Table 2.
Pan-cancer analysis of PTEN deletion prognostic value.
| Description | PTEN Loss | PTEN Del | OS p PTEN Loss | OS p PTEN Del | DFS p PTEN Loss | DFS p PTEN Del |
|---|---|---|---|---|---|---|
| Brain LGG | 1% | 22% | 2.45E-14 | 6.58E-27 | 2.15E-10 | 4.30E-24 |
| CCRCC | 1% | 18% | 3.16E-11 | 2.68E-01 | 1.85E-07 | 1.44E-01 |
| Pancreatic Adenocarcinoma | 1% | 18% | 4.70E-04 | 8.23E-01 | 2.23E-06 | 5.87E-01 |
| UCEC | 4% | 15% | 6.63E-03 | 1.78E-03 | 7.52E-05 | 1.13E-03 |
| Multiform GBM | 10% | 89% | 1.67E-02 | 1.67E-05 | 7.96E-05 | 4.26E-06 |
| Sarcoma | 6% | 54% | 1.04E-02 | 1.28E-01 | 6.73E-04 | 1.25E-01 |
| Head and Neck Squamous Cell Carcinoma | 3% | 27% | 3.45E-01 | 7.66E-01 | 4.73E-02 | 7.55E-01 |
| Prostate Adenocarcinoma | 19% | 32% | 8.59E-01 | 8.33E-01 | 1.31E-01 | 7.68E-02 |
| Bladder Urothelial Carcinoma | 2% | 43% | 2.59E-01 | 9.70E-01 | 2.68E-01 | 8.37E-01 |
| Breast Invasive Carcinoma | 5% | 30% | 5.72E-01 | 4.17E-01 | 2.82E-01 | 5.97E-02 |
| Diffuse Large B-cell Lymphoma | 6% | 15% | 2.91E-01 | 3.95E-01 | 4.64E-01 | 6.38E-01 |
| Liver Hepatocellular Carcinoma | 4% | 26% | 9.83E-01 | 2.52E-01 | 4.92E-01 | 2.09E-01 |
| Thyroid Carcinoma | 1% | 3% | 7.20E-01 | 5.57E-01 | 5.02E-01 | 3.48E-01 |
| Testicular Germ Cell Cancer | 1% | 46% | 8.85E-01 | 3.19E-01 | 5.33E-01 | 2.01E-01 |
| Colorectal Adenocarcinoma | 3% | 26% | 1.93E-01 | 1.52E-01 | 5.33E-01 | 1.02E-01 |
| Lung Squamous Cell Carcinoma | 10% | 54% | 7.25E-02 | 1.79E-01 | 5.70E-01 | 2.35E-01 |
| Skin Cutaneous Melanoma | 7% | 63% | 2.11E-01 | 2.71E-01 | 6.04E-01 | 5.46E-02 |
| Papillary Thyroid Carcinoma | 1% | 2% | 6.85E-01 | 6.57E-01 | 6.08E-01 | 5.13E-01 |
| Kidney Renal Papillary Cell Carcinoma | 0% | 7% | 7.59E-01 | 9.27E-03 | 6.75E-01 | 1.28E-02 |
| Stomach Adenocarcinoma | 5% | 27% | 1.96E-02 | 4.46E-02 | 6.75E-01 | 5.17E-02 |
| Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma | 5% | 30% | 6.45E-01 | 2.33E-01 | 6.92E-01 | 2.05E-01 |
| Esophageal Carcinoma | 4% | 37% | 5.00E-01 | 9.30E-01 | 7.20E-01 | 1.88E-01 |
| Kidney Chromophobe | 2% | 74% | 1.00E+00 | 1.70E-01 | 7.39E-01 | 4.74E-01 |
| Lung Adenocarcinoma | 1% | 28% | 3.02E-01 | 3.32E-01 | 7.59E-01 | 4.51E-01 |
| Ovarian Serous Cystadenocarcinoma | 4% | 39% | 4.74E-01 | 7.10E-02 | 9.93E-01 | 4.56E-01 |
| AML | 1% | 2% | 2.83E-07 | 3.72E-10 | NA | NA |
| Adrenocortical Carcinoma | 0% | 11% | NA | 2.33E-01 | NA | 3.50E-01 |
| Cholangiocarcinoma | 0% | 17% | NA | 8.36E-01 | NA | 9.60E-01 |
| Esophagus-Stomach Cancers | 7% | 40% | 9.99E-01 | 5.45E-01 | NA | NA |
| Thymoma | 0% | 3% | NA | 6.27E-01 | NA | 6.04E-01 |
| Uveal Melanoma | 0% | 1% | NA | 6.86E-05 | NA | NA |
PTEN Del, PTEN Deletion; OS, overall survival; p, p-value; DFS, disease-free survival; LGG, lower grade glioma; CCRCC, clear cell renal cell carcinoma; UCEC, uterine corpus endometrial carcinoma; AML, acute myeloid leukemia. Significant terms highlighted in bold. The survival tests were calculated via the survfit function of the “survival” R package. Patients were partitioned in each dataset accordingly to Copy Number Variation (CNV) data on the PTEN gene. Endpoint for OS was deceased/living and disease-free/recurred for DFS. PTEN Loss: genomic identification of significant targets in cancer (GISTIC) CNV score < −1. PTEN-Del: GISTIC CNV score < 0.