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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
attractin	ENSG00000088812	ATRN	chr20:3471040-3651122:+	0.39	0	2	0
ATP binding cassette subfamily C member 5	ENSG00000114770	ABCC5	chr3:183919934-184018015:-	0.39	0	2	0
adaptor related protein complex 2 subunit mu 1	ENSG00000161203	AP2M1	chr3:184174689-184184091:+	0.39	0	2	0
abhydrolase domain containing 2, acylglycerol lipase	ENSG00000140526	ABHD2	chr15:89087459-89202360:+	0.39	0	2	0
chloride voltage-gated channel 2	ENSG00000114859	CLCN2	chr3:184346185-184361651:-	0.39	0.1	2	1
EPH receptor B3	ENSG00000182580	EPHB3	chr3:184561784-184582409:+	0.39	0	2	0
immunoglobulin superfamily member 8	ENSG00000162729	IGSF8	chr1:160091340-160098943:-	0.38	0	2	0
vomeronasal 1 receptor 1	ENSG00000178201	VN1R1	chr19:57454790-57457142:-	0.38	0.18	2	1
G protein-coupled receptor 132	ENSG00000183484	GPR132	chr14:105049389-105065445:-	0.37	0	1	0
immunoglobulin superfamily member 9	ENSG00000085552	IGSF9	chr1:159927039-159945604:-	0.37	0	2	0
transmembrane protein 117	ENSG00000139173	TMEM117	chr12:43835967-44389762:+	0.37	0	1	0
leucine rich repeat and fibronectin type III domain containing 4	ENSG00000173621	LRFN4	chr11:66856647-66860475:+	0.36	0	2	0
solute carrier organic anion transporter family member 5A1	ENSG00000137571	SLCO5A1	chr8:69667047-69835064:-	0.36	0	2	0
insulin receptor	ENSG00000171105	INSR	chr19:7112255-7294034:-	0.36	0	1	0
serine incorporator 3	ENSG00000132824	SERINC3	chr20:44496221-44522109:-	0.36	0	2	0
aspartate beta-hydroxylase	ENSG00000198363	ASPH	chr8:61500556-61714640:-	0.34	0	2	0
fibroblast growth factor receptor 4	ENSG00000160867	FGFR4	chr5:177086886-177098144:+	0.34	0	1	0
protein tyrosine phosphatase receptor type A	ENSG00000132670	PTPRA	chr20:2864184-3039076:+	0.34	0	1	0
lectin, mannose binding 2	ENSG00000169223	LMAN2	chr5:177331562-177351852:-	0.34	0.11	1	1
solute carrier family 34 member 1	ENSG00000131183	SLC34A1	chr5:177379235-177398848:+	0.34	0	1	0

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