Table 2.
Summary of biomarker subgroup co-alterations for all subtypes.
| Pathway | Gene/protein | PIK3CA-AKT1- | PIK3CA | AKT1 | PTEN | PIK3CA-PTEN | AKT1-PTEN | PIK3CA-AKT1- |
|---|---|---|---|---|---|---|---|---|
| PTEN WT (%) | MT (%) | MT (%) | MT (%) | MT (%) | MT (%) | PTEN MT* (%) | ||
| Homologous recombination | BRCA1 | 2.7 | 0.5* | 0.0 | 5.3** | 0.3* | 0.0 | 3.0 |
| BRCA2 | 5.4 | 3.9 | 0.0 | 5.2 | 2.3* | 1.1 | 4.1 | |
| PALB2 | 1.3 | 0.3* | 1.4 | 0.8 | 0.8 | 1.1 | 0.7* | |
| Possible predictors of IO benefit | PD-1 | 50.0 | 43.4 | 66.7 | 57.3 | 34.0 | 66.7 | 49.7 |
| PD-L1 TC (SP142) | 4.2 | 3.2 | 1.6 | 8.7** | 6.8** | 5.7 | 6.9** | |
| PD-L1 IC (SP142) | 26.6 | 16.2 | 25.0 | 39.7** | 13.3* | 25.0 | 29.2 | |
| MSI | 0.6 | 0.3 | 0.0 | 0.9 | 1.2 | 0.0 | 0.7 | |
| TMB-High (≥10/Mb) | 18.8 | 27.1** | 24.3 | 19.8 | 26.7** | 21.3 | 22.9** | |
| Chromatin remodeling | ARID1A | 18.6 | 18.6 | 5.6 | 9.1* | 16.0 | 2.8* | 12.4* |
| ARID2 | 0.8 | 0.8 | 1.5 | 0.4 | 1.2 | 0.0 | 0.7 | |
| RAS-RAF-MEK-ERK | HRAS | 0.1 | 0.8** | 0.0 | 0.4 | 1.5** | 1.1 | 0.7** |
| KRAS | 1.1 | 2.1 | 1.4 | 1.5 | 3.2** | 1.1 | 2.0** | |
| NRAS | 0.0 | 0.3 | 0.0 | 0.2 | 0.3** | 0.0 | 0.2 | |
| BRAF | 0.1 | 0.8** | 0.0 | 0.3 | 0.5 | 5.4** | 0.5 | |
| Others | TP53 | 53.1 | 47.0* | 43.9 | 72.1** | 46.7* | 56.2 | 60.9** |
| CDH1 | 6.1 | 15.8** | 20.3** | 4.8 | 18.4** | 10.6 | 10.3** | |
| NF1 | 2.1 | 5.6** | 12.1** | 4.4** | 11.7** | 7.2** | 6.2** | |
| RB1 | 2.6 | 3.8 | 3.1 | 6.2** | 6.0** | 4.3 | 5.5** | |
| ERBB2 | 3.4 | 3.9 | 1.4 | 1.7 | 2.3 | 0.0 | 2.3* |
PIK3CA-AKT1-PTEN-MT* = pathogenic alteration in PIK3CA, AKT1, or PTEN.
All other MT cohorts = pathogenic alteration in genes included in cohort name and no mutation in genes not included in cohort name for PIK3CA, AKT1, and PTEN.
WT = no pathogenic mutations in PIK3CA, AKT1, and PTEN.
TMB = tumor mutational burden.
*
/
**
= statistically significant decrease/increase, respectively between MT and WT cohorts.