Integration of genome scale data for identifying new players in colorectal cancer

Table 1 Relevant studies that integrated copy number variations and gene expression data when studying colorectal cancer

Ref.	Case series		Chr 20q (gain)	Chr 8p (loss)	Additional genes/chromosomes
	CNV	mRNA
Ali Hassan et al[24]	64 couples (4 A, 33 B, 27 C1)	15/64 couples	20q12	8p23.2	Gains: 8q21-22, 8q24, 13q21, 13q34, 20p11-13, 20q11-13
			PTPRT2	CSMD1
			CHD6	DLC1
			EMILIN3
			LPIN3
			PLCG12
			TOP12
			ZHX3
			MAFB
Loo et al[25]	40 couples	40 couples	20q11-13	8p	Gains: 20pter-p12 (PCNA), 20p13 (CDC25B), 13q34 (CUL4A)
			AHCY	FBXO25
			POFUT1 RPN2	MTUS12
			TH1L	EPHX2
			PRPF6	KIF13B
			AURKA	PPP2CB2
Yoshida et al[26]	70 couples	70 couples			Gains: 1q21 (S1000A2), 18p11 (RALBP1, TYMS, RAB12, RNMT), 15q26 (ABHD2), 20p11 (ABHD12)
					Losses: 3q29 (LOC440995), 4q13 (UGT2B28, SULT1B1), 4q21 (CXCL6, CXCL3), 10q22 (OIT3), 12p12 (ARHGDIB)
Kikuchi et al[27]	122 couples (18 I, 42 II, 37 III, 25 IV3)	115/122 couples (16 I, 41 II, 35 III, 23 IV3)			Gains: 1q32.1 (NUCKS1), 1q42 (TMEM63A), 3p14.2 (SYNPR)
Reid et al[18]	48 couples (1 I, 10 II, 10 III, 23 IV3, 4 N.I.)	36/48 couples (1 I, 5 II, 8 III, 19 IV3, 4 N.I.)	20q11-13		Gains: 7p12 (EGFR), 8q24 (NDRG1), 13q (TFDP1, CDK8, GAS6, SPATA13)
			PLCG1	8p21-24
			ADRM1	BIN	Losses: 6p21, 8p, 18q (MAPRE2, INO80C, ARKL1), 20p (FKBP12)
			JAG1	DBC1
			AURKA	TNFRSF10A
			C20ORF20	TNFRSF10B
			C20ORF24 TCFL5	EXTL3
			TH1L
			AHCY
			TGIF2

¹Duke’s;

²CRC-related;

³Stage. Chr: Chromosome; CNV: Copy number variations; CRC: Colorectal cancer; Couple: Tumor tissue matched with its normal colorectal mucosa. Genes identified in more than one study are shown in bold font.