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1. Case report: Immune response characterization of a pseudoprogression in a PD-L1-negative, TMB-low, KEAP1/STK11 co-mutated metastatic NSCLC

Author

Nicolas Roussot, Marion Thibaudin, Jean-David Fumet, Susy Daumoine, Léa Hampe, Cédric Rébé, Emeric Limagne, Aurélie Lagrange, Victor Herreros, Julie Lecuelle, Hugo Mananet, Alis Ilie, David Rageot, Romain Boidot, Vincent Goussot, Anthony Comte, Pierre Jacob, Françoise Beltjens, Anthony Bergeron, Céline Charon-Barra, Laurent Arnould, Valentin Derangère, Sylvain Ladoire, Caroline Truntzer, and François Ghiringhelli

Subjects
case report, NSCLC, pseudoprogression, chemoimmunotherapy, neoantigen, cold tumor, Immunologic diseases. Allergy, RC581-607
Abstract

A patient with a PD-L1-negative, TMB-low, KEAP1/STK11 co-mutated metastatic non-small cell lung cancer (NSCLC) experienced a multisite radiological progression at 3 months after initiation of chemoimmunotherapy as first-line treatment for metastatic disease. After the radiological progression, while she was not undergoing treatment, the patient had spontaneous lesions shrinkage and further achieved a prolonged complete response. Genomic and transcriptomic data collected at baseline and at the time of pseudoprogression allowed us to biologically characterize this rare response pattern. We observed the presence of a tumor-specific T-cell response against tumor-specific neoantigens (TNAs). Endogenous retroviruses (ERVs) expression following chemoimmunotherapy was also observed, concurrent with biological features of an anti-viral-like innate immune response with type I IFN signaling and production of CXCR3-associated chemokines. This is the first biological characterization of a NSCLC pseudoprogression under chemoimmunotherapy followed by a prolonged complete response in a PD-L1-negative, TMB-low, KEAP1/STK11 co-mutated NSCLC. These clinical and biological data underline that even patients with multiple factors of resistance to immune checkpoint inhibitors could trigger a tumor-specific immune response to tumor neoantigen, leading to complete eradication of the tumor and probably a vaccinal immune response.

Published
2024
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2. Atypical cancer risk profile in carriers of Italian founder BRCA1 variant p.His1673del: Implications for classification and clinical management

Author

Giovanni Innella, Cristina Fortuno, Laura Caleca, Bing‐Jian Feng, Courtney Carroll, Michael T. Parsons, Sara Miccoli, Marco Montagna, Daniele Calistri, Laura Cortesi, Barbara Pasini, Siranoush Manoukian, Daniela Giachino, Laura Matricardi, Maria Cristina Foti, Valentina Zampiga, Claudia Piombino, Elena Barbieri, Francesca Vignolo Lutati, Jacopo Azzolini, Rita Danesi, Valentina Arcangeli, Sandrine M. Caputo, Nadia Boutry‐Kryza, Vincent Goussot, Susan Hiraki, Marcy Richardson, Hereditary Breast/Ovarian Cancer IOV network (HBOC IOVnet), Simona Ferrari, Paolo Radice, Amanda B. Spurdle, and Daniela Turchetti

Subjects
BRCA1, breast cancer, cancer risk, classification, clinical management, ovarian cancer, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background BRCA1:c.5017_5019del (p.His1673del) is a founder variant relatively frequent in Northern Italy. Despite previous suggestion of pathogenicity, variant classification in public databases is still conflicting, needing additional evidence. Methods Maximum likelihood penetrance of breast/ovarian and other cancer types was estimated using full pedigree data from 53 informative Italian families. The effect of the variant on BRCA1‐ABRAXAS1 interaction was assessed using a GFP‐fragment reassembly‐based PPI assay. Results were combined with additional data from multiple sources to classify the variant according to ACMG/AMP classification rules specified for BRCA1/2. Results Variant‐carriers displayed increased risk for ovarian cancer (HR = 33.0, 95% CI = 7.0–155.0; cumulative risk at age 70 = 27.6%, 95% CI = 12.6–40.0%) but not for breast cancer (HR = 0.7, 95% CI = 0.2–2.2). An increased risk of uterine cancer (HR = 8.0, 95% CI = 1.03–61.6) emerged, warranting further evaluation. Likelihood‐ratio in favor of pathogenicity was 98898642.82 under assumption of standard BRCA1 breast and ovarian penetrance, and 104240832.84 after excluding breast cancer diagnoses (based on penetrance results). Functional analysis demonstrated that the variant abrogates the BRCA1‐ABRAXAS1 binding, supporting the PS3 code assignment within the ACMG/AMP rule‐based model. Collectively, these findings allowed to classify the variant as pathogenic. Conclusion Pathogenicity of BRCA1:c.5017_5019del(p.His1673del) has been confirmed; however, breast cancer risk in Italian families is not increased, unlike in families from other countries and in carriers of most BRCA1 pathogenic variants. The knowledge of atypical risk profiles for this and other variants will pave the way for personalized management based on specific genotype.

Published
2024
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3. Advancing precision oncology through systematic germline and tumor genetic analysis: The oncogenetic point of view on findings from a prospective multicenter clinical trial of 666 patients

Author

Benoit Mazel, Geoffrey Bertolone, Amandine Baurand, Elodie Cosset, Caroline Sawka, Marion Robert, Elodie Gautier, Allan Lançon, Manon Réda, Laure Favier, Valentin Dérangère, Corentin Richard, Christine Binquet, Romain Boidot, Vincent Goussot, Juliette Albuisson, François Ghiringhelli, Laurence Faivre, and Sophie Nambot

Subjects
genetic counseling, incidental findings, information, oncogenetic, theranostic exome sequencing, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Introduction With the emergence of targeted therapies, there is a need to accurately identify more tumor biomarkers. The EXOMA trial was designed to offer tumor and germline exome sequencing (ES) to patients with solid malignant tumors and facing therapeutic failure. As hereditary cancer predispositions could be identified, with genetic counseling and health management implications, a genetic consultation was systematically established. This design needs to be discussed as genetic human resources are limited and indication of theranostic tests will increase. Methods Genetic counseling was conducted within 15 days following inclusion in the study for patients recruited between December 2015 and July 2019. In silico analyses from theranostic ES were limited to 317 genes involved in oncogenesis, from both tumor and blood DNA. Results Six hundred and sixty six patients had a genetic consultation before ES. In 65/666 patients, 66 germline pathogenic or likely pathogenic (P/LP) variants were identified in 16 actionable genes and seven non‐actionable genes according to French guidelines. 24/65 patients had previously received genetic analysis for diagnostic purposes, and for 17 of them, a P/LP variant had already been identified. Among the 48/65 remaining cases for which the EXOMA protocol revealed a previously unknown P/LP variant, only 19 met the criteria for genetic testing for inherited cancer risk after familial survey. These criteria had not been identified by the oncologist in 10 cases. In 21/65 cases, the variant was considered incidental. Discussion In 7.4% of patients, an undiagnosed hereditary genetic predisposition was identified, whether or not related to the clinical presentation, and germline analysis impacted oncological management for only 6.3% of the cohort. This low percentage should be weighed against the burden of systematic genetic consultation and urgent circuits. Information or training tools to form oncologists to the prescription of germline genetic analyses should be explored, as well as information supports and patient preferences.

Published
2023
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4. Custom multi‑tumor next‑generation sequencing panel for routine molecular diagnosis of solid tumors: Validation and results from three‑year clinical use

Author

Sandy, Chevrier, Astrid, Brasselet, Marion, Carnet, Angélique, Chevriaux, Anne, Gibeaud, Marine, Jourdain, Hugo, Mananet, Caroline, Truntzer, Françoise, Beltjens, Céline, Charon-Barra, Laurent, Arnould, Juliette, Albuisson, Anthony, Comte, Valentin, Derangère, Vincent, Goussot, and Romain, Boidot

Subjects
Gene Frequency, Biopsy, Neoplasms, Mutation, Genetics, High-Throughput Nucleotide Sequencing, Humans, General Medicine
Abstract

Molecular testing is extremely important in cancer care, starting as early as at diagnosis. In order to address the challenge of providing reliable results within the timeframe adapted to patient management and suitable to guide clinical decisions, a capture‑based next‑generation sequencing (NGS) panel focusing on ten genes known to harbor genetic variations which may be targeted by approved drugs in patients with cancer was designed and validated. Very favorable analytical performances were obtained for both solid and liquid biopsies. For solid biopsies, a low read depth (80X per nucleotide) led to the genotype detection accuracy of 100%. The read of raw data for liquid biopsies resulted in the 91.19% result concordance between paired solid and liquid samples. The present method met all the requirements for the ISO15189 certification. During our three‑year experience of routinely using this panel, almost 2,300 samples from lung and colorectal cancers, melanomas and gastrointestinal stromal tumors have been analyzed. It was found that our panel detected slightly more gain‑of‑function variants than described in the literature. Surprisingly, loss‑of‑function variants were also detected in certain of the analyzed genes. Finally, liquid biopsy data revealed statistically different mutated allele frequencies between tumor types, but also between mutated genes and variants themselves. In conclusion, the use of our capture‑based NGS panel is perfectly adapted to perform relevant molecular diagnosis in a time frame compatible with patient care.

Published
2022
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5. TCR Clonality and Genomic Instability Signatures as Prognostic Biomarkers in High Grade Serous Ovarian Cancer

Author

François Ghiringhelli, Isabelle Ray Coquard, Hugo Mananet, Caroline Truntzer, Zoé Tharin, Jean-David Fumet, Julie Lecuelle, Juliette Albuisson, Valentin Derangère, Laurent Arnould, Vincent Goussot, and Romain Boidot

Subjects
Genome instability, Cancer Research, Tumor microenvironment, medicine.medical_treatment, T cell, T-cell receptor, TCR clonality, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, biomarkers, Immunotherapy, Biology, HGSC, Article, Serous fluid, Immune system, medicine.anatomical_structure, Oncology, HRD, medicine, Cancer research, Copy-number variation, prognostic, RC254-282
Abstract

Simple Summary High-grade serous ovarian carcinoma (HGSC) could be analyzed with a molecular stratification defined by different genomic instability signatures associated with specific mutational process and prognostic biomarkers. Immune infiltrate is known to be a robust biomarker in HGSC. We aimed to investigate immune parameters according to genomic instability signatures. We observed that homologous recombination deficiency positive, copy cumber variant signature 7 and TCR (T cells receptor) clonality are good prognostic biomarkers in HGSC. Combining TCR clonality and genomic instability signature or T cell infiltration improved the prognostic value compared to each variable taken alone. We provided a description of immune parameters according to different genomic instability signatures. We identified TCR clonality, alone or combined with genomic instability, as a promising prognostic biomarker in HGSC. Abstract Purpose: Immune infiltration is a prognostic factor in high-grade serous ovarian carcinoma (HGSC) but immunotherapy efficacy is disappointing. Genomic instability is now used to guide the therapeutic value of PARP inhibitors. We aimed to investigate exome-derived parameters to assess the tumor microenvironment according to genomic instability profile. Methods: We used the HGSC TCGA (the cancer genome atlas) dataset with genomic characteristics, including homologous recombination deficiency (HRD), copy number variant (CNV) signatures, TCR (T cell receptor) clonality and abundance of tissue-infiltrating immune and stromal cell populations. We then investigated the relationship with survival data. Results: In 578 HGSC patients, HRD status, CNV signature 7 and TCR clonality were associated with longer survival. The combination of high CNV signature 7 expression and HRD status or high CNV signature 3 expression and high TCR clonality was associated with a trend towards longer survival compared to each variable alone. Combining T cell infiltrate and TCR clonality improved the prognostic value compared to T cells infiltration alone. Prognostic value of TCR clonality was confirmed in an independent cohort. Conclusions: TCR clonality is an emerging prognostic biomarker that improves T cell infiltrate information. Analysis of TCR clonality combined with genomic instability could be an interesting prognostic biomarker.

Published
2021

6. TUMOSPEC: A Nation-Wide Study of Hereditary Breast and Ovarian Cancer Families with a Predicted Pathogenic Variant Identified through Multigene Panel Testing

Author

Celine Garrec, Monique Mozelle-Nivoix, Jérôme Lemonnier, Etienne Rouleau, Tan Dat Nguyen, Dominique Vaur, Elodie Lacaze, Sarah Bonnet-Boissinot, Sophie Nambot, Jean Chiesa, Sophie Giraud, Dominique Stoppa-Lyonnet, Michel Longy, Alain Lortholary, Jean-Marc Rey, Olivier Caron, Christine Lasset, Claude Houdayer, Christine Maugard, Virginie Bubien, Véronique Mari, Marie-Emmanuelle Morin-Meschin, Nadine Andrieu, Nancy Uhrhammer, Louise Crivelli, Hélène Dreyfus, Vincent Goussot, Stephanie Chieze-Valéro, Nicolas Sevenet, Lisa Golmard, Séverine Eon-Marchais, Mathilde Martinez, Isabelle Coupier, Marie-Gabrielle Dondon, Odile Béra, Paul Vilquin, Capucine Delnatte, Odile Cohen-Haguenauer, Cornel Popovici, Christine Toulas, Laurence Gladieff, Marie-Agnès Collonge-Rame, Chrystelle Colas, Paul Gesta, Catherine Noguès, Fanny Brayotel, Audrey Mailliez, Fabienne Lesueur, Julie Tinat, Marie Bidart, Yves-Jean Bignon, Florence Coulet, Nadia Boutry-Kryza, Fabienne Prieur, Juana Beauvallet, Philippe Denizeau, Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Institut Curie [Paris]-MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Curie [Paris], Institut Gustave Roussy (IGR), Génétique (Biologie pathologie), Département de biologie et pathologie médicales [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Hôtel-Dieu de Nantes, CHU Rouen, Normandie Université (NU), Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse - Oncopole (IUCT Oncopole - UMR 1037), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Jean Godinot [Reims], UNICANCER, Centre Eugène Marquis (CRLCC), Institut de Cancérologie de Strasbourg Europe (ICANS), Centre Paul Strauss, CRLCC Paul Strauss, Institut Bergonié [Bordeaux], Actions for OnCogenesis understanding and Target Identification in ONcology (ACTION), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bordeaux Segalen - Bordeaux 2-Institut Bergonié [Bordeaux], UNICANCER-UNICANCER, Centre Hospitalier Georges Renon [Niort] (CH Georges Renon Niort), Genetic and Immunology Medical Institute (GIMI), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté]), Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] (UNICANCER/CAL), UNICANCER-Université Côte d'Azur (UCA), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), CHU de Saint-Étienne Hôpital Nord [Saint Etienne], Hôpital Nord (Saint Etienne), Institut de Cancérologie de l'Ouest [Angers/Nantes] (UNICANCER/ICO), CHU Bordeaux [Bordeaux], Centre Catherine-de-Sienne [Nantes] (CCS), Hôpital privé du Confluent [Nantes], Institut Sainte Catherine [Avignon], hôpital couple-enfant [CHU Grenoble Alpes], Centre Hospitalier Universitaire [Grenoble] (CHU), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Centre Hospitalier de Troyes, Hospices Civils de Lyon (HCL), Groupement Hospitalier Lyon-Est (GHE), Hôpital Universitaire Carémeau [Nîmes] (CHU Nîmes), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Hôpital Sud [CHU Rennes], CHU Pontchaillou [Rennes], Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), Immunologie humaine, physiopathologie & immunothérapie (HIPI (UMR_S_976 / U976)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Régional de Lutte contre le Cancer Oscar Lambret [Lille] (UNICANCER/Lille), Université Lille Nord de France (COMUE)-UNICANCER, Hôpital Arnaud de Villeneuve [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut de recherche en cancérologie de Montpellier (IRCM - U896 Inserm - UM1), Université Montpellier 1 (UM1)-CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Groupe Hospitalier du Havre, CHU de la Martinique [Fort de France], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CRLCC René Gauducheau, Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre Léon Bérard [Lyon], Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Régional de Lutte contre le Cancer François Baclesse [Caen] (UNICANCER/CRLC), UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU), Centre médical de Bligny, Onco-génétique, Département de médecine oncologique [Gustave Roussy], COLO, Mouniati, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM), UNICANCER-UNICANCER-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de médecine génomique et d’immunothérapie (Genomic and Immunotherapy Medical Institute) (institut GIMI), UNICANCER-UNICANCER-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-FHU TRANSLAD (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Université de Lille-UNICANCER, Institut de Recherche en Cancérologie de Montpellier (IRCM - U1194 Inserm - UM), CRLCC Val d'Aurelle - Paul Lamarque-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM), UNICANCER-UNICANCER-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS BFC)-FHU TRANSLAD (CHU de Dijon), and Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)

Subjects
0301 basic medicine, Cancer Research, medicine.medical_specialty, Sequencing data, [SDV.CAN]Life Sciences [q-bio]/Cancer, Context (language use), [SDV.GEN.GH] Life Sciences [q-bio]/Genetics/Human genetics, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, 030105 genetics & heredity, Article, 03 medical and health sciences, 0302 clinical medicine, [SDV.CAN] Life Sciences [q-bio]/Cancer, Care plan, Internal medicine, Epidemiology, medicine, RC254-282, Genetic testing, medicine.diagnostic_test, business.industry, Cancer, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, 3. Good health, genetic predisposition to breast and ovarian cancer, [SDV.MHEP.GEO] Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Oncology, 030220 oncology & carcinogenesis, multigene panels, Cancer risk, Ovarian cancer, business, cancer risk estimate, penetrance of pathogenic variants
Abstract

Simple Summary TUMOSPEC was designed for estimating the risk of cancer for carriers of a predicted pathogenic variant (PPV) in a gene usually tested in a hereditary breast and ovarian cancer context. Index cases are enrolled consecutively among patients who undergo genetic testing as part of their care plan in France. First- and second-degree relatives and cousins of PPV carriers are invited to participate whether they are affected by cancer or not, and are tested for the familial PPV. Genetic, clinical, family and epidemiological data are centralized at the coordinating centre. The three-year feasibility study included 4431 prospective index cases, with 19.1% of them carrying a PPV. This showed that the study logistics are well adapted to clinical and laboratory constraints, and collaboration between partners (clinicians, biologists, coordinating centre and participants) is smooth. Hence, TUMOSPEC is being pursued, with the aim of optimizing clinical management guidelines specific to each gene. Abstract Assessment of age-dependent cancer risk for carriers of a predicted pathogenic variant (PPV) is often hampered by biases in data collection, with a frequent under-representation of cancer-free PPV carriers. TUMOSPEC was designed to estimate the cumulative risk of cancer for carriers of a PPV in a gene that is usually tested in a hereditary breast and ovarian cancer context. Index cases are enrolled consecutively among patients who undergo genetic testing as part of their care plan in France. First- and second-degree relatives and cousins of PPV carriers are invited to participate whether they are affected by cancer or not, and genotyped for the familial PPV. Clinical, family and epidemiological data are collected, and all data including sequencing data are centralized at the coordinating centre. The three-year feasibility study included 4431 prospective index cases, with 19.1% of them carrying a PPV. When invited by the coordinating centre, 65.3% of the relatives of index cases (5.7 relatives per family, on average) accepted the invitation to participate. The study logistics were well adapted to clinical and laboratory constraints, and collaboration between partners (clinicians, biologists, coordinating centre and participants) was smooth. Hence, TUMOSPEC is being pursued, with the aim of optimizing clinical management guidelines specific to each gene.

Published
2021
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7. Classification of 101 BRCA1 and BRCA2 variants of uncertain significance by cosegregation study: A powerful approach

Author

Marie-Noëlle Bonnet-Dupeyron, Helene Dreyfus, Nadia Boutry-Kryza, Cornel Popovici, Laurent Castera, Nancy Uhrhammer, Anthony Laugé, Yves-Jean Bignon, Hélène Delhomelle, Alice Fiévet, Christophe Guy, Noémie Bronnec, Bruno Buecher, Fabienne Prieur, Sophie Demontety, Vincent Goussot, Emmanuelle Mouret-Fourme, Claire Saule, Helene Zattara, Sarah Malsa, Paul Gesta, Cindy Meira, Erell Guillerm, Isabelle Turbiez, Agathe Ricou, Mélanie Léoné, Pierre Vande Perre, Sarab Lizard, Pascaline Berthet, Norbert Lignon, Adrien Buisson, Anne-Marie Birot, Philippe Denizeau, Etienne Rouleau, Odile Cohen-Haguenauer, Veronica Goldbarg, Virginie Moncoutier, Charlotte Benigni, Emmanuelle Barouk-Simonet, Flavie Boulouard, Caroline Jacquot-Sawka, Alice Yvard, Hakima Lallaoui, Veronica Cusin, Angélina Legros, Muriel Belotti, Christine Maugard, Marine Guillaud-Bataille, Jean-Marc Limacher, Marion Gauthier-Villars, Louise Crivelli, Afane Brahimi, Odile Cabaret, Ophelie Bertrand, Michel Longy, Gabrielle Le Guyadec, Doriane Livon, Amelie Bloucard, Dominique Stoppa-Lyonnet, Capucine Delnatte, Caroline Lecerf, Jennifer Carriere, Virginie Guibert, Véronique Mari, Anne-Sophie Allary, Florence Coulet, Françoise Bonnet, Paul Vilquin, Noémie Basset, Khadija Abidallah, Pierre Macquere, Nicolas Derive, Manon Boulaire, Stephanie Chieze-Valéro, Marine Le Mentec, Mathilde Gay-Bellile, Anne-Laure Conoy, Henri Margot, Pierre Devulder, Mathias Schwartz, Isabelle Tennevet, Stéphane Bézieau, Francesca Damiola, Violaine Bourdon, Audrey Mailliez, Zoe Nevière, Nicolas Viellard, Laurence Venat, Antoine De Pauw, Brigitte Bressac-de Paillerets, Agnès Hardouin, Sofiane Lacoste, Sandra Fert-Ferrer, Maud Privat, Helene Larbre, Dominique Vaur, Etienne Muller, Françoise Revillion, Clémentine Legrand, Rosette Lidereau, Laurence Gladieff, Sabine Raad, Jean Chiesa, Diane Molière, Ahmed Bouras, Nicolas Sevenet, Patrick R. Benusiglio, Sophie Giraud, Christine Toulas, Voreak Suybeng, Florine Oca, Tetsuro Noguchi, Catherine Dehainault, Sophie Lejeune, Céline Heude, Catherine Dubois d’Enghein, Thien-vu Nguyen Minh Tuan, Olivier Caron, Mathilde Warcoin, Christine Lasset, Claude Houdayer, Jessica Moretta-Serra, Julie Tinat, Hagay Sobol, Natalie Jones, Fanny Brayotel, Anne Fajac, Virginie Bubien, Maud Blanluet, Jean-Marc Rey, Anne Durlach, Sandrine M. Caputo, Isabelle Coupier, Fatoumata Simaga, Sophie Krieger, Catherine Noguès, Fabrice Airaud, Robin Fouillet, Celine Garrec, Valérie Bonadona, Julie Menjard, Bérengère Legendre, Chrystelle Colas, Christelle Berthemin, Camille Cohen, Caroline Abadie, Olivier Ingster, Audrey Remenieras, Anaïs Dupré, Jessica Le Gall, Lisa Golmard, Marie Bidart, Henrique Tenreiro, J Bombled, Marie-Charlotte Villy, Marie-Agnès Collonge-Rame, Sophie Dussart, Alain Lortholary, Lucie Salle, Samira Fekairi, Service de Génétique Oncologique, Institut Curie [Paris], Université Paris sciences et lettres (PSL), Département de Biologie des Tumeurs, Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Hospices Civils de Lyon (HCL), Centre Léon Bérard [Lyon], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut Gustave Roussy (IGR), Génétique (Biologie pathologie), Département de biologie et pathologie médicales [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre de Références Cancers Rares (PREDIR), INCA, Institut national du cancer [Boulogne] (INCA), Hôpital Européen Georges Pompidou [APHP] (HEGP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpitaux Universitaires Paris Ouest - Hôpitaux Universitaires Île de France Ouest (HUPO), Institut de Cancérologie de l'Ouest [Angers/Nantes] (UNICANCER/ICO), Centre Hospitalier Universitaire de Reims (CHU Reims), dormoy, valerian, Unité fonctionnelle de neurogénétique moléculaire et cellulaire, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière]

Subjects
Cosegregation, Genotype, [SDV]Life Sciences [q-bio], Breast Neoplasms, Biology, Article, 03 medical and health sciences, Likely benign, Genetics, medicine, Humans, Clinical significance, Genetic Predisposition to Disease, Genetic Testing, Uncertain significance, Gene, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 030304 developmental biology, BRCA2 Protein, Ovarian Neoplasms, 0303 health sciences, Cancer predisposition, BRCA1 Protein, 030305 genetics & heredity, Cancer, Genetic Variation, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], Classification methods, Female
Abstract

Up to 80% of BRCA1 and BRCA2 genetic variants remain of uncertain clinical significance (VUSs). Only variants classified as pathogenic or likely pathogenic can guide breast and ovarian cancer prevention measures and treatment by PARP inhibitors. We report the first results of the ongoing French national COVAR (cosegregation variant) study, the aim of which is to classify BRCA1/2 VUSs. The classification method was a multifactorial model combining different associations between VUSs and cancer, including cosegregation data. At this time, among the 653 variants selected, 101 (15%) distinct variants shared by 1,624 families were classified as pathogenic/likely pathogenic or benign/likely benign by the COVAR study. Sixty-six of the 101 (65%) variants classified by COVAR would have remained VUSs without cosegregation data. Of note, among the 34 variants classified as pathogenic by COVAR, 16 remained VUSs or likely pathogenic when following the ACMG/AMP variant classification guidelines. Although the initiation and organization of cosegregation analyses require a considerable effort, the growing number of available genetic tests results in an increasing number of families sharing a particular variant, and thereby increases the power of such analyses. Here we demonstrate that variant cosegregation analyses are a powerful tool for the classification of variants in the BRCA1/2 breast-ovarian cancer predisposition genes.

Published
2021
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8. Seroprevalence of SARs-CoV-2 among the staff and patients of a French cancer centre after first lockdown: the canSEROcov study

Author

Laurent Arnould, Julie Vincent, Elise Ballot, Vincent Goussot, Cléa Fraisse, Charles Coutant, Anne-Laure Simonet-Lamm, Jean-David Fumet, Emilie Redersdorff, Nathalie Bremaud, Siavoshe Ayati, Adele Cueff, François Ghiringhelli, Sylvie Zanetta, Caroline Truntzer, Silvia Ilie, Didier Mayeur, Roxana Hanu, Bruno Coudert, Alice Hervieu, Sylvain Ladoire, Aurélie Lagrange, Aurélie Bertaut, Nils Martin, Coureche Kaderbhai, Leila Bengrine-Lefevre, Irina Mazilu, Laure Favier, Isabelle Desmoulins, Rémi Palmier, and Audrey Hennequin

Subjects
0301 basic medicine, Male, Cancer Research, Serology, 0302 clinical medicine, Hygiene, Seroepidemiologic Studies, Epidemiology, Medicine, Prospective cohort study, Child, media_common, Original Research, Aged, 80 and over, serodiagnosis, seroprevalence, Social distance, Middle Aged, Oncology, 030220 oncology & carcinogenesis, Child, Preschool, Carrier State, Female, France, medicine.symptom, Adult, medicine.medical_specialty, Adolescent, media_common.quotation_subject, Health Personnel, SARS-COV-2, Cancer Care Facilities, Asymptomatic, COVID-19 Serological Testing, staff, 03 medical and health sciences, Young Adult, Seroprevalence, Humans, Antibody, Aged, business.industry, healthcare workers, Cancer, COVID-19, cancer center, Cancer patients, medicine.disease, Personnel, Hospital, 030104 developmental biology, Family medicine, business
Abstract

Background In view of the potential gravity of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection for patients with cancer, epidemiological data are vital to assess virus circulation among patients and staff of cancer centres. We performed a prospective study to investigate seroprevalence of SARS-CoV-2 antibodies among staff and patients with cancer at a large cancer centre, at the end of the period of first national lockdown in France and to determine factors associated with the risk of SARS-CoV-2 infection. Methods After the first lockdown, all medical and non-medical staff, as well as all patients attending the medical oncology department were invited to undergo serological testing for SARS-CoV-2 between 11 May and 30 June 2020. All participants were also invited to complete a questionnaire collecting data about their living and working conditions, and for patients, medical management during lockdown. Findings A total of 1,674 subjects (663 staff members, 1011 patients) were included. Seroprevalence was low in both staff (1.8%) and patients (1.7%), despite more features of high risk for severe forms among patients. None of the risk factors tested in our analysis (working or living conditions, comorbidities, management characteristics during lockdown) was found to be statistically associated with seroprevalence in either staff or patients. There was no significant difference in the proportion of symptomatic and asymptomatic subjects between staff and patients. Only fever, loss of smell, and loss of taste were significantly more frequent among seropositive patients, in both staff and patients. Interpretation We report very low seroprevalence of antibodies against SARS-CoV-2 in the staff (caregiving and non-caregiving) and patients of a large cancer care centre in which strict hygiene, personal protection, and social distancing measures were implemented.

Published
2021

9. Author response for 'Further delineation of the NTHL1 associated syndrome: a report from the French oncogenetic consortium'

Author

Vincent Goussot, Véronica Cusin, Flavie Boulouard, Nancy Uhrhammer, Jacques Mauillon, Sophie Lejeune, Stéphanie Vasseur, Michel Bahuau, Stéphanie Baert-Desurmont, Emmanuelle Barouk Simonet, Lisa Golmard, Marion Dhooge, Camille Tlemsani, Sandrine Manase, Thierry Frebourg, Gwendoline Lienard, Marie-Pascale Beaumont, Edwige Kasper, Marie-Pierre Buisine, Gaëlle Bougeard, Virginie Bubien, Nadim Hamzaoui, Jean-Marc Rey, Stéphane Pinson, Florence Coulet, Claude Houdayer, Elodie Lacaze, and Christine Toulas

Published
2020
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10. Further delineation of the NTHL1 associated syndrome: A report from the French Oncogenetic Consortium

Author

Thierry Frebourg, Gwendoline Lienard, Stéphanie Baert-Desurmont, Camille Tlemsani, Nadim Hamzaoui, Lisa Golmard, Michel Bahuau, Gaëlle Bougeard, Edwige Kasper, Vincent Goussot, Stéphane Pinson, Elodie Lacaze, Marie-Pascale Beaumont, Emmanuelle Barouk Simonet, Sandrine Manase, Christine Toulas, Sophie Lejeune, Nancy Uhrhammer, Flavie Boulouard, Jacques Mauillon, Véronica Cusin, Stéphanie Vasseur, Marion Dhooge, Marie-Pierre Buisine, Claude Houdayer, Virginie Bubien, Florence Coulet, and Jean-Marc Rey

Subjects
0301 basic medicine, Oncology, Adult, Male, medicine.medical_specialty, Heterozygote, Colorectal cancer, Colonoscopy, Breast Neoplasms, 030105 genetics & heredity, 03 medical and health sciences, Deoxyribonuclease (Pyrimidine Dimer), Breast cancer, MUTYH, Neoplastic Syndromes, Hereditary, Internal medicine, Genetics, medicine, Biomarkers, Tumor, Humans, Basal cell carcinoma, Genetics (clinical), Germ-Line Mutation, Aged, Ovarian Neoplasms, medicine.diagnostic_test, business.industry, Reverse Transcriptase Polymerase Chain Reaction, Melanoma, Cancer, Middle Aged, medicine.disease, Pedigree, 030104 developmental biology, Adenomatous Polyposis Coli, Female, Sarcoma, business, Colorectal Neoplasms
Abstract

Biallelic pathogenic variants in the NTHL1 (Nth Like DNA Glycosylase 1) gene cause a recently identified autosomal recessive hereditary cancer syndrome predisposing to adenomatous polyposis and colorectal cancer. Half of biallelic carriers also display multiple colonic or extra-colonic primary tumors, mainly breast, endometrium, urothelium and brain tumors. Published data designate NTHL1 as an important contributor to hereditary cancers but also underline the scarcity of available informations. Thanks to the French oncogenetic consortium (Groupe Genetique et Cancer), we collected NTHL1 variants from 7765 patients attending for hereditary colorectal cancer or polyposis (n =3936) or other hereditary cancers (n =3829). Here, we describe ten patients with pathogenic biallelic NTHL1 germline variants i.e. the second largest NTHL1 series. All carriers were from the "colorectal cancer or polyposis" series. All 9 biallelic carriers who underwent colonoscopy presented adenomatous polyps. For digestive cancers, average age at diagnosis was 56.2 and we reported colorectal, duodenal, caecal and pancreatic cancers. Extra-digestive malignancies included sarcoma, basal cell carcinoma, breast cancer, urothelial carcinoma and melanoma. Although tumor risks remain to be precisely defined, these novel data support NTHL1 inclusion in diagnostic panel testing. Colonic surveillance should be conducted based on MUTYH recommendations while extra-colonic surveillance has to be defined. This article is protected by copyright. All rights reserved.

Published
2020

11. Does large NGS panel analysed using exome tumour sequencing improve the management of advanced non-small-cell lung cancers?

Author

François Ghiringhelli, Laure Favier, Cléa Fraisse, Valentin Derangère, Pascal Foucher, Lorraine Dalens, Caroline Truntzer, Vincent Goussot, Laurent Arnould, Sandy Chevrier, Juliette Albuisson, Aurélie Lagrange, Virginie Westeel, Romain Boidot, Julie Niogret, Courèche-Guillaume Kaderbhai, Ayoub Zouak, and Bruno Coudert

Subjects
Pulmonary and Respiratory Medicine, Oncology, Cancer Research, medicine.medical_specialty, Lung Neoplasms, medicine.medical_treatment, Germline, Targeted therapy, Internal medicine, Carcinoma, Non-Small-Cell Lung, Medicine, Humans, Exome, Lung cancer, Lung, business.industry, High-Throughput Nucleotide Sequencing, Oncogenes, Precision medicine, medicine.disease, Cancer related genes, medicine.anatomical_structure, Mutation, Non small cell, business
Abstract

Introduction Non-small-cell lung cancer (NSCLC) is one of the most common and deadly cancers. Several molecular drivers of oncogene addiction are now known to be strong predictive biomarkers for target therapies. Advances in large Next Generation Sequencing (LNGS) have improved the ability to detect potentially targetable mutations. However, the integration of LNGS into clinical management in an individualized manner remains challenging. Methods In this single-center observational study we included all patients with advanced NSCLC who underwent LNGS. Somatic and germline exome analysis was performed with a restriction on 323 cancer related genes. Variants were classified and Molecular Tumour Board (MTB) made therapeutic propositions. Results We performed LNGS analysis in 281 patients with advanced NSCLC between March 2015 and January 2018. Technical failure occurred in only 3% of cases. Three hundred and fifty-six targetable mutations were detected. At least one targetable mutation was found in 209 patients. For all these patients, the MTB was able to recommend treatment with a targeted agent based on the evaluation of the tumour’s genetic profile and treatment history. Twenty-nine patients (13.9%) were subsequently treated with an MTB-recommended targeted therapy. We did not observe any improvement in terms of clinical benefit for these patients. Conclusions In this case series, we show that including LNGS into routine clinical management was feasible but does not appear to provide clinical benefit in the management of patients with advanced NSCLC.

Published
2020

12. A novel POLD1 pathogenic variant identified in two families with a cancer spectrum mimicking Lynch syndrome

Author

Clémentine Legrand, Marine Lebrun, Pierre Naïbo, Magalie Peysselon, Fabienne Prieur, Caroline Kientz, Françoise Desseigne, Sandrine Handallou, Jean-Marc Rey, Sophie Nambot, Vincent Goussot, Nadim Hamzaoui, and Qing Wang

Subjects
Adult, Aged, 80 and over, Male, Heterozygote, Colonic Polyps, General Medicine, Middle Aged, Colorectal Neoplasms, Hereditary Nonpolyposis, Pedigree, Diagnosis, Differential, Phenotype, Mutation, Genetics, Humans, Female, Genetics (clinical), Aged, DNA Polymerase III
Abstract

The POLD1 gene is involved in DNA proofreading to ensure accurate DNA replication. Some germline alterations in its exonuclease domain are associated with predisposition to cancers and colonic polyps. Only a few pathogenic variants have been clearly identified so far. Here we report a novel variant: c.1458GT p.(Lys486Asn) that we classified as pathogenic, detected in two putatively unrelated families. The cancer spectrum was very similar to Lynch syndrome, implying an overlapped tissue susceptibility. The common presence of colonic polyps in carriers and the MMR proficient phenotype in tumors were distinctive features suggesting POLD1 implication. Some clinical characteristics observed in the carriers of this variant differed from those reported previously, suggesting a potential genotype/phenotype correlation, and very likely in relation to the functional importance of affected residues. Our findings provide further insight into understanding the role of POLD1 in cancer-related risk.

Published
2022
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13. Clinical value of CEA for detection of distant metastases in newly diagnosed breast cancer: comparison with CA 15-3

Author

Alina Berriolo-Riedinger, Guillaume Maccio, Jean-Marc Riedinger, and Vincent Goussot

Subjects
Adult, Oncology, medicine.medical_specialty, Population, CA 15-3, Breast Neoplasms, Newly diagnosed, Sensitivity and Specificity, 01 natural sciences, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Carcinoembryonic antigen, Predictive Value of Tests, Internal medicine, Biomarkers, Tumor, medicine, Humans, Neoplasm Metastasis, education, Aged, Retrospective Studies, Aged, 80 and over, education.field_of_study, biology, business.industry, Mucin-1, 010401 analytical chemistry, Cancer, Retrospective cohort study, General Medicine, Middle Aged, medicine.disease, Metastatic breast cancer, Carcinoembryonic Antigen, 0104 chemical sciences, ROC Curve, Disease Progression, 030221 ophthalmology & optometry, biology.protein, Female, business
Abstract

The aim of the study is to investigate the clinical value of CEA (carcinoembryonic antigen) for detection of distant metastases (DM) in newly diagnosed breast cancer. This retrospective study focuses on a population of 929 patients with locally advanced breast cancer (n=521) or metastatic breast cancer (n=408) diagnosed at the CGFL (Centre Georges Francois Leclerc) from 1998 to 2014. These patients underwent a measurement of CA 15-3, a measurement of CEA and an assessment of extension before any treatment. The initial concentrations of CEA are correlated with conventional prognostic factors. The cut-off value of CEA was determined and verified on two independents subpopulations determined in drawing lots. The ROC curve shows an AUC of 0.82 (p0.0001). At the threshold of 6.7 μg/L, CEA before treatment has a predictive value on the existence of DM independently of the CA 15-3 and other prognostic factors. The combination of CEA and CA 15-3 increases significantly the predictive value of CA 15-3 on the whole population (sensitivity increased by 9%) and on tumors expressing hormonal receptors. Concerning the only CEA the rate of false negative is of 52% and depends on the number and the type of the metastatic localization. Among the 28 patients without DM and a CEA6.7 μg/L, 15 have developed DM and 2 a new cancer. Thirteen will die of cancer. In conclusion, these facts confirm the independently predictive value of CEA before treatment on the existence of DM and its complementarity with CA 15-3 during the assessment of extension by imagery.

Published
2017
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14. ACE et diagnostic précoce de récidive dans les différents sous-types moléculaires de cancer du sein : comparaison au CA 15-3

Author

Jean-Marc Riedinger, Véronique Lorgis, Françoise Beltjens, Vincent Goussot, Charles Coutant, Sarab Lizard, Isabelle Desmoulins, and Pierre Fumoleau

Subjects
Gynecology, Cancer Research, medicine.medical_specialty, business.industry, CA 15-3, Early detection, Hematology, General Medicine, medicine.disease, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Oncology, 030220 oncology & carcinogenesis, medicine, Radiology, Nuclear Medicine and imaging, 030212 general & internal medicine, business
Abstract

Resume Cette etude retrospective evalue l’interet du dosage de l’ACE pour la detection precoce des recidives des cancers du sein. Sur une population de 804 patientes porteuses d’un cancer du sein invasif, nous avons etudie 260 patientes dont 97 patientes sans recidive (SR) depuis plus de 5 ans, 32 patientes avec une recidive locale (RL) isolee et 131 patientes avec au moins une metastase a distance (MAD). Des concentrations elevees d’ACE et de CA 15-3 (> 3,1 μg/L et > 26 kU/L) ont ete trouvees chez 6 et 22 % des patientes avec une RL et chez 49 et 69 % des patientes avec MAD respectivement. L’ACE et le CA 15-3 ont une valeur predictive independante au diagnostic de MAD. Les elevations de l’ACE et du CA 15-3 sont etroitement correlees a la positivite des recepteurs hormonaux. Les sensibilites de l’ACE et du CA 15-3 sont respectivement de 23 et 65 % dans le groupe des tumeurs de profil triple negatif, de 58 et 75 % pour les tumeurs de type luminal, 56 et 78 % chez les tumeurs luminal-HER2, 50 et 30 % chez les tumeurs HER2 -enriched ( p = 0,0094 et 0,0252 respectivement). La combinaison de l’ACE et du CA 15-3 augmente la sensibilite de CA 15-3 dans les profils luminal et HER2 -enriched . En conclusion, l’elevation de l’ACE et du CA 15-3 au diagnostic de MAD est tres correlee a la positivite des recepteurs hormonaux et au profil moleculaire de la tumeur. L’association de l’ACE et du CA 15-3 apparait utile specialement dans les profils luminal et HER2 -enriched .

Published
2016
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15. [CA 125 assay in the extension assessment of newly diagnosed breast cancers: why and how?]

Author

Anne, Laffont, Vincent, Goussot, Alina, Berriolo-Riedinger, and Jean-Marc, Riedinger

Subjects
Adult, Aged, 80 and over, Mucin-1, Aftercare, Breast Neoplasms, Middle Aged, Sensitivity and Specificity, Carcinoembryonic Antigen, Cystadenocarcinoma, Serous, ROC Curve, Predictive Value of Tests, CA-125 Antigen, Biomarkers, Tumor, Humans, Female, Inflammatory Breast Neoplasms, Neoplasm Metastasis, Aged, Retrospective Studies
Abstract

CA 125 assay is sometimes combined in practice with the one of CA 15-3 and CEA in the extension assessment of breast cancers. The purpose of this work is to evaluate the contribution of the initial CA 125 as an indicator of distant metastases (DM) or of serous inflammation (SI). This retrospective study concerns a population of 620 patients with breast cancer without metastatic extension (n=325) or metastatic breast cancer (n=295) diagnosed at the Georges-François Leclerc center from 1998 to 2014. Seventy-four patients had SI. We showed that initial CA 125 level is linked to the TNM clinic status, the HER2 status, the nature and the number of metastatic locations, the inflammation of the tumor or serous. The ROC curves and logistic regression analyses show that CA 125 is an independent predictive criterion of DM presence (threshold of 55 kU/L): this is the only positive marker in 7% of patients with DM. At the threshold of 110 kU/L, the CA 125 is the only predictive biologic factor for SI. In conclusion, these data present the independent predictive value of CA 125 on the presence of DM or SI on condition of usinga specific threshold for each of these uses.

Published
2018

16. Intérêt clinique du CA 15-3 dans la détection précoce des récidives de cancer du sein localement avancé

Author

Pierre Fumoleau, Françoise Beltjens, Véronique Lorgis, Sarab Lizard, Jean-Marc Riedinger, C. Dalban, Vincent Goussot, Charles Coutant, Stéphane Konan, and Isabelle Desmoulins

Subjects
Oncology, Cancer Research, medicine.medical_specialty, Receptor Status, business.industry, CA 15-3, Early detection, Distant metastasis, Retrospective cohort study, Hematology, General Medicine, medicine.disease, Breast cancer, Internal medicine, Predictive value of tests, medicine, Radiology, Nuclear Medicine and imaging, Differential diagnosis, business
Abstract

This retrospective study evaluates the interest of CA 15-3 measurement for early detection of breast cancer recurrences. Among 804 patients with invasive breast cancer we selected 117 patients without recurrence (WR) for 5 years or more, 33 with a local recurrence (LR) and 149 with at least one distant metastasis (DM). The sensitivity of CA 15-3 depends on the type of recurrence ([LR] or [DM]), the localization of unique DM, the presence and the number of metastatic sites, on hormonal receptor status and tumor subtypes. The number of metastatic sites and hormonal receptor status are independent predictive criteria of an elevation of CA 15-3. The analysis of ROC curve in order to separate patients with DM and patients WR shows an AUC of 0.87 (p

Published
2015
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17. Identification and validation of a factor of commutability between platelet counts performed on EDTA and citrate

Author

Vincent Goussot, Sarab Lizard, Jean-Marc Riedinger, Alice David, and Pierre Dumont

Subjects
Adult, Male, medicine.medical_specialty, 040301 veterinary sciences, medicine.drug_class, Giemsa stain, Citric Acid, 0403 veterinary science, Andrology, chemistry.chemical_compound, Internal medicine, 0502 economics and business, medicine, Prevalence, Humans, Platelet, False Positive Reactions, Diagnostic Errors, Edetic Acid, Aged, Aged, 80 and over, Hematology, business.industry, Platelet Count, 05 social sciences, Anticoagulant, Anticoagulants, 04 agricultural and veterinary sciences, General Medicine, Middle Aged, Thrombocytopenia, Blood smear, chemistry, 050211 marketing, Female, Citric acid, business, Artifacts
Abstract

The anticoagulant mostly employed for platelet count is EDTA. The Francophone Group of Cellular Hematology recommends checking of blood smear stained with May-Grunwald Giemsa any thrombocytopenia less than 100 G/L without medical history or whether an alarm is generated by the cell counter. The pseudo-thrombocytopenia (PTP) with EDTA is the best known artifact in platelet count. A sample of blood on citrated tube is necessary to get rid of the interference. The objective of this study was to compare the platelet counts obtained on EDTA (numEDTA) and citrate (numCTAD) tubes and to define, then validate a factor of conversion between both methods. The prevalence of PTP EDTA is 0.26%. The PTP was transient in 80% of the patients. The numEDTA and numCTAD+10% (numCTAD increased by 10% to take dilution into account) are correlated but are not equivalent. The numCTAD+10% underestimate numEDTA significantly. The systematic bias is removed if we increase by 17% numCTAD. The factor of correction is stable over a period of 3 hours.

Published
2017

18. [Validation steps for the detection of L858R mutation in EGFR gene by real time quantitative PCR]

Author

Anne Gibeaud, Muriel Cadouot, Jean-Marc Riedinger, Astrid Brasselet, Sarab Lizard, Emeline Saitta, Vincent Goussot, Didier Bozonnet, and Marine Jourdain

Subjects
Oncology, Fastidious organism, medicine.medical_specialty, Lung Neoplasms, DNA Mutational Analysis, Mutation, Missense, Arginine, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Egfr tki, Leucine, Limit of Detection, Internal medicine, Carcinoma, Non-Small-Cell Lung, medicine, Humans, Gene, Cells, Cultured, business.industry, Cancer, Reproducibility of Results, Amino acid substitution, General Medicine, medicine.disease, respiratory tract diseases, ErbB Receptors, Real-time polymerase chain reaction, Amino Acid Substitution, Non small lung cancer, MCF-7 Cells, business, L858r mutation
Abstract

Since January 16(th) 2010, the French legislation requires that the medical laboratories must be accredited according to ISO 15189 standards. This concerned all the biological medical technics, including molecular biology technics. In this work, we described the validation steps by real time quantitative PCR of L858R mutation in EGFR gene, frequently detected in non-small lung cancers (NSCLC). Epidermal growth factor - tyrosine kinase inhibitors (EGFR-TKIs) are authorized in Europe for the treatment of metastatic NSCLC after failure of, at least one, prior chemotherapy. Thus, in view of accreditation of this analysis, we have used the recommendation of the COFRAC (Comite francais d'accreditation) and INCa (Institut national du cancer). Several parameters have been tested, such as the primers, the limit of detection, and the sensitivity and specificity of the method. In addition, a risk study has been evaluated. Although long and fastidious, the method of validation is required to perform analysis in optimal conditions to guaranty optimal results for the patients.

Published
2016

19. Restoring Anticancer Immune Response by Targeting Tumor-Derived Exosomes With a HSP70 Peptide Aptamer

Author

Cédric Rébé, Hajare Mjahed, Nicolas Pernet, Victor Clausse, Carmen Garrido, Renaud Seigneuric, Sarah Richaud, Pierre Fumoleau, Alexandre M.M. Dias, François Ghiringhelli, Guillaume Marcion, Nicolas Isambert, Vincent Goussot, Marine Cordonnier, Frédéric Lirussi, Jessica Gobbo, Aurélie de Thonel, Aurélie Bertaut, Arlette Hammann, Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Laboratoire d'Excellence : Lipoprotéines et Santé : prévention et Traitement des maladies Inflammatoires et du Cancer (LabEx LipSTIC), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Paris-Sud - Paris 11 (UP11)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Gustave Roussy (IGR)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Bourgogne (UB)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Fédération Francophone de la Cancérologie Digestive, FFCD-Université de Montpellier (UM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS BFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Département d'oncologie médicale [Centre Georges-François Leclerc], Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER, Institut Charles Sadron (ICS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), UNICANCER, Unité de biostatistiques [Centre Georges-François Leclerc], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Physiologie de la Nutrition et Toxicologie (NUTox) (U866, Lipides et nutrition, équipe 7) (NUTox), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA)-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Institut National du Cancer, Conseil Regional de Bourgogne, ANR-11-LABX-0021,Lipstic,Lipoprotéines et santé : prévention et traitement des maladies inflammatoires non vasculaires et du cancer(2011), European Project: 248835,EC:FP7:ICT,FP7-ICT-2009-4,SPEDOC(2010), Centre épigénétique et destin cellulaire (EDC (UMR_7216)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Paris-Sud - Paris 11 (UP11)-École pratique des hautes études (EPHE)-Institut Gustave Roussy (IGR)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Université de Bourgogne (UB)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc (CRLCC - CGFL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Fédération Francophone de la Cancérologie Digestive, FFCD-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement français du sang [Bourgogne-France-Comté] (EFS [Bourgogne-France-Comté])-Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon)-Université de Franche-Comté (UFC)-Université de Montpellier (UM), Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc (CRLCC - CGFL), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), ANR-11-LABX-0021/11-LABX-0021,Lipstic,Lipoprotéines et santé : prévention et traitement des maladies inflammatoires non vasculaires et du(2011), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Paris-Sud - Paris 11 (UP11)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Gustave Roussy (IGR)-Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy)-Université de Bourgogne (UB)-Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon)-Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Fédération Francophone de la Cancérologie Digestive, FFCD-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Montpellier (UM), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0021,Lipstic,Lipoprotéines et santé : prévention et traitement des maladies inflammatoires non vasculaires et du(2011), UNICANCER-UNICANCER-Institut National de la Santé et de la Recherche Médicale (INSERM)-Fédération Francophone de la Cancérologie Digestive, FFCD-Université de Montpellier (UM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), and Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace (FMNGE)

Subjects
Male, 0301 basic medicine, Cancer Research, Lung Neoplasms, [SDV]Life Sciences [q-bio], Exosomes, Mice, Mechanisms, Myeloid Cells, ComputingMilieux_MISCELLANEOUS, Cancer, Ovarian Neoplasms, 3. Good health, Phenotype, Oncology, Colonic Neoplasms, Female, medicine.drug, Myeloid suppressor-Cells, B-cells, Antineoplastic Agents, Breast Neoplasms, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, 03 medical and health sciences, Lymphocytes, Tumor-Infiltrating, Immune system, Cell Line, Tumor, medicine, Animals, Humans, HSP70 Heat-Shock Proteins, Cell Proliferation, Cisplatin, Macrophages, Neoplasms, Experimental, medicine.disease, Molecular biology, Toll-Like Receptor 2, Microvesicles, Mice, Inbred C57BL, Membrane heat-shock-protein-70 Hsp70, TLR2, Interferometry, 030104 developmental biology, Tumor progression, Release, Cancer cell, Myeloid-derived Suppressor Cell, Aptamers, Peptide, Spleen
Abstract

International audience; Background: Exosomes, via heat shock protein 70 (HSP70) expressed in their membrane, are able to interact with the toll-like receptor 2 (TLR2) on myeloid-derived suppressive cells (MDSCs), thereby activating them.Methods: We analyzed exosomes from mouse (C57Bl/6) and breast, lung, and ovarian cancer patient samples and cultured cancer cells with different approaches, including nanoparticle tracking analysis, biolayer interferometry, FACS, and electron microscopy. Data were analyzed with the Student's t and Mann-Whitney tests. All statistical tests were two-sided.Results: We showed that the A8 peptide aptamer binds to the extracellular domain of membrane HSP70 and used the aptamer to capture HSP70 exosomes from cancer patient samples. The number of HSP70 exosomes was higher in cancer patients than in healthy donors (mean, ng/mL +/- SD = 3.5 +/- 1.7 vs 0.17 +/- 0.11, respectively, P = .004). Accordingly, all cancer cell lines examined abundantly released HSP70 exosomes, whereas "normal" cells did not. HSP70 had higher affinity for A8 than for TLR2; thus, A8 blocked HSP70/TLR2 association and the ability of tumor-derived exosomes to activate MDSCs. Treatment of tumor-bearing C57Bl/6 mice with A8 induced a decrease in the number of MDSCs in the spleen and inhibited tumor progression (n = 6 mice per group). Chemotherapeutic agents such as cisplatin or 5FU increase the amount of HSP70 exosomes, favoring the activation of MDSCs and hampering the development of an antitumor immune response. In contrast, this MDSC activation was not observed if cisplatin or 5FU was combined with A8. As a result, the antitumor effect of the drugs was strongly potentiated.Conclusions: A8 might be useful for quantifying tumor-derived exosomes and for cancer therapy through MDSC inhibition.

Published
2016
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20. [CEA and early detection of relapse in breast cancer subtypes: Comparison with CA 15-3]

Author

Jean-Marc, Riedinger, Vincent, Goussot, Isabelle, Desmoulins, Véronique, Lorgis, Charles, Coutant, Françoise, Beltjens, Sarab, Lizard, and Pierre, Fumoleau

Subjects
Adult, Aged, 80 and over, Time Factors, Receptor, ErbB-2, Mucin-1, Breast Neoplasms, Triple Negative Breast Neoplasms, Middle Aged, Sensitivity and Specificity, Carcinoembryonic Antigen, Predictive Value of Tests, Humans, Female, Neoplasm Recurrence, Local, Early Detection of Cancer, Aged, Retrospective Studies
Abstract

This retrospective study evaluates the interest of CEA measurement for early detection of breast cancer recurrences. Among 804 patients with invasive breast cancer, we selected 97 patients without recurrence (WR) for 5 years or more, 32 with a local recurrence (LR) and 131 with at least one distant metastasis (DM). Elevated CEA and CA 15-3 levels (3.1 μg/L and26 kU/L respectively) were found in 6 % and 22 % of patients with RL respectively and in 49 % and 69 % of patients with DM. Both CEA and CA 15-3 retained a significant value in predicting DM by univariate and multivariate analysis. Higher sensitivity of CEA and CA 15-3 were found in tumors with positive hormonal receptor status. CEA and CA 15-3 levels at DM were raised respectively in 23 and 65 % of the triple negative group, 58 and 75 % of the luminal, 56 and 78 % of the luminal-HER2 and 50 and 30 % of HER2-enriched group (P=0.0094 and 0.0252 respectively). The combination of CEA and CA 15-3 increased CA 15-3 sensitivity in especially luminal and HER2-enriched groups. In conclusion, elevated CA 15-3 and CEA levels at initial diagnosis of recurrence were found to be associated with hormonal receptor status and breast cancer subtypes. The combination of CEA and CA 15-3 appeared useful especially luminal and HER2-enriched groups.

Published
2015

21. [Clinical value of CA 15-3 for early detection of relapse in locally advanced breast cancer]

Author

Stéphane, Konan, Vincent, Goussot, Isabelle, Desmoulins, Véronique, Lorgis, Charles, Coutant, Pierre, Fumoleau, Françoise, Beltjens, Cécile, Dalban, Sarab, Lizard, and Jean-Marc, Riedinger

Subjects
Adult, Aged, 80 and over, Mucin-1, Breast Neoplasms, Middle Aged, Sensitivity and Specificity, Diagnosis, Differential, ROC Curve, Predictive Value of Tests, Humans, Regression Analysis, Female, Neoplasm Recurrence, Local, Early Detection of Cancer, Aged, Retrospective Studies
Abstract

This retrospective study evaluates the interest of CA 15-3 measurement for early detection of breast cancer recurrences. Among 804 patients with invasive breast cancer we selected 117 patients without recurrence (WR) for 5 years or more, 33 with a local recurrence (LR) and 149 with at least one distant metastasis (DM). The sensitivity of CA 15-3 depends on the type of recurrence ([LR] or [DM]), the localization of unique DM, the presence and the number of metastatic sites, on hormonal receptor status and tumor subtypes. The number of metastatic sites and hormonal receptor status are independent predictive criteria of an elevation of CA 15-3. The analysis of ROC curve in order to separate patients with DM and patients WR shows an AUC of 0.87 (p0.0001). The optimal discriminative threshold is 26 kU/L. In conclusion, these data confirm that CA 15-3 increase depends on the kind of evolution and on initial tumor's hormonal status.

Published
2015

22. A new hybrid record linkage process to make epidemiological databases interoperable: application to the GEMO and GENEPSO studies involving BRCA1 and BRCA2 mutation carriers

Author

Jiao, Yue, Lesueur, Fabienne, Azencott, Chloé-Agathe, Laurent, Maïté, Mebirouk, Noura, Laborde, Lilian, Beauvallet, Juana, Dondon, Marie-Gabrielle, Eon-Marchais, Séverine, Laugé, Anthony, Noguès, Catherine, Andrieu, Nadine, Stoppa-Lyonnet, Dominique, Caputo, Sandrine, Boutry-Kryza, Nadia, Calender, Alain, Giraud, Sophie, Léone, Mélanie, Bressac- de Paillerets, Brigitte, Caron, Olivier, Guillaud-Bataille, Marine, Bignon, Yves-Jean, Uhrhammer, Nancy, Bonadona, Valérie, Lasset, Christine, Berthet, Pascaline, Castera, Laurent, Vaur, Dominique, Bourdon, Violaine, Noguchi, Tetsuro, Popovici, Cornel, Remenieras, Audrey, Sobol, Hagay, Coupier, Isabelle, Harmand, Pierre-Olivier, Pujol, Pascal, Vilquin, Paul, Dumont, Aurélie, Révillion, Françoise, Muller, Danièle, Barouk-Simonet, Emmanuelle, Bonnet, Françoise, Bubien, Virginie, Longy, Michel, Sevenet, Nicolas, Gladieff, Laurence, Guimbaud, Rosine, Feillel, Viviane, Toulas, Christine, Dreyfus, Hélène, Leroux, Dominique, Peysselon, Magalie, Rebischung, Christine, Baurand, Amandine, Bertolone, Geoffrey, Coron, Fanny, Faivre, Laurence, Goussot, Vincent, Jacquot, Caroline, Sawka, Caroline, Kientz, Caroline, Lebrun, Marine, Prieur, Fabienne, Fert-Ferrer, Sandra, Mari, Véronique, Venat-Bouvet, Laurence, Bézieau, Stéphane, Delnatte, Capucine, Mortemousque, Isabelle, Coulet, Florence, Soubrier, Florent, Warcoin, Mathilde, Bronner, Myriam, Lizard, Sarab, Sokolowska, Johanna, Collonge-Rame, Marie-Agnès, Damette, Alexandre, Gesta, Paul, Lallaoui, Hakima, Chiesa, Jean, Molina-Gomes, Denise, Ingster, Olivier, Manouvrier-Hanu, Sylvie, Lejeune, Sophie, Pontois, Pauline, Lyonnet, Dominique Stoppa, Gauthier-Villars, Marion, Buecher, Bruno, Mouret-Fourme, Emmanuelle, Fricker, Jean-Pierre, Luporsi, Elisabeth, Frenay, Marc, Eisinger, Francois, Moretta, Jessica, Dugast, Catherine, Colas, Chrystelle, Lortholary, Alain, Vennin, Philippe, Adenis, Claude, Nguyen, Tan Dat, Rossi, Annick, Tinat, Julie, Tennevet, Isabelle, Limacher, Jean-Marc, Maugard, Christine, Bignon, Jean-Yves, Demange, Liliane, Cohen-Haguenauer, Odile, Gilbert, Brigitte, Zattara-Cannoni, Hélène, Institut Curie [Paris], Université Paris sciences et lettres (PSL), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Bioinformatique (CBIO), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Unité de génétique et biologie des cancers (U830), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Descartes - Paris 5 (UPD5), Aix Marseille Université (AMU), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Paris (UP), Nadia Boutry-Kryza, Alain Calender, Sophie Giraud, Mélanie Léone, Brigitte Bressac-de-Paillerets, Olivier Caron, Marine Guillaud-Bataille, Yves-Jean Bignon, Nancy Uhrhammer, Valérie Bonadona, Christine Lasset, Pascaline Berthet, Laurent Castera, Dominique Vaur, Violaine Bourdon, Catherine Noguès, Tetsuro Noguchi, Cornel Popovici, Audrey Remenieras, Hagay Sobol, Isabelle Coupier, Pierre-Olivier Harmand, Pascal Pujol, Paul Vilquin, Aurélie Dumont, Françoise Révillion, Danièle Muller, Emmanuelle Barouk-Simonet, Françoise Bonnet, Virginie Bubien, Michel Longy, Nicolas Sévenet, Laurence Gladieff, Rosine Guimbaud, Viviane Feillel, Christine Toulas, Hélène Dreyfus, Dominique Leroux, Magalie Peysselon, Christine Rebischung, Amandine Baurand, Geoffrey Bertolone, Fanny Coron, Laurence Faivre, Vincent Goussot, Caroline Jacquot, Caroline Sawka, Caroline Kientz, Marine Lebrun, Fabienne Prieur, Sandra Fert-Ferrer, Véronique Mari, Laurence Vénat-Bouvet, Stéphane Bézieau, Capucine Delnatte, Isabelle Mortemousque, Florence Coulet, Florent Soubrier, Mathilde Warcoin, Myriam Bronner, Sarab Lizard, Johanna Sokolowska, Marie-Agnès Collonge-Rame, Alexandre Damette, Paul Gesta, Hakima Lallaoui, Jean Chiesa, Denise Molina-Gomes, Olivier Ingster, Sylvie Manouvrier-Hanu, Sophie Lejeune, Catherine Noguès, Lilian Laborde, Pauline Pontois, Dominique Stoppa-Lyonnet, Marion Gauthier-Villars, Bruno Buecher, Olivier Caron, Emmanuelle Mouret-Fourme, Jean-Pierre Fricker, Christine Lasset, Valérie Bonadona, Pascaline Berthet, Laurence Faivre, Elisabeth Luporsi, Marc Frénay, Laurence Gladieff, Paul Gesta, Hagay Sobol, François Eisinger, Jessica Moretta, Michel Longy, Catherine Dugast, Chrystelle Colas, Florent Soubrier, Isabelle Coupier, Pascal Pujol, Alain Lortholary, Philippe Vennin, Claude Adenis, Tan Dat Nguyen, Capucine Delnatte, Annick Rossi, Julie Tinat, Isabelle Tennevet, Jean-Marc Limacher, Christine Maugard, Yves-Jean Bignon, Liliane Demange, Hélène Dreyfus, Odile Cohen-Haguenauer, Brigitte Gilbert, Dominique Leroux, Hélène Zattara-Cannoni, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris Cité (UPCité), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Malbec, Odile, and Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC)

Subjects
Risk, Medicine (General), Databases, Factual, Epidemiology, Computer science, [SDV]Life Sciences [q-bio], Breast Neoplasms, Health Informatics, computer.software_genre, Cohort Studies, 03 medical and health sciences, Record linkage, R5-920, 0302 clinical medicine, Humans, Genetic Predisposition to Disease, Prospective Studies, 030212 general & internal medicine, AdaBoost, Supervised machine learning, BRCA2 Protein, Linkage (software), [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Database, BRCA1 Protein, Random forest, Support vector machine, Identifier, [SDV] Life Sciences [q-bio], Identification (information), Probabilistic linkage, Hybrid process, 030220 oncology & carcinogenesis, Mutation, Mutation (genetic algorithm), Female, computer, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Research Article
Abstract

Background Linking independent sources of data describing the same individuals enable innovative epidemiological and health studies but require a robust record linkage approach. We describe a hybrid record linkage process to link databases from two independent ongoing French national studies, GEMO (Genetic Modifiers of BRCA1 and BRCA2), which focuses on the identification of genetic factors modifying cancer risk of BRCA1 and BRCA2 mutation carriers, and GENEPSO (prospective cohort of BRCAx mutation carriers), which focuses on environmental and lifestyle risk factors. Methods To identify as many as possible of the individuals participating in the two studies but not registered by a shared identifier, we combined probabilistic record linkage (PRL) and supervised machine learning (ML). This approach (named “PRL + ML”) combined together the candidate matches identified by both approaches. We built the ML model using the gold standard on a first version of the two databases as a training dataset. This gold standard was obtained from PRL-derived matches verified by an exhaustive manual review. Results The Random Forest (RF) algorithm showed a highest recall (0.985) among six widely used ML algorithms: RF, Bagged trees, AdaBoost, Support Vector Machine, Neural Network. Therefore, RF was selected to build the ML model since our goal was to identify the maximum number of true matches. Our combined linkage PRL + ML showed a higher recall (range 0.988–0.992) than either PRL (range 0.916–0.991) or ML (0.981) alone. It identified 1995 individuals participating in both GEMO (6375 participants) and GENEPSO (4925 participants). Conclusions Our hybrid linkage process represents an efficient tool for linking GEMO and GENEPSO. It may be generalizable to other epidemiological studies involving other databases and registries.

Published
2021
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