Table 3.
ISWI subunits with high frequence of abnormal copy numbers in malignancies
| Tumor | Gene | Cytoband | Type of CNA | Case number with CNA | Percentage (total number) |
|---|---|---|---|---|---|
| Acral Melanoma | RSF1 | 11q14.1 | AMP | 6 | 15.8%(38) |
| BAZ2A | 12q13.3 | AMP | 2 | 5.3%(38) | |
| Adenoid Cystic Carcinoma | BAZ2A | 12q13.3 | HOMDEL | 6 | 10%(60) |
| BAZ1A | 14q13.1-q13 | HOMDEL | 4 | 6.7%(60) | |
| Adrenocortical Carcinoma | BAZ2A | 12q13.3 | AMP | 3 | 3.3%(90) |
| POLE3 | 9q32 | AMP | 3 | 3.3%(90) | |
| Adult Soft Tissue Sarcomas | CHRAC1 | 8q24.3 | AMP | 9 | 4.4%(206) |
| Angiosarcoma | RBBP4 | 1p35.1 | AMP | 3 | 3.6%(83) |
| BPTF | 17q24.2 | AMP | 3 | 3.6%(83) | |
| CHRAC1 | 8q24.3 | AMP | 3 | 3.6%(83) | |
| Bladder Cancer | CHRAC1 | 8q24.3 | AMP | 21 | 5.1%(408) |
| RSF1 | 11q14.1 | AMP | 16 | 3.9%(408) | |
| BAZ2B | 2q24.2 | AMP | 5 | 1.1%(442) | |
| Brain Lower Grade Glioma | CHRAC1 | 8q24.3 | AMP | 18 | 3.5%(511) |
| Breast Cancer | CHRAC1 | 8q24.3 | AMP | 449 | 20.7%(2173) |
| RSF1 | 11q14.1 | AMP | 204 | 9.4%(2173) | |
| BPTF | 17q24.2 | AMP | 167 | 7.7%(2173) | |
| BAZ1A | 14q13.1-q13.2 | AMP | 10 | 4.2%(237) | |
| CECR2 | 22q11.1-q11.21 | HOMDEL | 10 | 4.2%(237) | |
| RBBP4 | 1p35.1 | AMP | 7 | 3%(237) | |
| Colon cancer | BPTF | 17q24.2 | HOMDEL | 8 | 7.6%(105) |
| BAZ2B | 2q24.2 | AMP | 2 | 1.9%(105) | |
| 2q24.2 | HOMDEL | 1 | 1.0%(105) | ||
| Colorectal Adenocarcinoma | CHRAC1 | 8q24.3 | AMP | 21 | 3.5%(592) |
| Esophageal Carcinoma | CHRAC1 | 8q24.3 | AMP | 21 | 11.5%(182) |
| RSF1 | 11q14.1 | AMP | 18 | 4.8%(378) | |
| SMARCA5 | 4q31.21 | AMP | 6 | 3.3%(182) | |
| BPTF | 17q24.2 | AMP | 12 | 3.2%(378) | |
| BAZ2B | 2q24.2 | AMP | 2 | 1.1%(184) | |
| Gastric Cancer | SMARCA1 | Xq25-q26.1 | HOMDEL | 106 | 98.1%(108) |
| RBBP7 | Xp22.2 | HOMDEL | 105 | 97.2%(108) | |
| CHRAC1 | 8q24.3 | AMP | 22 | 20.4%(108) | |
| BAZ1B | 7q11.23 | AMP | 7 | 6.5%(108) | |
| BPTF | 17q24.2 | AMP | 5 | 4.6%(108) | |
| RSF1 | 11q14.1 | AMP | 5 | 4.6%(108) | |
| POLE3 | 9q32 | AMP | 4 | 3.7%(108) | |
| Head and Neck Squamous Cell Carcinoma | CHRAC1 | 8q24.3 | AMP | 41 | 7.9%(517) |
| RSF1 | 11q14.1 | AMP | 18 | 3.5%(517) | |
| Liver Hepatocellular Carcinoma | CHRAC1 | 8q24.3 | AMP | 60 | 16.2%(370) |
| BPTF | 17q24.2 | AMP | 16 | 4.3%(370) | |
| BAZ2B | 2q24.2 | AMP | 4 | 1.1%(370) | |
| Lung Adenocarcinoma | BAZ1A | 14q13.1-q13 | AMP | 60 | 11.6%(516) |
| CHRAC1 | 8q24.3 | AMP | 15 | 5.0%(302) | |
| RSF1 | 11q14.1 | AMP | 20 | 3.9%(516) | |
| BPTF | 17q24.2 | AMP | 19 | 3.7%(516) | |
| Lung Squamous Cell Carcinoma | CHRAC1 | 8q24.3 | AMP | 36 | 7.2%(501) |
| BPTF | 17q24.2 | AMP | 18 | 3.6%(501) | |
| BAZ2B | 2q24.2 | AMP | 4 | 1.1%(370) | |
| 2q24.2 | HOMDEL | 8 | 1.6%(501) | ||
| Melanoma | CHRAC1 | 8q24.3 | AMP | 17 | 26.6%(64) |
| BAZ1B | 7q11.23 | AMP | 11 | 17.2%(64) | |
| BPTF | 17q24.2 | AMP | 5 | 7.8%(64) | |
| RSF1 | 11q14.1 | AMP | 4 | 6.3%(64) | |
| SMARCA5 | 4q31.21 | AMP | 2 | 3.1%(64) | |
| BAZ2A | 12q13.3 | AMP | 2 | 3.1%(64) | |
| 12q13.3 | HOMDEL | 2 | 3.1%(64) | ||
| POLE3 | 9q32 | AMP | 2 | 3.1%(64) | |
| 9q32 | HOMDEL | 3 | 4.7%(64) | ||
| BAZ2B | 2q24.2 | AMP | 3 | 4.7%(64) | |
| 2q24.2 | HOMDEL | 1 | 1.6%(64) | ||
| Mesothelioma | BPTF | 17q24.2 | AMP | 5 | 5.7%(87) |
| Ovarian Serous Cystadenocarcinoma | CHRAC1 | 8q24.3 | AMP | 156 | 27.3%(572) |
| RSF1 | 11q14.1 | AMP | 57 | 10%(572) | |
| RBBP4 | 1p35.1 | AMP | 27 | 4.7%(572) | |
| Pancreatic Cancer | CHRAC1 | 8q24.3 | AMP | 14 | 12.8%(109) |
| BAZ1B | 7q11.23 | AMP | 7 | 6.4%(109) | |
| RBBP4 | 1p35.1 | HOMDEL | 6 | 5.5%(109) | |
| SMARCA5 | 4q31.21 | HOMDEL | 6 | 5.5%(109) | |
| BPTF | 17q24.2 | HOMDEL | 4 | 3.7%(109) | |
| BAZ2B | 2q24.2 | AMP | 2 | 1.8%(109) | |
| Pediatric Neuroblastoma | BPTF | 17q24.2 | AMP | 2 | 3.4%(59) |
| Prostate Cancer | CHRAC1 | 8q24.3 | AMP | 87 | 19.6%(444) |
| RBBP7 | Xp22.2 | AMP | 47 | 10.6%(444) | |
| BAZ1B | 7q11.23 | AMP | 25 | 5.6%(444) | |
| BPTF | 17q24.2 | AMP | 22 | 5%(444) | |
| POLE3 | 9q32 | AMP | 21 | 4.7%(444) | |
| BAZ1A | 14q13.1-q13.2 | AMP | 18 | 4.1%(444) | |
| SMARCA1 | Xq25-q26.1 | AMP | 16 | 3.6%(444) | |
| BAZ1B | 7q11.23 | AMP | 5 | 3.3%(150) | |
| RBBP4 | 1p35.1 | AMP | 1 | 3.3%(30) | |
| Stomach Adenocarcinoma | CHRAC1 | 8q24.3 | AMP | 32 | 7.3%(441) |
| RSF1 | 11q14.1 | AMP | 16 | 3.6%(441) | |
| Urothelial Carcinoma | BPTF | 17q24.2 | AMP | 13 | 24.5%(53) |
| CHRAC1 | 8q24.3 | AMP | 8 | 15.1%(53) | |
| CECR2 | 22q11.1-q11.21 | AMP | 3 | 5.7%(53) | |
| RSF1 | 11q14.1 | AMP | 3 | 5.7%(53) | |
| BAZ1A | 14q13.1-q13.2 | AMP | 3 | 5.7%(53) | |
| BAZ1B | 7q11.23 | AMP | 2 | 3.8%(53) | |
| BAZ2B | 2q24.2 | AMP | 3 | 5.7%(53) | |
| Uterine Carcinosarcoma | CHRAC1 | 8q24.3 | AMP | 5 | 8.9%(56) |
| BPTF | 17q24.2 | AMP | 3 | 5.4%(56) | |
| SMARCA1 | Xq25-q26.1 | HOMDEL | 2 | 3.6%(56) | |
| BAZ2B | 2q24.2 | AMP | 1 | 1.8%(56) | |
| Uterine Corpus Endometrial Carcinoma | CHRAC1 | 8q24.3 | AMP | 24 | 4.5%(539) |
| BAZ2B | 2q24.2 | AMP | 6 | 1.1%(539) | |
| Uveal melanoma | CHRAC1 | 8q24.3 | AMP | 14 | 17.5%(80) |
| Invasive ductal cancer | BAZ1A | 14q12-q13 | AMP | 7 | 5.74%(122) |
All data come from the TCGA database
HOMDEL homozygouse deletion, AMP amplification