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Pozzorini C, Andre G, Coletta T, Buisson A, Bieler J, Ferrer L, Kempfer R, Saintigny P, Harlé A, Vacirca D, Barberis M, Gilson P, Roma C, Saitta A, Smith E, Consales Barras F, Ripol L, Fritzsche M, Marques AC, Alkodsi A, Marin R, Normanno N, Grimm C, Müllauer L, Harter P, Pignata S, Gonzalez-Martin A, Denison U, Fujiwara K, Vergote I, Colombo N, Willig A, Pujade-Lauraine E, Just PA, Ray-Coquard I, Xu Z. GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles. Cell Rep Med 2023; 4:101344. [PMID: 38118421 PMCID: PMC10772634 DOI: 10.1016/j.xcrm.2023.101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/11/2023] [Accepted: 11/23/2023] [Indexed: 12/22/2023]
Abstract
Homologous recombination deficiency (HRD) is a predictive biomarker for poly(ADP-ribose) polymerase 1 inhibitor (PARPi) sensitivity. Routine HRD testing relies on identifying BRCA mutations, but additional HRD-positive patients can be identified by measuring genomic instability (GI), a consequence of HRD. However, the cost and complexity of available solutions hamper GI testing. We introduce a deep learning framework, GIInger, that identifies GI from HRD-induced scarring observed in low-pass whole-genome sequencing data. GIInger seamlessly integrates into standard BRCA testing workflows and yields reproducible results concordant with a reference method in a multisite study of 327 ovarian cancer samples. Applied to a BRCA wild-type enriched subgroup of 195 PAOLA-1 clinical trial patients, GIInger identified HRD-positive patients who experienced significantly extended progression-free survival when treated with PARPi. GIInger is, therefore, a cost-effective and easy-to-implement method for accurately stratifying patients with ovarian cancer for first-line PARPi treatment.
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Affiliation(s)
| | | | | | - Adrien Buisson
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | | | - Loïc Ferrer
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Rieke Kempfer
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Pierre Saintigny
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France; University of Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Alexandre Harlé
- Institut de Cancérologie de Lorraine, Service de Biopathologie, CNRS UMR 7039 CRAN, Vandoeuvre-lès-Nancy, France
| | | | | | - Pauline Gilson
- Institut de Cancérologie de Lorraine, Service de Biopathologie, CNRS UMR 7039 CRAN, Vandoeuvre-lès-Nancy, France
| | - Cristin Roma
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | | | - Ewan Smith
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | | | - Lucia Ripol
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | | | | | - Amjad Alkodsi
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Ray Marin
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | - Nicola Normanno
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy
| | | | | | | | - Sandro Pignata
- Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, and Multicenter Italian Trials in Ovarian Cancer and Gynecologic Malignancies (MITO), Naples, Italy
| | - Antonio Gonzalez-Martin
- Cancer Center Clinica Universidad de Navarra, Madrid, Spain; GEICO, Madrid, Spain; Program In Solid Tumors, CIMA, Pamplona, Spain
| | - Ursula Denison
- Department for Gynaecology and Obstetrics, Klinik Hietzing, Vienna, Austria
| | - Keiichi Fujiwara
- Saitama Medical University International Medical Center, Saitama, Japan
| | - Ignace Vergote
- University Hospital Leuven, Leuven Cancer Institute, Leuven, Belgium
| | | | - Adrian Willig
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland
| | | | - Pierre-Alexandre Just
- Service de Pathologie, APHM (Assistance Publique - Hôpitaux de Marseille), Marseille, Provence-Alpes-Côte d'Azur, France
| | - Isabelle Ray-Coquard
- Centre Léon BERARD, and University Claude Bernard Lyon I, Lyon, France; Groupe d'Investigateurs Nationaux pour l'Etude des Cancers Ovariens (GINECO), Lyon, France
| | - Zhenyu Xu
- SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
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Callens C, Rodrigues M, Briaux A, Frouin E, Eeckhoutte A, Pujade-Lauraine E, Renault V, Stoppa-Lyonnet D, Bieche I, Bataillon G, Karayan-Tapon L, Rochelle T, Heitz F, Cecere SC, Pérez MJR, Grimm C, Nøttrup TJ, Colombo N, Vergote I, Yonemori K, Ray-Coquard I, Stern MH, Popova T. Shallow whole genome sequencing approach to detect Homologous Recombination Deficiency in the PAOLA-1/ENGOT-OV25 phase-III trial. Oncogene 2023; 42:3556-3563. [PMID: 37945748 PMCID: PMC10673712 DOI: 10.1038/s41388-023-02839-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 11/12/2023]
Abstract
The bevacizumab (bev)/olaparib (ola) maintenance regimen was approved for BRCA1/2-mutated (BRCAmut) and Homologous Recombination Deficient (HRD) high-grade Advanced Ovarian Cancer (AOC) first line setting, based on a significantly improved progression-free survival (PFS) compared to bev alone in the PAOLA-1/ENGOT-ov25 trial (NCT02477644), where HRD was detected by MyChoice CDx PLUS test. The academic shallowHRDv2 test was developed based on shallow whole-genome sequencing as an alternative to MyChoice. Analytical and clinical validities of shallowHRDv2 as compared to MyChoice on 449 PAOLA-1 tumor samples are presented. The overall agreement between shallowHRDv2 and MyChoice was 94% (369/394). Less non-contributive tests were observed with shallowHRDv2 (15/449; 3%) than with MyChoice (51/449; 11%). Patients with HRD tumors according to shallowHRDv2 (including BRCAmut) showed a significantly prolonged PFS with bev+ola versus bev (median PFS: 65.7 versus 20.3 months, hazard ratio (HR): 0.36 [95% CI: 0.24-0.53]). This benefit was significant also for BRCA1/2 wild-type tumors (40.8 versus 19.5 months, HR: 0.45 [95% CI: 0.26-0.76]). ShallowHRDv2 is a performant, clinically validated, and cost-effective test for HRD detection.
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Affiliation(s)
- Celine Callens
- Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France.
| | - Manuel Rodrigues
- Medical Oncology Department, Institut Curie and Paris Sciences Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Adrien Briaux
- Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Eleonore Frouin
- Clinic Bioinformatics Unit, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Alexandre Eeckhoutte
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | | | - Victor Renault
- Clinic Bioinformatics Unit, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Ivan Bieche
- Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Guillaume Bataillon
- Department of Pathology, University Cancer Institute of Toulouse-Oncopole, Toulouse, France
| | - Lucie Karayan-Tapon
- Biology of Cancer laboratory, University Hospital of Poitiers, Poitiers, France
| | - Tristan Rochelle
- Biology of Cancer laboratory, University Hospital of Poitiers, Poitiers, France
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
- Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, and AGO, Berlin, Germany
| | - Sabrina Chiara Cecere
- Department of Urology and Gynecology, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, and MITO, Napoli, Italy
| | | | - Christoph Grimm
- Division of General Gynecology and Gynecologic Oncology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, and AGO Austria, Vienna, Austria
| | - Trine Jakobi Nøttrup
- Department of Oncology, Copenhagen University Hospital-Rigshospitalet and NSGO, Copenhagen, Denmark
| | - Nicoletta Colombo
- Dipartimento Medicina e Chirurgia, Università Milano-Bicocca, Istituto Europeo Oncologia, Milano, and MaNGO, Milano, Italy
| | - Ignace Vergote
- University Hospital Leuven, Leuven Cancer Institute, and BGOG, Leuven, Belgium
| | - Kan Yonemori
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo, and GOTIC, Tokyo, Japan
| | - Isabelle Ray-Coquard
- Centre Léon BERARD, and University Claude Bernard Lyon I, Lyon, and GINECO, Lyon, France
| | - Marc-Henri Stern
- Genetics Laboratory, Department of Diagnostic and Theranostic Medicine, Institut Curie and Paris Sciences Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie and Paris Sciences Lettres Research University, Paris, France
| | - Tatiana Popova
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie and Paris Sciences Lettres Research University, Paris, France
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