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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
adrenoceptor alpha 1A	ENSG00000120907	ADRA1A	chr8:26748150-26867273:-	0	0.11	0	1
protein O-mannosyltransferase 2	ENSG00000009830	POMT2	chr14:77274956-77320884:-	0	0.11	0	1
vascular cell adhesion molecule 1	ENSG00000162692	VCAM1	chr1:100719742-100739045:+	0	0.11	0	1
cadherin 13	ENSG00000140945	CDH13	chr16:82626803-83800640:+	0	0.11	0	1
TNF receptor superfamily member 8	ENSG00000120949	TNFRSF8	chr1:12063377-12144207:+	0	0.11	0	1
solute carrier family 7 member 5	ENSG00000103257	SLC7A5	chr16:87830023-87869488:-	0	0.11	0	1
cadherin EGF LAG seven-pass G-type receptor 1	ENSG00000075275	CELSR1	chr22:46360834-46537170:-	0	0.11	0	1
adhesion G protein-coupled receptor D1	ENSG00000111452	ADGRD1	chr12:130953907-131141469:+	0	0.11	0	1
potassium two pore domain channel subfamily K member 10	ENSG00000100433	KCNK10	chr14:88180103-88326907:-	0	0.11	0	1
phospholipase D family member 3	ENSG00000105223	PLD3	chr19:40348456-40380439:+	0	0.11	0	1
dystrophin	ENSG00000198947	DMD	chrX:31097677-33339441:-	0	0.11	0	1
periaxin	ENSG00000105227	PRX	chr19:40393768-40413366:-	0	0.11	0	1
solute carrier family 8 member A3	ENSG00000100678	SLC8A3	chr14:70044217-70189070:-	0	0.11	0	1
dipeptidase 1	ENSG00000015413	DPEP1	chr16:89613308-89638456:+	0	0.11	0	1
protein tyrosine phosphatase receptor type N2	ENSG00000155093	PTPRN2	chr7:157539056-158587788:-	0	0.11	0	1
ATP binding cassette subfamily A member 4	ENSG00000198691	ABCA4	chr1:93992835-94121132:-	0	0.11	0	1
polycystin 2, transient receptor potential cation channel	ENSG00000118762	PKD2	chr4:88007668-88077777:+	0	0.11	0	1
ATP binding cassette subfamily G member 2 (Junior blood group)	ENSG00000118777	ABCG2	chr4:88090264-88231322:-	0	0.11	0	1
heparan sulfate 2-O-sulfotransferase 1	ENSG00000153936	HS2ST1	chr1:86914648-87109998:+	0	0.11	0	1
solute carrier family 44 member 3	ENSG00000143036	SLC44A3	chr1:94820342-94895246:+	0	0.11	0	1

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