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GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles.
Pozzorini, Christian; Andre, Gregoire; Coletta, Tommaso; Buisson, Adrien; Bieler, Jonathan; Ferrer, Loïc; Kempfer, Rieke; Saintigny, Pierre; Harlé, Alexandre; Vacirca, Davide; Barberis, Massimo; Gilson, Pauline; Roma, Cristin; Saitta, Alexandra; Smith, Ewan; Consales Barras, Floriane; Ripol, Lucia; Fritzsche, Martin; Marques, Ana Claudia; Alkodsi, Amjad; Marin, Ray; Normanno, Nicola; Grimm, Christoph; Müllauer, Leonhard; Harter, Philipp; Pignata, Sandro; Gonzalez-Martin, Antonio; Denison, Ursula; Fujiwara, Keiichi; Vergote, Ignace; Colombo, Nicoletta; Willig, Adrian; Pujade-Lauraine, Eric; Just, Pierre-Alexandre; Ray-Coquard, Isabelle; Xu, Zhenyu.
Afiliación
  • Pozzorini C; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Andre G; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Coletta T; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Buisson A; Department of Medical Oncology, Centre Léon Bérard, Lyon, France.
  • Bieler J; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Ferrer L; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Kempfer R; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Saintigny P; 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.
  • Harlé A; Institut de Cancérologie de Lorraine, Service de Biopathologie, CNRS UMR 7039 CRAN, Vandoeuvre-lès-Nancy, France.
  • Vacirca D; European Institute of Oncology, Milan, Italy.
  • Barberis M; European Institute of Oncology, Milan, Italy.
  • Gilson P; Institut de Cancérologie de Lorraine, Service de Biopathologie, CNRS UMR 7039 CRAN, Vandoeuvre-lès-Nancy, France.
  • Roma C; Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy.
  • Saitta A; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Smith E; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Consales Barras F; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Ripol L; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Fritzsche M; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Marques AC; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Alkodsi A; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Marin R; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Normanno N; Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Naples, Italy.
  • Grimm C; Medical University of Vienna, Vienna, Austria.
  • Müllauer L; Medical University of Vienna, Vienna, Austria.
  • Harter P; Kliniken Essen Mitte, Essen, Germany.
  • Pignata S; Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, and Multicenter Italian Trials in Ovarian Cancer and Gynecologic Malignancies (MITO), Naples, Italy.
  • Gonzalez-Martin A; Cancer Center Clinica Universidad de Navarra, Madrid, Spain; GEICO, Madrid, Spain; Program In Solid Tumors, CIMA, Pamplona, Spain.
  • Denison U; Department for Gynaecology and Obstetrics, Klinik Hietzing, Vienna, Austria.
  • Fujiwara K; Saitama Medical University International Medical Center, Saitama, Japan.
  • Vergote I; University Hospital Leuven, Leuven Cancer Institute, Leuven, Belgium.
  • Colombo N; European Institute of Oncology, Milan, Italy.
  • Willig A; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland.
  • Pujade-Lauraine E; Association de Recherche Cancers Gynécologiques (ARCAGY), Paris, France.
  • Just PA; Service de Pathologie, APHM (Assistance Publique - Hôpitaux de Marseille), Marseille, Provence-Alpes-Côte d'Azur, France.
  • Ray-Coquard I; Centre Léon BERARD, and University Claude Bernard Lyon I, Lyon, France; Groupe d'Investigateurs Nationaux pour l'Etude des Cancers Ovariens (GINECO), Lyon, France.
  • Xu Z; SOPHiA GENETICS, La Piéce 12, 1180 Rolle, Switzerland. Electronic address: zxu@sophiagenetics.com.
Cell Rep Med ; 4(12): 101344, 2023 12 19.
Article en En | MEDLINE | ID: mdl-38118421
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias Ováricas Límite: Female / Humans Idioma: En Revista: Cell Rep Med Año: 2023 Tipo del documento: Article País de afiliación: Suiza Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias Ováricas Límite: Female / Humans Idioma: En Revista: Cell Rep Med Año: 2023 Tipo del documento: Article País de afiliación: Suiza Pais de publicación: Estados Unidos