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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
thyroid stimulating hormone receptor	ENSG00000165409	TSHR	chr14:80954989-81146302:+	0	0.11	0	1
delta like canonical Notch ligand 4	ENSG00000128917	DLL4	chr15:40929340-40939072:+	0	0.11	0	1
coagulation factor III, tissue factor	ENSG00000117525	F3	chr1:94529225-94541800:-	0	0.11	0	1
adducin 3	ENSG00000148700	ADD3	chr10:109996368-110135565:+	0	0.11	0	1
fibronectin leucine rich transmembrane protein 2	ENSG00000185070	FLRT2	chr14:85530144-85654426:+	0	0.1	0	1
cholinergic receptor nicotinic alpha 7 subunit	ENSG00000175344	CHRNA7	chr15:32030488-32172521:+	0	0.1	0	1
N-acylsphingosine amidohydrolase 2	ENSG00000188611	ASAH2	chr10:50182778-50248610:-	0	0.1	0	1
cadherin 15	ENSG00000129910	CDH15	chr16:89171767-89195492:+	0	0.1	0	1
scavenger receptor class B member 1	ENSG00000073060	SCARB1	chr12:124776856-124882668:-	0	0.1	0	1
5'-nucleotidase ecto	ENSG00000135318	NT5E	chr6:85449584-85495791:+	0	0.1	0	1
solute carrier family 16 member 3	ENSG00000141526	SLC16A3	chr17:82228397-82261129:+	0	0.1	0	1

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