Table 3.
Significantly Copy Number Altered Genes by Tumor Subtype*
|
Overall (257) |
Invasive Ductal Carcinoma (221) |
Invasive Lobular Carcinoma (19) |
HER2-/HR+ (165) |
TNBC (60) |
HER2+/HR+ (24) |
HER2+/HR- (8) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P Value | % | P Value | % | P Value | % | P Value | % | P Value | % | P Value | % | P Value | % | |
| FGFR1 | 13.30/−0.59 | 0.101 | 11.99/−0.62 | 0.104 | 0.53 | 0.0526 | 11.68/−0.80 | 0.115 | 1.35 | 0.0667 | 1.67 | 0.125 | 0 | 0 |
| NOTCH1 | −1.79/9.29 | 0.0856 | 7.13/−1.73 | 0.0814 | 2.13 | 0.211 | −1.23/6.33 | 0.097 | −0.99/1.85 | 0.0667 | 0.56 | 0 | 0.94 | 0.25 |
| GNAS | 6.35 | 0.0739 | 6.52 | 0.0814 | 0.00 | 0 | 4.82 | 0.0788 | 0.43 | 0.05 | 1.67 | 0.125 | 0.41 | 0 |
| SMARCA4 | 5.14 | 0.0623 | 4.60 | 0.0633 | 0.92 | 0.105 | 2.49 | 0.0545 | 2.55 | 0.0833 | 0.00 | 0 | 0.94 | 0.25 |
| ERBB2 | 5.14 | 0.0584 | 5.88 | 0.0679 | 0.00 | 0 | 0.14 | 0.0182 | 0.00 | 0 | 8.89 | 0.333 | 2.29 | 0.5 |
| NOTCH3 | 4.10 | 0.0545 | 2.80 | 0.0498 | 0.92 | 0.105 | 2.49 | 0.0545 | 0.90 | 0.0333 | 0.00 | 0 | 1.05 | 0.375 |
| CPAMD8 | 4.10 | 0.0545 | 2.29 | 0.0452 | 1.57 | 0.158 | 2.49 | 0.0545 | 0.90 | 0.0333 | 0.00 | 0 | 1.05 | 0.375 |
| CRIPAK | −1.00/4.10 | 0.0623 | −1.08/3.38 | 0.0633 | 0.92 | 0.105 | −0.80/4.25 | 0.0727 | 0.25/−0.99 | 0.0333 | 0.00 | 0 | 0.94 | 0.25 |
| GATA3 | 4.10 | 0.0584 | 4.60 | 0.0679 | 0.00 | 0 | 1.35 | 0.0424 | 3.36 | 0.117 | 0.56 | 0.0417 | 0 | 0 |
| FGFR3 | −1.00/4.10 | 0.0623 | −1.08/3.38 | 0.0633 | 0.92 | 0.105 | −0.80/4.25 | 0.0727 | −0.99/0.25 | 0.0333 | 0.00 | 0 | 0.94 | 0.25 |
| CSMD1 | −3.75/0.00 | 0.0233 | −3.94/0.01 | 0.0271 | 0.00 | 0 | 0.04/−3.22 | 0.0303 | 0.00 | 0 | 0.00 | 0 | −1.97 | 0.125 |
| NF1 | −3.75 | 0.0156 | −3.94 | 0.0181 | 0.00 | 0 | −1.23 | 0.00606 | −2.60 | 0.05 | 0.00 | 0 | 0 | 0 |
| CREBBP | 3.51 | 0.0467 | 1.84 | 0.0362 | 2.13 | 0.211 | 3.57 | 0.0545 | 0.25 | 0.0167 | 0.00 | 0 | 0.94 | 0.25 |
| HNF1A | 2.95 | 0.0467 | 1.84 | 0.0407 | 1.57 | 0.158 | 3.02 | 0.0545 | 0.25 | 0.0167 | 0.00 | 0 | 0.94 | 0.25 |
| NOTCH2 | 2.50 | 0.0428 | 1.84 | 0.0452 | 0.53 | 0.0526 | 0.14 | 0.0182 | 5.19 | 0.133 | 0.00 | 0 | 0 | 0 |
| NFKB2 | 2.50 | 0.0428 | 1.51 | 0.0362 | 1.57 | 0.158 | 3.02 | 0.0545 | 0.00 | 0 | 0.00 | 0 | 0.94 | 0.25 |
| LRP1 | 2.50 | 0.0428 | 2.29 | 0.0452 | 0.53 | 0.0526 | 2.49 | 0.0485 | 0.00 | 0 | 0.56 | 0.0417 | 0.94 | 0.25 |
| TSC2 | 2.50 | 0.0389 | 1.51 | 0.0317 | 1.57 | 0.158 | 3.02 | 0.0485 | 0.00 | 0 | 0.00 | 0 | 0.94 | 0.25 |
| IL6R | 2.02 | 0.0428 | 1.51 | 0.0407 | 0.53 | 0.0526 | 0.98 | 0.0364 | 1.85 | 0.0833 | 0.00 | 0 | 0 | 0 |
| ZNF536 | 2.02 | 0.0428 | 1.51 | 0.0407 | 0.53 | 0.0526 | 0.33 | 0.0242 | 1.35 | 0.0667 | 0.00 | 0 | 1.05 | 0.375 |
| MAP2K4 | −0.59 | 0.00389 | −0.62 | 0.00452 | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | −2.27 | 0.0417 | 0 | 0 |
*
The number represent –log10 (P Value) from a Poisson test of copy number alteration rate in targeted regions against a random distribution. Genes 2 or more are significant at P<0.01. #negative value represents copy number losses. #positive value represents copy number gains