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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 protein 255B	ENSG00000184497	TMEM255B	chr13:113759240-113816995:+	0.33	0	2	0
G protein regulated inducer of neurite outgrowth 1	ENSG00000169258	GPRIN1	chr5:176595802-176610133:-	0.33	0.11	1	1
tetraspanin 17	ENSG00000048140	TSPAN17	chr5:176647387-176659054:+	0.33	0.11	1	1
unc-5 netrin receptor A	ENSG00000113763	UNC5A	chr5:176810477-176880895:+	0.33	0	1	0
cadherin related family member 2	ENSG00000074276	CDHR2	chr5:176542511-176595974:+	0.33	0	1	0
histamine receptor H2	ENSG00000113749	HRH2	chr5:175658030-175686242:+	0.33	0.11	1	1
solute carrier family 52 member 3	ENSG00000101276	SLC52A3	chr20:760080-776015:-	0.33	0	1	0
solute carrier family 19 member 2	ENSG00000117479	SLC19A2	chr1:169463909-169486003:-	0.33	0	2	0
solute carrier family 12 member 4	ENSG00000124067	SLC12A4	chr16:67943474-67969601:-	0.32	0.47	2	2
KIAA1549 like	ENSG00000110427	KIAA1549L	chr11:33542072-33674102:+	0.32	0	2	0
solute carrier family 29 member 4	ENSG00000164638	SLC29A4	chr7:5274369-5306870:+	0.32	0.41	2	1
adrenoceptor alpha 1B	ENSG00000170214	ADRA1B	chr5:159916783-159972544:+	0.32	0.12	1	1
protein tyrosine phosphatase non-receptor type 4	ENSG00000088179	PTPN4	chr2:119759631-119983818:+	0.31	0	1	0
ATP binding cassette subfamily C member 10	ENSG00000124574	ABCC10	chr6:43427366-43450430:+	0.31	0	2	0
Yip1 domain family member 3	ENSG00000137207	YIPF3	chr6:43511827-43516990:-	0.31	0	2	0
hydroxysteroid 17-beta dehydrogenase 7	ENSG00000132196	HSD17B7	chr1:162790702-162812817:+	0.31	0	2	0
hepatitis A virus cellular receptor 2	ENSG00000135077	HAVCR2	chr5:157085832-157142869:-	0.31	0	1	0
hepatitis A virus cellular receptor 1	ENSG00000113249	HAVCR1	chr5:157029413-157059119:-	0.31	0	1	0
solute carrier family 26 member 2	ENSG00000155850	SLC26A2	chr5:149960737-149993455:+	0.31	0.14	1	1
solute carrier family 36 member 1	ENSG00000123643	SLC36A1	chr5:151437046-151492381:+	0.31	0.14	1	1

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