Machine Learning for Better Prognostic Stratification and Driver Gene Identification Using Somatic Copy Number Variations in Anaplastic Oligodendroglioma

Autor: Luc Bauchet, Denys Fontaine, D. Larrieu‐Ciron, M. Andraud, H. Aubriot‐Lorton, Fabien Forest, G. Runavot, Shai Rosenberg, I. Carpiuc, François Labrousse, Christine Desenclos, Annie Laquerrière, Georges Noël, Olivier Chinot, Catherine Godfraind, Patrick Beauchesne, Jean-Yves Delattre, Caroline Dehais, T. Cruel, Danchristian Chiforeanu, F. Dhermain, Dominique Cazals-Hatem, Claude Gaultier, W. Lahiani, Marie-Laure Tanguy, C. Dehais, S. Elouadhani‐Hamdi, Pomone Richard, François Ghiringhelli, Olivier Langlois, Ca. Maurage, Dominique Figarella-Branger, Ahmed Idbaih, Carole Ramirez, Philippe Menei, François Ducray, Benoit Lhermitte, Nabila Elarouci, M. Campone, F. Vandenbos‐Burel, Mj. Motso‐Fotso, C. Blechet, Nicolas Desse, Sandrine Eimer, Valérie Rigau, Agusti Alentorn, Anne Jouvet, Damien Ricard, Mc. Tortel, T. Khallil, Clovis Adam, Hugues Loiseau, L. Bekaert, Henri Sevestre, Chiara Villa, M. Fesneau, Isabelle Quintin-Roue, Antoine Petit, Philippe Colin, Elodie Vauleon, S. Lopez, S. Gaillard, Guillaume Gauchotte, Antoine F. Carpentier, Phong Dam-Hieu, Md. Diebold, Yannick Marie, Thierry Faillot, Serge Milin, Aurélien de Reyniès, Emmanuelle Lechapt-Zalcman, Fabrice Parker, E. Cohen‐Moyal, Delphine Loussouarn, Emmanuelle Uro-Coste, Em. Gueye, Audrey Rousseau, F. Ducray, M‐I Mihai, Aurelie Kamoun, Karima Mokhtari
Přispěvatelé: Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), (le programme) Cartes d'identité des tumeurs (CIT), Ligue Nationales Contre le Cancer (LNCC), Biologie des Interactions Neurones / Glie, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de neurophysiopathologie (INP), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anatomie Pathologique-Neuropathologique [AP-HM Hôpital La Timone], Hôpital de la Timone [CHU - APHM] (TIMONE), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)
Rok vydání: 2018
Předmět:
Zdroj: Oncologist
Oncologist, AlphaMed Press, 2018, ⟨10.1634/theoncologist.2017-0495⟩
Oncologist, 2018, ⟨10.1634/theoncologist.2017-0495⟩
ISSN: 1549-490X
1083-7159
Popis: Background 1p/19q-codeleted anaplastic gliomas have variable clinical behavior. We have recently shown that the common 9p21.3 allelic loss is an independent prognostic factor in this tumor type. The aim of this study is to identify less frequent genomic copy number variations (CNVs) with clinical importance that may shed light on molecular oncogenesis of this tumor type. Materials and Methods A cohort of 197 patients with anaplastic oligodendroglioma was collected as part of the French POLA network. Clinical, pathological, and molecular information was recorded. CNV analysis was performed using single-nucleotide polymorphism arrays. Computational biology and feature selection based on the random forests method were used to identify CNV events associated with overall survival and other clinical-pathological variables. Results Recurrent chromosomal events were identified in chromosomes 4, 9, and 11. Forty-six focal amplification events and 22 focal deletion events were identified. Twenty-four focal CNV areas were associated with survival, and five of them were significantly associated with survival after multivariable analysis. Nine out of 24 CNV events were validated using an external cohort of The Cancer Genome Atlas. Five of the validated events contain a cancer-related gene or microRNA: CDKN2A deletion, SS18L1 amplification, RHOA/MIR191 copy-neutral loss of heterozygosity, FGFR3 amplification, and ARNT amplification. The CNV profile contributes to better survival prediction compared with clinical-based risk assessment. Conclusion Several recurrent CNV events, detected in anaplastic oligodendroglioma, enable better survival prediction. More importantly, they help in identifying potential genes for understanding oncogenesis and for personalized therapy. Implications for Practice Genomic analysis of 197 anaplastic oligodendroglioma tumors reveals recurrent somatic copy number variation areas that may help in understanding oncogenesis and target identification for precision medicine. A machine learning multivariable model built using this genomic information enables better survival prediction.
Databáze: OpenAIRE
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