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

From: Histotype-specific copy-number alterations in ovarian cancer

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

  1. 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.
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BMC Medical Genomics

ISSN: 1755-8794

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