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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
immunoglobulin superfamily member 9B	ENSG00000080854	IGSF9B	chr11:133908564-133956985:-	0	0.21	0	1
N-acetylated alpha-linked acidic dipeptidase like 2	ENSG00000177694	NAALADL2	chr3:174438573-175810552:+	0	0.21	0	1
interferon lambda receptor 1	ENSG00000185436	IFNLR1	chr1:24154157-24187959:-	0	0.21	0	1
interleukin 22 receptor subunit alpha 1	ENSG00000142677	IL22RA1	chr1:24119771-24143121:-	0	0.2	0	1
olfactomedin 4	ENSG00000102837	OLFM4	chr13:53028759-53052057:+	0	0.2	0	1
syndecan 3	ENSG00000162512	SDC3	chr1:30869467-30908761:-	0	0.2	0	1
cadherin related family member 4	ENSG00000187492	CDHR4	chr3:49790732-49799835:-	0	0.2	0	1
ATPase H+ transporting V0 subunit a1	ENSG00000033627	ATP6V0A1	chr17:42458844-42522611:+	0	0.2	0	1
RAB5C, member RAS oncogene family	ENSG00000108774	RAB5C	chr17:42124976-42155044:-	0	0.2	0	1
transmembrane protein 231	ENSG00000205084	TMEM231	chr16:75536744-75556286:-	0	0.19	0	1
leukocyte receptor tyrosine kinase	ENSG00000062524	LTK	chr15:41503638-41513887:-	0	0.19	0	1
serine incorporator 2	ENSG00000168528	SERINC2	chr1:31409565-31434680:+	0	0.19	0	1
solute carrier family 1 member 1	ENSG00000106688	SLC1A1	chr9:4490444-4587469:+	0	0.19	0	1
solute carrier family 2 member 8	ENSG00000136856	SLC2A8	chr9:127397138-127408424:+	0	0.19	0	1
leucine rich repeat containing 37A	ENSG00000176681	LRRC37A	chr17:46292733-46337794:+	0	0.19	0	1
leucine rich repeat containing 37 member A2	ENSG00000238083	LRRC37A2	chr17:46511511-46555650:+	0	0.19	0	1
C-X-C motif chemokine receptor 2	ENSG00000180871	CXCR2	chr2:218125289-218137253:+	0	0.19	0	1
scavenger receptor cysteine rich family member with 5 domains	ENSG00000179954	SSC5D	chr19:55488404-55519098:+	0	0.19	0	1
5-hydroxytryptamine receptor 2B	ENSG00000135914	HTR2B	chr2:231108230-231125118:-	0	0.19	0	1
histamine receptor H1	ENSG00000196639	HRH1	chr3:11137093-11263557:+	0	0.18	0	1

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