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# PTEN

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npj Precision Oncology Oct 16, 2026
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.
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.
Boston Children's Hospital Universität Greifswald University Hospital Heidelberg Universitätsmedizin Greifswald Technical University of Munich Heidelberg University Harvard University Technische Universität Dresden
Irina A Kerle（First author, Corresponding author）
XGBoost Copy Number Variation Detection PTEN TruSight Oncology 500 MASTERsg precision oncology program
bioRxiv Sep 22, 2026
Passenger co-deletion confounds glutaminolysis signatures anchored on PTEN loss: a cautionary case for location-aware signature design
Using GISTIC copy number from the TCGA PanCancer Atlas to classify tumors as PTEN intact, hemizygous, or homozygous deletion, this study scored a five-gene glutaminolysis signature (GLS, SLC1A5, GOT1, GLUD1, GPT2) against loss severity across fourteen tumor types and found that the signature decreased with PTEN loss in all fourteen (significantly in twelve) but was not MYC-mediated; instead the decline tracked chromosomal position, since GLUD1 and GOT1 flank PTEN on 10q and thirty-seven neighboring genes carrying no glutaminolysis annotation tracked PTEN copy number just as closely (mean rho 0.843 versus 0.842), with co-deletion fidelity falling monotonically with distance from PTEN (rho = -0.
Using GISTIC copy number from the TCGA PanCancer Atlas to classify tumors as PTEN intact, hemizygous, or homozygous deletion, this study scored a five-gene glutaminolysis signature (GLS, SLC1A5, GOT1, GLUD1, GPT2) against loss severity across fourteen tumor types and found that the signature decreased with PTEN loss in all fourteen (significantly in twelve) but was not MYC-mediated; instead the decline tracked chromosomal position, since GLUD1 and GOT1 flank PTEN on 10q and thirty-seven neighboring genes carrying no glutaminolysis annotation tracked PTEN copy number just as closely (mean rho 0.843 versus 0.842), with co-deletion fidelity falling monotonically with distance from PTEN (rho = -0.
University of Benghazi
Abdelmuhsen Abusneina（First author, Corresponding author）
Passenger co-deletion PTEN Glutaminolysis signature TCGA PanCancer Atlas

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