Standard pipeline called these tumors PTEN wild-type; a gradient-boosting model found 33 more deletions, and 75% of stainable cases lost the protein
At the Dresden University Cancer Center's MASTERsg precision oncology program, a gradient-boosting model re-reads the raw bin-level copy-number data from TSO500 panel sequencing to find focal PTEN deletions that the standard pipeline misses. TSO500 averages read counts across bins within a gene, so focal events fall short of its fold-change threshold; the model flagged deletions in 33 of 204 samples classified as PTEN wild-type, and 15 of the 20 stainable cases showed absent or reduced PTEN protein.