Copy number signatures in targeted gene panels associate with patient outcomes in routine clinical data

Authors

Netz, E., Moris, C., Hasanovic, A., Möbs, M., Schlomm, T., Frost, N., Mohr, R., Stintzing, S., Braicu, E., Sehouli, J., Rieke, D. T., Benary, M., Horst, D., Dubois, F.

Abstract

Targeted gene panels (TGPs) dominate clinical sequencing, yet most copy-number (CN) signature studies rely on genome-wide assays. Whether signatures can be recovered from TGPs and retain clinical relevance remains unclear. We analyzed two real-world TGP cohorts comprising 1,726 patients across 62 tumor types, including 825 with clinical annotations, and made the underlying data publicly available. TGP-derived signatures recapitulated established biological associations, including links to homologous recombination deficiency and TP53 alterations, concordant with published genome-wide assay-derived CN signatures. Using our detailed clinical data, we found TGP-derived CN signatures associated with overall survival under standard therapies in ovarian, pancreatic, and colorectal cancer. In ovarian cancer, CN2 was associated with CCNE1 amplification and shorter survival under paclitaxel/carboplatin, with the survival association validated in an independent SNP-array cohort. These findings demonstrate that routine TGPs yield biologically and clinically relevant CN signatures with potential as biomarkers for therapy stratification.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 26 Sep 2026.

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