250	NOTCH2	chr1:119911553-120069626:-	0.68	0.16	3	1
transmembrane protein 67	ENSG00000164953	TMEM67	chr8:93754844-93819234:+	0.67	0	3	0
dpy-19 like 4	ENSG00000156162	DPY19L4	chr8:94719703-94793836:+	0.67	0	3	0
dual specificity phosphatase 15	ENSG00000149599	DUSP15	chr20:31847637-31870747:-	0.67	0	3	0
zinc activated ion channel	ENSG00000186919	ZACN	chr17:76071961-76083666:+	0.67	0	3	0
transmembrane protein 64	ENSG00000180694	TMEM64	chr8:90621995-90791632:-	0.66	0	3	0
potassium calcium-activated channel subfamily M regulatory beta subunit 3	ENSG00000171121	KCNMB3	chr3:179236691-179267002:-	0.65	0	3	0
exocyst complex component 1	ENSG00000090989	EXOC1	chr4:55853616-55905034:+	0.65	0	3	0
ATP binding cassette subfamily A member 5	ENSG00000154265	ABCA5	chr17:69244311-69327244:-	0.64	0	3	0
ethanolamine kinase 1	ENSG00000139163	ETNK1	chr12:22625075-22690665:+	0.64	0	1	0
T cell immune regulator 1, ATPase H+ transporting V0 subunit a3	ENSG00000110719	TCIRG1	chr11:68039016-68050895:+	0.63	0	1	0
ATP binding cassette subfamily C member 9	ENSG00000069431	ABCC9	chr12:21797401-21941402:-	0.62	0	1	0
peripheral myelin protein 22	ENSG00000109099	PMP22	chr17:15229777-15265326:-	0.62	0	1	0
ADAM metallopeptidase domain 15	ENSG00000143537	ADAM15	chr1:155050566-155062775:+	0.61	0	3	0
WW domain containing E3 ubiquitin protein ligase 1	ENSG00000123124	WWP1	chr8:86342738-86478420:+	0.61	0	3	0
calsyntenin 3	ENSG00000139182	CLSTN3	chr12:7129698-7158945:+	0.6	0	1	0
glyceraldehyde-3-phosphate dehydrogenase	ENSG00000111640	GAPDH	chr12:6533927-6538374:+	0.6	0	1	0

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