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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
prostate stem cell antigen	ENSG00000167653	PSCA	chr8:142670308-142682724:+	0.24	0	1	0
Lck interacting transmembrane adaptor 1	ENSG00000203896	LIME1	chr20:63736283-63739103:+	0.24	0	2	0
mannose receptor C type 2	ENSG00000011028	MRC2	chr17:62627401-62693597:+	0.24	0	1	0
nectin cell adhesion molecule 2	ENSG00000130202	PVRL2	chr19:44846175-44889228:+	0.24	0.46	1	2
PVR cell adhesion molecule	ENSG00000073008	PVR	chr19:44643798-44663583:+	0.24	0.45	1	2
notch receptor 3	ENSG00000074181	NOTCH3	chr19:15159038-15200981:-	0.23	0	1	0
integrin subunit beta 4	ENSG00000132470	ITGB4	chr17:75721328-75757818:+	0.23	0	1	0
prostate transmembrane protein, androgen induced 1	ENSG00000124225	PMEPA1	chr20:57648392-57711536:-	0.23	0	1	0
neurofibromin 2	ENSG00000186575	NF2	chr22:29603556-29698598:+	0.23	0.26	1	1
sarcoglycan beta	ENSG00000163069	SGCB	chr4:52020706-52038482:-	0.23	0	1	0
LMBR1 domain containing 2	ENSG00000164187	LMBRD2	chr5:36098412-36151961:-	0.23	0	1	0
semaphorin 6A	ENSG00000092421	SEMA6A	chr5:116443616-116574934:-	0.23	0	1	0
potassium voltage-gated channel subfamily C member 3	ENSG00000131398	KCNC3	chr19:50311937-50333515:-	0.23	0.32	1	1
V-set and immunoglobulin domain containing 10 like	ENSG00000186806	VSIG10L	chr19:51331536-51342124:-	0.23	0	1	0
SH3 and multiple ankyrin repeat domains 1	ENSG00000161681	SHANK1	chr19:50661827-50719450:-	0.23	0	1	0
interleukin 6 receptor	ENSG00000160712	IL6R	chr1:154405193-154469450:+	0.22	0	1	0
erb-b2 receptor tyrosine kinase 3	ENSG00000065361	ERBB3	chr12:56079857-56103505:+	0.22	0	1	0
phosphoprotein membrane anchor with glycosphingolipid microdomains 1	ENSG00000076641	PAG1	chr8:80967810-81112068:-	0.22	0	1	0
lymphocyte antigen 96	ENSG00000154589	LY96	chr8:73991352-74029087:+	0.22	0	1	0
junctophilin 1	ENSG00000104369	JPH1	chr8:74234700-74321328:-	0.22	0	1	0

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