1. The Scarface Score: Deciphering Response to DNA Damage Agents in High-Grade Serous Ovarian Cancer—A GEICO Study
- Author
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Fernandez-Serra, Antonio, López-Reig, Raquel, Márquez, Raúl, Gallego, Alejandro, De Sande-González, Luis Miguel, Yubero Esteban, Alfonso, OAKNIN, ANA, Institut Català de la Salut, [Fernández-Serra A, López-Reig R] Molecular Biology Lab, Molecular Biology Department, Instituto Valenciano de Oncologia, Valencia, Spain. Joint IVO-CIPF Cancer Research Unit, Valencia, Spain. [Márquez R] Medical Oncology Department, MD Anderson Cancer Center, Madrid, Spain. [Gallego A] Medical Oncology Department, Hospital Universitario La Paz, Madrid, Spain. [de Sande LM] Medical Oncology Department, Hospital Universitario de León, León, Spain. [Yubero A] Medical Oncology Department, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain. [Oaknin A] Servei d’Oncologia Mèdica, Vall d’Hebron Hospital Universitari, Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus
- Subjects
Genòmica ,Anomalies cromosòmiques ,Neoplasms::Neoplasms by Site::Endocrine Gland Neoplasms::Ovarian Neoplasms [DISEASES] ,Genetic Phenomena::Genetic Variation::Mutation::Genetic Phenomena::Genomic Instability [PHENOMENA AND PROCESSES] ,Ovaris - Càncer - Aspectes genètics ,neoplasias::neoplasias por localización::neoplasias de las glándulas endocrinas::neoplasias ováricas [ENFERMEDADES] ,fenómenos genéticos::variación genética::mutación::fenómenos genéticos::inestabilidad genómica [FENÓMENOS Y PROCESOS] - Abstract
Genomic instability; Machine learning Inestabilidad genómica; Aprendizaje automático Inestabilitat genòmica; Aprenentatge automàtic Genomic Instability (GI) is a transversal phenomenon shared by several tumor types that provide both prognostic and predictive information. In the context of high-grade serous ovarian cancer (HGSOC), response to DNA-damaging agents such as platinum-based and poly(ADP-ribose) polymerase inhibitors (PARPi) has been closely linked to deficiencies in the DNA repair machinery by homologous recombination repair (HRR) and GI. In this study, we have developed the Scarface score, an integrative algorithm based on genomic and transcriptomic data obtained from the NGS analysis of a prospective GEICO cohort of 190 formalin-fixed paraffin-embedded (FFPE) tumor samples from patients diagnosed with HGSOC with a median follow up of 31.03 months (5.87–159.27 months). In the first step, three single-source models, including the SNP-based model (accuracy = 0.8077), analyzing 8 SNPs distributed along the genome; the GI-based model (accuracy = 0.9038) interrogating 28 parameters of GI; and the HTG-based model (accuracy = 0.8077), evaluating the expression of 7 genes related with tumor biology; were proved to predict response. Then, an ensemble model called the Scarface score was found to predict response to DNA-damaging agents with an accuracy of 0.9615 and a kappa index of 0.9128 (p < 0.0001). The Scarface Score approaches the routine establishment of GI in the clinical setting, enabling its incorporation as a predictive and prognostic tool in the management of HGSOC. This research was partially funded by GVA Grants “Subvencions per a la realització de projectes d’i+d+i desenvolupats per grups d’investigació emergents (GV/2020/158)” and “Ayudas para la contratación de personal investigador en formación de carácter predoctoral” (ACIF/2016/008) and “Beca de investigación traslacional Andrés Poveda 2020” from GEICO group. This study was awarded the Prize “Antonio Llombart Rodriguez-FINCIVO 2020” from the Royal Academy of Medicine of the Valencian Community.
- Published
- 2023