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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
CD3d molecule	ENSG00000167286	CD3D	chr11:118338954-118342744:-	0	0.23	0	1
CD3g molecule	ENSG00000160654	CD3G	chr11:118344344-118355161:+	0	0.23	0	1
MAM domain containing 4	ENSG00000177943	MAMDC4	chr9:136850943-136860799:+	0	0.23	0	1
notch receptor 1	ENSG00000148400	NOTCH1	chr9:136494444-136545862:-	0	0.23	0	1
CD3e molecule	ENSG00000198851	CD3E	chr11:118304545-118316175:+	0	0.23	0	1
quiescin sulfhydryl oxidase 2	ENSG00000165661	QSOX2	chr9:136206333-136245841:-	0	0.22	0	1
TNF superfamily member 11	ENSG00000120659	TNFSF11	chr13:42562736-42608013:+	0	0.22	0	1
sushi domain containing 4	ENSG00000143502	SUSD4	chr1:223220819-223364202:-	0	0.22	0	1
phospholipase A2 group IIA	ENSG00000188257	PLA2G2A	chr1:19975431-19980416:-	0	0.22	0	1
phospholipid phosphatase 1	ENSG00000067113	PPAP2A	chr5:55424854-55535050:-	0	0.22	0	1
phospholipase B domain containing 2	ENSG00000151176	PLBD2	chr12:113358566-113391625:+	0	0.22	0	1
cytoskeleton associated protein 4	ENSG00000136026	CKAP4	chr12:106237877-106304279:-	0	0.22	0	1
ectonucleoside triphosphate diphosphohydrolase 2	ENSG00000054179	ENTPD2	chr9:137048098-137054045:-	0	0.22	0	1
leucine rich repeat containing 8 VRAC subunit B	ENSG00000197147	LRRC8B	chr1:89524836-89597864:+	0	0.22	0	2
leucine rich repeat containing 8 VRAC subunit C	ENSG00000171488	LRRC8C	chr1:89633072-89769903:+	0	0.22	0	2
neurexin 3	ENSG00000021645	NRXN3	chr14:78242391-79868290:+	0	0.22	0	2
solute carrier family 30 member 2	ENSG00000158014	SLC30A2	chr1:26037252-26046133:-	0	0.21	0	1
blood vessel epicardial substance	ENSG00000112276	BVES	chr6:105096822-105137174:-	0	0.21	0	2
ATPase phospholipid transporting 8B1	ENSG00000081923	ATP8B1	chr18:57646426-57803101:-	0	0.21	0	2
ATPase H+ transporting V0 subunit a2	ENSG00000185344	ATP6V0A2	chr12:123712318-123761755:+	0	0.21	0	1

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