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.