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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
kirre like nephrin family adhesion molecule 3	ENSG00000149571	KIRREL3	chr11:126423359-127003460:-	0	0.17	0	1
leukocyte immunoglobulin like receptor B1	ENSG00000104972	LILRB1	chr19:54617158-54700954:+	0	0.17	0	1
leukocyte immunoglobulin like receptor A1	ENSG00000104974	LILRA1	chr19:54573879-54602090:+	0	0.17	0	1
osteoclast associated Ig-like receptor	ENSG00000170909	OSCAR	chr19:54094668-54102692:-	0	0.17	0	1
leukocyte immunoglobulin like receptor B3	ENSG00000204577	LILRB3	chr19:54216278-54223506:-	0	0.17	0	1
leukocyte immunoglobulin like receptor B2	ENSG00000131042	LILRB2	chr19:54238904-54281184:-	0	0.17	0	1
leukocyte immunoglobulin like receptor A2	ENSG00000239998	LILRA2	chr19:54572920-54590287:+	0	0.17	0	1
leukocyte immunoglobulin like receptor B4	ENSG00000186818	LILRB4	chr19:54643889-54670359:+	0	0.17	0	1
sodium voltage-gated channel beta subunit 3	ENSG00000166257	SCN3B	chr11:123629187-123655244:-	0	0.17	0	1
calcium voltage-gated channel auxiliary subunit gamma 7	ENSG00000105605	CACNG7	chr19:53909335-53943941:+	0	0.17	0	1
V-set and immunoglobulin domain containing 2	ENSG00000019102	VSIG2	chr11:124747472-124752238:-	0	0.17	0	1
myeloid associated differentiation marker	ENSG00000179820	MYADM	chr19:53866223-53876437:+	0	0.17	0	1
RAB35, member RAS oncogene family	ENSG00000111737	RAB35	chr12:120095095-120117502:-	0	0.17	0	1
activin A receptor type 2A	ENSG00000121989	ACVR2A	chr2:147844517-147930826:+	0	0.17	0	1
calcium voltage-gated channel auxiliary subunit alpha2delta 2	ENSG00000007402	CACNA2D2	chr3:50362799-50504244:-	0	0.17	0	1
LDL receptor related protein 6	ENSG00000070018	LRP6	chr12:12116025-12267012:-	0	0.17	0	1
potassium voltage-gated channel subfamily Q member 1	ENSG00000053918	KCNQ1	chr11:2444684-2849109:+	0	0.17	0	1
LMBR1 domain containing 1	ENSG00000168216	LMBRD1	chr6:69675802-69797111:-	0	0.17	0	1
myosin VI	ENSG00000196586	MYO6	chr6:75749192-75919537:+	0	0.17	0	1
ATPase phospholipid transporting 8B3	ENSG00000130270	ATP8B3	chr19:1782075-1812276:-	0	0.17	0	1

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