Histotype-specific copy-number alterations in ovarian cancer

BMC Medical Genomics

Table 1 Summary of copy number alterations and potential driver cancer genes

Region	AMP				DEL				Cancer genes
	C	E	M	S	C	E	M	S
1p36.11								D	MDS2
1q21.2-1q21.3		A							ARNT,TPM3
1q21.1-1q23.1		A		A					BCL9,MUC1,PRCC,NTRK1
1q42.13-1q44				A					FH
3q21.1-3q26.1				A					FOXL2,GMPS,MLF1
3q26.31-3q29				A					PIK3CA,ETV5,EIF4A2,BCL6,LPP,TFRC
4q21.22-4q31.3								D	RAP1GDS1,TET2,IL2,FBXW7
5q11.2-5q23.1								D	IL6ST,PIK3R1,APC
6p22.1-6p25.3				A					IRF4,DEK,HIST1H4I
6q22.2-6q27								D	ROS1,GOPC,STL,MYB,TNFAIP3,FGFR1OP,MLLT4
7q32.1-7q36.3				A					SMO,CREB3L2,KIAA1549,BRAF,EZH2
8p12-8p23.3								D	PCM1,WRN,WHSC1L1
8q11.21-8q24.3	A			A					HOOK3,TCEA1,CHCHD7,PLAG1,NCOA2,COX6C,EXT1,MYC,RECQL4
9p21.3-9p24.1							D		JAK2,MLLT3
11p15.4								D	CARS,NUP98,LMO1
11q13.3-11q21				A					NUMA1,PICALM,MAML2
12p11.21-12p13.33				A					KDM5A,CCND2,ZNF384,ETV6,KRAS
13q12.2-13q14.3								D	CDX2,FLT3,BRCA2,LHFP,LCP1
13q14.2					D			D	RB1
15q14-15q15.1								D	BUB1B
16q13-16q23.3								D	HERPUD1,CBFB,CDH1,MAF
17p11.2-17p13.2							D	D	USP6,TP53,PER1,GAS7,MAP2K4
17q11.1-17q21.31								D	NF1,SUZ12,TAF15,MLLT6,LASP1,RARA,BRCA1
17q12			A					D	ERBB2
18q21.32-18q22.2								D	MALT1,BCL2
19p13.3								D	FSTL3,STK11,TCF3,SH3GL1,MLLT1
20q11.21-20q13.33				A					ASXL1,GNAS,SS18L1
22q11.21-22q13.33								D	CLTCL1,MN1,CHEK2,EWSR1,NF2,MYH9,PDGFB,MKL1,MKL1,EP300
Xp11.3-Xp22.33								D	P2RY8,KDM6A
Xq25								D	ELF4

For simplicity, the altered regions are summarized into cytobands in the first column. Second (AMP) and third (DEL) columns indicate the amplification and deletion respectively for each histotype (C-clear cell, E-endometrioid, M-mucinous, S-serous). The amplification (A) and deletion (D) status for each histotype are indicated in each cytoband. The last column shows known cancer genes (from Sanger COSMIC database) that are within the altered regions. In total, 76 genes are listed in this table. Cancer genes which are potential drivers (i.e. significant correlation between gene expression and copy number alterations) are highlighted in bold.

ISSN: 1755-8794