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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
mucin 20, cell surface associated	ENSG00000176945	MUC20	chr3:195720882-195741123:+	0.19	0	1	0
potassium voltage-gated channel subfamily Q member 2	ENSG00000075043	KCNQ2	chr20:63400210-63472677:-	0.19	0	1	0
milk fat globule EGF and factor V/VIII domain containing	ENSG00000140545	MFGE8	chr15:88898683-88913411:-	0.19	0	1	0
semaphorin 4C	ENSG00000168758	SEMA4C	chr2:96859716-96870757:-	0.19	0	1	0
lysosomal associated membrane protein 3	ENSG00000078081	LAMP3	chr3:183122213-183163839:-	0.19	0	1	0
discs large MAGUK scaffold protein 1	ENSG00000075711	DLG1	chr3:197042560-197299300:-	0.19	0.12	1	1
potassium calcium-activated channel subfamily M regulatory beta subunit 2	ENSG00000197584	KCNMB2	chr3:178272932-178844429:+	0.19	0	1	0
annexin A13	ENSG00000104537	ANXA13	chr8:123680794-123737407:-	0.19	0	1	0
CUB and Sushi multiple domains 3	ENSG00000164796	CSMD3	chr8:112222928-113437099:-	0.19	0	1	0
synaptic vesicle glycoprotein 2B	ENSG00000185518	SV2B	chr15:91099950-91301309:+	0.19	0	1	0
transmembrane protein 127	ENSG00000135956	TMEM127	chr2:96248516-96265994:-	0.19	0	1	0
CD82 molecule	ENSG00000085117	CD82	chr11:44564427-44620363:+	0.19	0	1	0
interleukin 2 receptor subunit alpha	ENSG00000134460	IL2RA	chr10:6010689-6062325:-	0.19	0	1	0
interleukin 15 receptor subunit alpha	ENSG00000134470	IL15RA	chr10:5937569-5978187:-	0.19	0	1	0
kirre like nephrin family adhesion molecule 1	ENSG00000183853	KIRREL	chr1:157993273-158100262:+	0.19	0	1	0
solute carrier family 9 member A3	ENSG00000066230	SLC9A3	chr5:473310-524332:-	0.18	0	1	0
chromosome 19 open reading frame 18	ENSG00000177025	C19orf18	chr19:57958437-57974534:-	0.18	0	1	0
symplekin	ENSG00000125755	SYMPK	chr19:45815410-45863290:-	0.18	0.49	1	2
cytohesin 2	ENSG00000105443	CYTH2	chr19:48469032-48482314:+	0.18	0.54	1	2
potassium inwardly rectifying channel subfamily J member 14	ENSG00000182324	KCNJ14	chr19:48455509-48466980:+	0.18	0.33	1	1

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