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282 results on '"Bernard, Virginie"'

2. Molecular diagnosis of retinoblastoma by circulating tumor DNA analysis

Author

Jiménez, Irene, Frouin, Éléonore, Chicard, Mathieu, Dehainault, Catherine, Le Gall, Jessica, Benoist, Camille, Gauthier, Arnaud, Lapouble, Eve, Houdayer, Claude, Radvanyi, François, Bernard, Virginie, Brisse, Hervé J., Gauthier-Villars, Marion, Stoppa-Lyonnet, Dominique, Baulande, Sylvain, Cassoux, Nathalie, Lumbroso, Livia, Matet, Alexandre, Aerts, Isabelle, Renault, Victor, Doz, François, Golmard, Lisa, Delattre, Olivier, and Schleiermacher, Gudrun

Published
2021
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3. Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

Author

Callens, Céline, Driouch, Keltouma, Boulai, Anaïs, Tariq, Zakia, Comte, Aurélie, Berger, Frédérique, Belin, Lisa, Bièche, Ivan, Servois, Vincent, Legoix, Patricia, Bernard, Virginie, Baulande, Sylvain, Chemlali, Walid, Bidard, François-Clément, Fourchotte, Virginie, Salomon, Anne Vincent-, Brain, Etienne, Lidereau, Rosette, Bachelot, Thomas, Saghatchian, Mahasti, Campone, Mario, Giacchetti, Sylvie, Zafrani, Brigitte Sigal, and Cottu, Paul

Published
2021
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4. Relevance of a molecular tumour board (MTB) for patients’ enrolment in clinical trials: experience of the Institut Curie

Author

Basse, Clémence, Morel, Claire, Alt, Marie, Sablin, Marie Paule, Franck, Coralie, Pierron, Gaëlle, Callens, Céline, Melaabi, Samia, Masliah-Planchon, Julien, Bataillon, Guillaume, Gardrat, Sophie, Lavigne, Marion, Bonsang, Benjamin, Vaflard, Pauline, Pons Tostivint, Elvire, Dubot, Coraline, Loirat, Delphine, Marous, Miguelle, Geiss, Romain, Clément, Nathalie, Schleiermacher, Gudrun, Kamoun, Choumouss, Girard, Elodie, Ardin, Maude, Benoist, Camille, Bernard, Virginie, Mariani, Odette, Rouzier, Roman, Tresca, Patricia, Servois, Vincent, Vincent-Salomon, Anne, Bieche, Ivan, Le Tourneau, Christophe, and Kamal, Maud

Published
2018
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6. The clonal and mutational evolution spectrum of primary triple-negative breast cancers

Author

Shah, Sohrab P, Roth, Andrew, Goya, Rodrigo, Oloumi, Arusha, Ha, Gavin, Zhao, Yongjun, Turashvili, Gulisa, Ding, Jiarui, Tse, Kane, Haffari, Gholamreza, Bashashati, Ali, Prentice, Leah M, Khattra, Jaswinder, Burleigh, Angela, Yap, Damian, Bernard, Virginie, McPherson, Andrew, Shumansky, Karey, Crisan, Anamaria, Giuliany, Ryan, Heravi-Moussavi, Alireza, Rosner, Jamie, Lai, Daniel, Birol, Inanc, Varhol, Richard, Tam, Angela, Dhalla, Noreen, Zeng, Thomas, Ma, Kevin, Chan, Simon K, Griffith, Malachi, Moradian, Annie, Cheng, S-W Grace, Morin, Gregg B, Watson, Peter, Gelmon, Karen, Chia, Stephen, Chin, Suet-Feung, Curtis, Christina, Rueda, Oscar M, Pharoah, Paul D, Damaraju, Sambasivarao, Mackey, John, Hoon, Kelly, Harkins, Timothy, Tadigotla, Vasisht, Sigaroudinia, Mahvash, Gascard, Philippe, Tlsty, Thea, Costello, Joseph F, Meyer, Irmtraud M, Eaves, Connie J, Wasserman, Wyeth W, Jones, Steven, Huntsman, David, Hirst, Martin, Caldas, Carlos, Marra, Marco A, and Aparicio, Samuel

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Breast Cancer, Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Alleles, Breast Neoplasms, Clone Cells, DNA Copy Number Variations, DNA Mutational Analysis, Disease Progression, Evolution, Molecular, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genotype, High-Throughput Nucleotide Sequencing, Humans, INDEL Mutation, Mutation, Point Mutation, Precision Medicine, Reproducibility of Results, Sequence Analysis, RNA, General Science & Technology
Abstract

Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.

Published
2012

7. PLK1 inhibition exhibits strong anti-tumoral activity in CCND1-driven breast cancer metastases with acquired palbociclib resistance

Author

Montaudon, Elodie, Nikitorowicz-Buniak, Joanna, Sourd, Laura, Morisset, Ludivine, El Botty, Rania, Huguet, Léa, Dahmani, Ahmed, Painsec, Pierre, Nemati, Fariba, Vacher, Sophie, Chemlali, Walid, Masliah-Planchon, Julien, Château-Joubert, Sophie, Rega, Camilla, Leal, Mariana Ferreira, Simigdala, Nikiana, Pancholi, Sunil, Ribas, Ricardo, Nicolas, André, Meseure, Didier, Vincent-Salomon, Anne, Reyes, Cécile, Rapinat, Audrey, Gentien, David, Larcher, Thibaut, Bohec, Mylène, Baulande, Sylvain, Bernard, Virginie, Decaudin, Didier, Coussy, Florence, Le Romancer, Muriel, Dutertre, Guillaume, Tariq, Zakia, Cottu, Paul, Driouch, Keltouma, Bièche, Ivan, Martin, Lesley-Ann, and Marangoni, Elisabetta

Published
2020
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8. Data from The European MAPPYACTS Trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

Author

Berlanga, Pablo, primary, Pierron, Gaelle, primary, Lacroix, Ludovic, primary, Chicard, Mathieu, primary, Adam de Beaumais, Tiphaine, primary, Marchais, Antonin, primary, Harttrampf, Anne C., primary, Iddir, Yasmine, primary, Larive, Alicia, primary, Soriano Fernandez, Aroa, primary, Hezam, Imene, primary, Chevassus, Cecile, primary, Bernard, Virginie, primary, Cotteret, Sophie, primary, Scoazec, Jean-Yves, primary, Gauthier, Arnaud, primary, Abbou, Samuel, primary, Corradini, Nadege, primary, André, Nicolas, primary, Aerts, Isabelle, primary, Thebaud, Estelle, primary, Casanova, Michela, primary, Owens, Cormac, primary, Hladun-Alvaro, Raquel, primary, Michiels, Stefan, primary, Delattre, Olivier, primary, Vassal, Gilles, primary, Schleiermacher, Gudrun, primary, and Geoerger, Birgit, primary

Published
2023
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9. Supplementary Data from The European MAPPYACTS Trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

Author

Berlanga, Pablo, primary, Pierron, Gaelle, primary, Lacroix, Ludovic, primary, Chicard, Mathieu, primary, Adam de Beaumais, Tiphaine, primary, Marchais, Antonin, primary, Harttrampf, Anne C., primary, Iddir, Yasmine, primary, Larive, Alicia, primary, Soriano Fernandez, Aroa, primary, Hezam, Imene, primary, Chevassus, Cecile, primary, Bernard, Virginie, primary, Cotteret, Sophie, primary, Scoazec, Jean-Yves, primary, Gauthier, Arnaud, primary, Abbou, Samuel, primary, Corradini, Nadege, primary, André, Nicolas, primary, Aerts, Isabelle, primary, Thebaud, Estelle, primary, Casanova, Michela, primary, Owens, Cormac, primary, Hladun-Alvaro, Raquel, primary, Michiels, Stefan, primary, Delattre, Olivier, primary, Vassal, Gilles, primary, Schleiermacher, Gudrun, primary, and Geoerger, Birgit, primary

Published
2023
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11. Supplementary Figure 2 from Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis

Author

Bellini, Angela, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Rio Frio, Thomas, primary, Pierron, Gaelle, primary, Combaret, Valérie, primary, Lapouble, Eve, primary, Clement, Nathalie, primary, Rubie, Herve, primary, Thebaud, Estelle, primary, Chastagner, Pascal, primary, Defachelles, Anne Sophie, primary, Bergeron, Christophe, primary, Buchbinder, Nimrod, primary, Taque, Sophie, primary, Auvrignon, Anne, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Janoueix-Lerosey, Isabelle, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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12. supplemental figure legend from Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis

Author

Bellini, Angela, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Rio Frio, Thomas, primary, Pierron, Gaelle, primary, Combaret, Valérie, primary, Lapouble, Eve, primary, Clement, Nathalie, primary, Rubie, Herve, primary, Thebaud, Estelle, primary, Chastagner, Pascal, primary, Defachelles, Anne Sophie, primary, Bergeron, Christophe, primary, Buchbinder, Nimrod, primary, Taque, Sophie, primary, Auvrignon, Anne, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Janoueix-Lerosey, Isabelle, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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13. Supplemental Figure 4 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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14. Supplemental Patient Information from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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15. Supplemental Figure 3 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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16. Supplementary Figure Legends, Supplementary Figures 1-8, Supplementary References, Supplemental Information (1) on treatment protocols from Whole-Exome Sequencing of Cell-Free DNA Reveals Temporo-spatial Heterogeneity and Identifies Treatment-Resistant Clones in Neuroblastoma

Author

Chicard, Mathieu, primary, Colmet-Daage, Leo, primary, Clement, Nathalie, primary, Danzon, Adrien, primary, Bohec, Mylène, primary, Bernard, Virginie, primary, Baulande, Sylvain, primary, Bellini, Angela, primary, Deveau, Paul, primary, Pierron, Gaëlle, primary, Lapouble, Eve, primary, Janoueix-Lerosey, Isabelle, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Defachelles, Anne Sophie, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Combaret, Valérie, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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17. supplementary table 2 from PIK3CA Pathway Mutations Predictive of Poor Response Following Standard Radiochemotherapy ± Cetuximab in Cervical Cancer Patients

Author

de la Rochefordiere, Anne, primary, Kamal, Maud, primary, Floquet, Anne, primary, Thomas, Laurence, primary, Petrow, Peter, primary, Petit, Thierry, primary, Pop, Marius, primary, Fabbro, Michel, primary, Kerr, Christine, primary, Joly, Florence, primary, Sevin, Emmanuel, primary, Maillard, Sophie, primary, Curé, Hervé, primary, Weber, Béatrice, primary, Brunaud, Claire, primary, Minsat, Mathieu, primary, Gonzague, Laurence, primary, Berton-Rigaud, Dominique, primary, Aumont, Maud, primary, Gladieff, Laurence, primary, Peignaux, Karine, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Bieche, Ivan, primary, Margogne, Audrey, primary, Nadan, AnaTereza, primary, Fourchotte, Virginie, primary, Diallo, Alhassane, primary, Asselain, Benard, primary, Plancher, Corine, primary, Armanet, Sébastien, primary, Beuzeboc, Philippe, primary, and Scholl, Suzy M., primary

Published
2023
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18. supplementary table 4 from PIK3CA Pathway Mutations Predictive of Poor Response Following Standard Radiochemotherapy ± Cetuximab in Cervical Cancer Patients

Author

de la Rochefordiere, Anne, primary, Kamal, Maud, primary, Floquet, Anne, primary, Thomas, Laurence, primary, Petrow, Peter, primary, Petit, Thierry, primary, Pop, Marius, primary, Fabbro, Michel, primary, Kerr, Christine, primary, Joly, Florence, primary, Sevin, Emmanuel, primary, Maillard, Sophie, primary, Curé, Hervé, primary, Weber, Béatrice, primary, Brunaud, Claire, primary, Minsat, Mathieu, primary, Gonzague, Laurence, primary, Berton-Rigaud, Dominique, primary, Aumont, Maud, primary, Gladieff, Laurence, primary, Peignaux, Karine, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Bieche, Ivan, primary, Margogne, Audrey, primary, Nadan, AnaTereza, primary, Fourchotte, Virginie, primary, Diallo, Alhassane, primary, Asselain, Benard, primary, Plancher, Corine, primary, Armanet, Sébastien, primary, Beuzeboc, Philippe, primary, and Scholl, Suzy M., primary

Published
2023
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19. supplementary table 1 from PIK3CA Pathway Mutations Predictive of Poor Response Following Standard Radiochemotherapy ± Cetuximab in Cervical Cancer Patients

Author

de la Rochefordiere, Anne, primary, Kamal, Maud, primary, Floquet, Anne, primary, Thomas, Laurence, primary, Petrow, Peter, primary, Petit, Thierry, primary, Pop, Marius, primary, Fabbro, Michel, primary, Kerr, Christine, primary, Joly, Florence, primary, Sevin, Emmanuel, primary, Maillard, Sophie, primary, Curé, Hervé, primary, Weber, Béatrice, primary, Brunaud, Claire, primary, Minsat, Mathieu, primary, Gonzague, Laurence, primary, Berton-Rigaud, Dominique, primary, Aumont, Maud, primary, Gladieff, Laurence, primary, Peignaux, Karine, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Bieche, Ivan, primary, Margogne, Audrey, primary, Nadan, AnaTereza, primary, Fourchotte, Virginie, primary, Diallo, Alhassane, primary, Asselain, Benard, primary, Plancher, Corine, primary, Armanet, Sébastien, primary, Beuzeboc, Philippe, primary, and Scholl, Suzy M., primary

Published
2023
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20. Supplementary Table 2 from Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis

Author

Bellini, Angela, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Rio Frio, Thomas, primary, Pierron, Gaelle, primary, Combaret, Valérie, primary, Lapouble, Eve, primary, Clement, Nathalie, primary, Rubie, Herve, primary, Thebaud, Estelle, primary, Chastagner, Pascal, primary, Defachelles, Anne Sophie, primary, Bergeron, Christophe, primary, Buchbinder, Nimrod, primary, Taque, Sophie, primary, Auvrignon, Anne, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Janoueix-Lerosey, Isabelle, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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21. supplementary table 3 from PIK3CA Pathway Mutations Predictive of Poor Response Following Standard Radiochemotherapy ± Cetuximab in Cervical Cancer Patients

Author

de la Rochefordiere, Anne, primary, Kamal, Maud, primary, Floquet, Anne, primary, Thomas, Laurence, primary, Petrow, Peter, primary, Petit, Thierry, primary, Pop, Marius, primary, Fabbro, Michel, primary, Kerr, Christine, primary, Joly, Florence, primary, Sevin, Emmanuel, primary, Maillard, Sophie, primary, Curé, Hervé, primary, Weber, Béatrice, primary, Brunaud, Claire, primary, Minsat, Mathieu, primary, Gonzague, Laurence, primary, Berton-Rigaud, Dominique, primary, Aumont, Maud, primary, Gladieff, Laurence, primary, Peignaux, Karine, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Bieche, Ivan, primary, Margogne, Audrey, primary, Nadan, AnaTereza, primary, Fourchotte, Virginie, primary, Diallo, Alhassane, primary, Asselain, Benard, primary, Plancher, Corine, primary, Armanet, Sébastien, primary, Beuzeboc, Philippe, primary, and Scholl, Suzy M., primary

Published
2023
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22. Supplementary Table 3 from Whole-Exome Sequencing of Cell-Free DNA Reveals Temporo-spatial Heterogeneity and Identifies Treatment-Resistant Clones in Neuroblastoma

Author

Chicard, Mathieu, primary, Colmet-Daage, Leo, primary, Clement, Nathalie, primary, Danzon, Adrien, primary, Bohec, Mylène, primary, Bernard, Virginie, primary, Baulande, Sylvain, primary, Bellini, Angela, primary, Deveau, Paul, primary, Pierron, Gaëlle, primary, Lapouble, Eve, primary, Janoueix-Lerosey, Isabelle, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Defachelles, Anne Sophie, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Combaret, Valérie, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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23. Supplemental Figure 5 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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24. Supplemental Table 1 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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25. Supplemental Figure 2 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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26. Supplementary Table 1 from Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis

Author

Bellini, Angela, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Rio Frio, Thomas, primary, Pierron, Gaelle, primary, Combaret, Valérie, primary, Lapouble, Eve, primary, Clement, Nathalie, primary, Rubie, Herve, primary, Thebaud, Estelle, primary, Chastagner, Pascal, primary, Defachelles, Anne Sophie, primary, Bergeron, Christophe, primary, Buchbinder, Nimrod, primary, Taque, Sophie, primary, Auvrignon, Anne, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Janoueix-Lerosey, Isabelle, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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27. Supplemental Table 2 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma

Author

Chicard, Mathieu, primary, Boyault, Sandrine, primary, Colmet Daage, Leo, primary, Richer, Wilfrid, primary, Gentien, David, primary, Pierron, Gaelle, primary, Lapouble, Eve, primary, Bellini, Angela, primary, Clement, Nathalie, primary, Iacono, Isabelle, primary, Bréjon, Stéphanie, primary, Carrere, Marjorie, primary, Reyes, Cécile, primary, Hocking, Toby, primary, Bernard, Virginie, primary, Peuchmaur, Michel, primary, Corradini, Nadège, primary, Faure-Conter, Cécile, primary, Coze, Carole, primary, Plantaz, Dominique, primary, Defachelles, Anne Sophie, primary, Thebaud, Estelle, primary, Gambart, Marion, primary, Millot, Frédéric, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Puisieux, Alain, primary, Delattre, Olivier, primary, Combaret, Valérie, primary, and Schleiermacher, Gudrun, primary

Published
2023
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28. Supplementary Figure 1 from Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis

Author

Bellini, Angela, primary, Bernard, Virginie, primary, Leroy, Quentin, primary, Rio Frio, Thomas, primary, Pierron, Gaelle, primary, Combaret, Valérie, primary, Lapouble, Eve, primary, Clement, Nathalie, primary, Rubie, Herve, primary, Thebaud, Estelle, primary, Chastagner, Pascal, primary, Defachelles, Anne Sophie, primary, Bergeron, Christophe, primary, Buchbinder, Nimrod, primary, Taque, Sophie, primary, Auvrignon, Anne, primary, Valteau-Couanet, Dominique, primary, Michon, Jean, primary, Janoueix-Lerosey, Isabelle, primary, Delattre, Olivier, primary, and Schleiermacher, Gudrun, primary

Published
2023
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30. Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial

Author

Le Tourneau, Christophe, Delord, Jean-Pierre, Gonçalves, Anthony, Gavoille, Céline, Dubot, Coraline, Isambert, Nicolas, Campone, Mario, Trédan, Olivier, Massiani, Marie-Ange, Mauborgne, Cécile, Armanet, Sebastien, Servant, Nicolas, Bièche, Ivan, Bernard, Virginie, Gentien, David, Jezequel, Pascal, Attignon, Valéry, Boyault, Sandrine, Vincent-Salomon, Anne, Servois, Vincent, Sablin, Marie-Paule, Kamal, Maud, and Paoletti, Xavier

Published
2015
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31. Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types

Author

Lebofsky, Ronald, Decraene, Charles, Bernard, Virginie, Kamal, Maud, Blin, Anthony, Leroy, Quentin, Rio Frio, Thomas, Pierron, Gaëlle, Callens, Céline, Bieche, Ivan, Saliou, Adrien, Madic, Jordan, Rouleau, Etienne, Bidard, François-Clément, Lantz, Olivier, Stern, Marc-Henri, Le Tourneau, Christophe, and Pierga, Jean-Yves

Published
2015
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32. Learning phenotypic patterns in genetic diseases by symptom interaction modeling

Author

Thevenon, Julien, primary, Yauy, Kevin, additional, Duforet-Frebourg, Nicolas, additional, Testard, Quentin, additional, Beaumeunier, Sacha, additional, Audoux, Jerome, additional, Simard, Benoit, additional, Larue, DImitri, additional, Blum, Michael, additional, Bernard, VIrginie, additional, Geneviève, David, additional, Bertrand, Denis, additional, and Philippe, Nicolas, additional

Published
2022
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34. Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite

Author

Grünewald, Thomas G P, Bernard, Virginie, Gilardi-Hebenstreit, Pascale, Raynal, Virginie, Surdez, Didier, Aynaud, Marie-Ming, Mirabeau, Olivier, Cidre-Aranaz, Florencia, Tirode, Franck, Zaidi, Sakina, Perot, Gaëlle, Jonker, Anneliene H, Lucchesi, Carlo, Le Deley, Marie-Cécile, Oberlin, Odile, Marec-Bérard, Perrine, Véron, Amélie S, Reynaud, Stephanie, Lapouble, Eve, Boeva, Valentina, Frio, Thomas Rio, Alonso, Javier, Bhatia, Smita, Pierron, Gaëlle, Cancel-Tassin, Geraldine, Cussenot, Olivier, Cox, David G, Morton, Lindsay M, Machiela, Mitchell J, Chanock, Stephen J, Charnay, Patrick, and Delattre, Olivier

Published
2015
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35. The European MAPPYACTS Trial: Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

Author

Berlanga, Pablo, primary, Pierron, Gaelle, additional, Lacroix, Ludovic, additional, Chicard, Mathieu, additional, Adam de Beaumais, Tiphaine, additional, Marchais, Antonin, additional, Harttrampf, Anne C., additional, Iddir, Yasmine, additional, Larive, Alicia, additional, Soriano Fernandez, Aroa, additional, Hezam, Imene, additional, Chevassus, Cecile, additional, Bernard, Virginie, additional, Cotteret, Sophie, additional, Scoazec, Jean-Yves, additional, Gauthier, Arnaud, additional, Abbou, Samuel, additional, Corradini, Nadege, additional, André, Nicolas, additional, Aerts, Isabelle, additional, Thebaud, Estelle, additional, Casanova, Michela, additional, Owens, Cormac, additional, Hladun-Alvaro, Raquel, additional, Michiels, Stefan, additional, Delattre, Olivier, additional, Vassal, Gilles, additional, Schleiermacher, Gudrun, additional, and Geoerger, Birgit, additional

Published
2022
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36. Frequency and Prognostic Impact of ALK Amplifications and Mutations in the European Neuroblastoma Study Group (SIOPEN) High-Risk Neuroblastoma Trial (HR-NBL1)

Author

Bellini, Angela, primary, Pötschger, Ulrike, additional, Bernard, Virginie, additional, Lapouble, Eve, additional, Baulande, Sylvain, additional, Ambros, Peter F., additional, Auger, Nathalie, additional, Beiske, Klaus, additional, Bernkopf, Marie, additional, Betts, David R., additional, Bhalshankar, Jaydutt, additional, Bown, Nick, additional, de Preter, Katleen, additional, Clément, Nathalie, additional, Combaret, Valérie, additional, Font de Mora, Jaime, additional, George, Sally L., additional, Jiménez, Irene, additional, Jeison, Marta, additional, Marques, Barbara, additional, Martinsson, Tommy, additional, Mazzocco, Katia, additional, Morini, Martina, additional, Mühlethaler-Mottet, Annick, additional, Noguera, Rosa, additional, Pierron, Gaelle, additional, Rossing, Maria, additional, Taschner-Mandl, Sabine, additional, Van Roy, Nadine, additional, Vicha, Ales, additional, Chesler, Louis, additional, Balwierz, Walentyna, additional, Castel, Victoria, additional, Elliott, Martin, additional, Kogner, Per, additional, Laureys, Geneviève, additional, Luksch, Roberto, additional, Malis, Josef, additional, Popovic-Beck, Maja, additional, Ash, Shifra, additional, Delattre, Olivier, additional, Valteau-Couanet, Dominique, additional, Tweddle, Deborah A., additional, Ladenstein, Ruth, additional, and Schleiermacher, Gudrun, additional

Published
2021
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37. Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients

Author

Madic, Jordan, Kiialainen, Anna, Bidard, Francois-Clement, Birzele, Fabian, Ramey, Guillemette, Leroy, Quentin, Frio, Thomas Rio, Vaucher, Isabelle, Raynal, Virginie, Bernard, Virginie, Lermine, Alban, Clausen, Inga, Giroud, Nicolas, Schmucki, Roland, Milder, Maud, Horn, Carsten, Spleiss, Olivia, Lantz, Olivier, Stern, Marc-Henri, Pierga, Jean-Yves, Weisser, Martin, and Lebofsky, Ronald

Published
2015
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39. Additional file 2 of Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

Author

Callens, Céline, Keltouma Driouch, Boulai, Anaïs, Tariq, Zakia, Comte, Aurélie, Berger, Frédérique, Belin, Lisa, Bièche, Ivan, Servois, Vincent, Legoix, Patricia, Bernard, Virginie, Baulande, Sylvain, Chemlali, Walid, François-Clément Bidard, Fourchotte, Virginie, Salomon, Anne Vincent, Brain, Etienne, Lidereau, Rosette, Bachelot, Thomas, Mahasti Saghatchian, Campone, Mario, Giacchetti, Sylvie, Zafrani, Brigitte Sigal, and Cottu, Paul

Abstract

Additional file 2. Supplementary Tables. This file contains 4 supplementary tables pertaining to the NGS gene panel, detailed patient characteristics, and additional multivariate analyses.

Published
2021
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40. Additional file 1 of Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

Author

Callens, Céline, Keltouma Driouch, Boulai, Anaïs, Tariq, Zakia, Comte, Aurélie, Berger, Frédérique, Belin, Lisa, Bièche, Ivan, Servois, Vincent, Legoix, Patricia, Bernard, Virginie, Baulande, Sylvain, Chemlali, Walid, François-Clément Bidard, Fourchotte, Virginie, Salomon, Anne Vincent, Brain, Etienne, Lidereau, Rosette, Bachelot, Thomas, Mahasti Saghatchian, Campone, Mario, Giacchetti, Sylvie, Zafrani, Brigitte Sigal, and Cottu, Paul

Abstract

Additional file 1. Supplementary Procedures and Methods. This file contains additional methods with regard to tissue handling (sampling, extraction), digital droplet PCR methods, and targeted and whole exome sequencing procedures.

Published
2021
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41. Additional file 3 of Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

Author

Callens, Céline, Keltouma Driouch, Boulai, Anaïs, Tariq, Zakia, Comte, Aurélie, Berger, Frédérique, Belin, Lisa, Bièche, Ivan, Servois, Vincent, Legoix, Patricia, Bernard, Virginie, Baulande, Sylvain, Chemlali, Walid, François-Clément Bidard, Fourchotte, Virginie, Salomon, Anne Vincent, Brain, Etienne, Lidereau, Rosette, Bachelot, Thomas, Mahasti Saghatchian, Campone, Mario, Giacchetti, Sylvie, Zafrani, Brigitte Sigal, and Cottu, Paul

Abstract

Additional file 3. Supplementary Figures. This file contains 7 supplementary figures further describing the sequencing results.

Published
2021
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42. Frequency and prognostic impact of alk amplifications and mutations in the european neuroblastoma study group (siopen) high-risk neuroblastoma trial (hr-nbl1)

Author

Bellini, Angela, Potschger, Ulrike, Bernard, Virginie, Lapouble, Eve, Baulande, Sylvain, Ambros, Peter F., Auger, Nathalie, Beiske, Klaus, Bernkopf, Marie, Betts, David R., Bhalshankar, Jaydutt, Bown, Nick, De Preter, Katleen, Clement, Nathalie, Combaret, Valerie, De Mora, Jaime Font, George, Sally L., Jimenez, Irene, Jeison, Marta, Marques, Barbara, Martinsson, Tommy, Mazzocco, Katia, Morini, Martina, Muhlethaler-Mottet, Annick, Noguera, Rosa, Pierron, Gaelle, Rossing, Maria, Taschner-Mandl, Sabine, Van Roy, Nadine, Vicha, Ales, Chesler, Louis, Balwierz, Walentyna, Castel, Victoria, Elliott, Martin, Kogner, Per, Laureys, Genevieve, Luksch, Roberto, Malis, Josef, Popovic-Beck, Maja, Ash, Shifra, Delattre, Olivier, Valteau-Couanet, Dominique, Tweddle, Deborah A., Ladenstein, Ruth, Schleiermacher, Gudrun, Bellini, Angela, Potschger, Ulrike, Bernard, Virginie, Lapouble, Eve, Baulande, Sylvain, Ambros, Peter F., Auger, Nathalie, Beiske, Klaus, Bernkopf, Marie, Betts, David R., Bhalshankar, Jaydutt, Bown, Nick, De Preter, Katleen, Clement, Nathalie, Combaret, Valerie, De Mora, Jaime Font, George, Sally L., Jimenez, Irene, Jeison, Marta, Marques, Barbara, Martinsson, Tommy, Mazzocco, Katia, Morini, Martina, Muhlethaler-Mottet, Annick, Noguera, Rosa, Pierron, Gaelle, Rossing, Maria, Taschner-Mandl, Sabine, Van Roy, Nadine, Vicha, Ales, Chesler, Louis, Balwierz, Walentyna, Castel, Victoria, Elliott, Martin, Kogner, Per, Laureys, Genevieve, Luksch, Roberto, Malis, Josef, Popovic-Beck, Maja, Ash, Shifra, Delattre, Olivier, Valteau-Couanet, Dominique, Tweddle, Deborah A., Ladenstein, Ruth, and Schleiermacher, Gudrun

Abstract

PURPOSE In neuroblastoma (NB), the ALK receptor tyrosine kinase can be constitutively activated through activating point mutations or genomic amplification. We studied ALK genetic alterations in high-risk (HR) patients on the HR-NBL1/SIOPEN trial to determine their frequency, correlation with clinical parameters, and prognostic impact. MATERIALS AND METHODS Diagnostic tumor samples were available from 1,092 HR-NBL1/SIOPEN patients to determine ALK amplification status (n 5 330), ALK mutational profile (n 5 191), or both (n 5 571). RESULTS Genomic ALK amplification (ALKa) was detected in 4.5% of cases (41 out of 901), all except one with MYCN amplification (MNA). ALKa was associated with a significantly poorer overall survival (OS) (5-year OS: ALKa [n 5 41] 28% [95% CI, 15 to 42]; no-ALKa [n 5 860] 51% [95% CI, 47 to 54], [P , .001]), particularly in cases with metastatic disease. ALK mutations (ALKm) were detected at a clonal level (. 20% mutated allele fraction) in 10% of cases (76 out of 762) and at a subclonal level (mutated allele fraction 0.1%-20%) in 3.9% of patients (30 out of 762), with a strong correlation between the presence of ALKm and MNA (P , .001). Among 571 cases with known ALKa and ALKm status, a statistically significant difference in OS was observed between cases with ALKa or clonal ALKm versus subclonal ALKm or no ALK alterations (5-year OS: ALKa [n 5 19], 26% [95% CI, 10 to 47], clonal ALKm[n565] 33% [95% CI, 21 to 44], subclonal ALKm(n522) 48% [95% CI, 26 to 67], and no alteration [n 5 465], 51% [95% CI, 46 to 55], respectively; P 5 .001). Importantly, in a multivariate model, involvement of more than one metastatic compartment (hazard ratio [HR], 2.87; P , .001), ALKa (HR, 2.38; P 5 .004), and clonal ALKm (HR, 1.77; P 5 .001) were independent predictors of poor outcome. CONCLUSION Genetic alterations of ALK (clonal mutations and amplifications) in HR-NB are independent predictors of poorer survival. These data provide a rationale for integr

Published
2021

43. Improved detection of motifs with preferential location in promoters

Author

Bernard, Virginie, Lecharny, Alain, and Brunaud, Veronique

Subjects
Gene expression -- Research, Promoters (Genetics) -- Research, Biological sciences
Abstract

Many transcription factor binding sites (TFBSs) involved in gene expression regulation are preferentially located relative to the transcription start site. This property is exploited in in silico prediction approaches, one of which involves studying the local overrepresentation of motifs using a sliding window to scan promoters with considerable accuracy. Nevertheless, the consequences of the choice of the sliding window size have never before been analysed. We propose an automatic adaptation of this size to each motif distribution profile. This approach allows a better characterization of the topological constraints of the motifs and the lists of genes containing them. Moreover, our approach allowed us to highlight a nonconstant frequency of occurrence of spurious motifs that could be counter-selected close to their functional area. Therefore, to improve the accuracy of in silico prediction of TFBSs and the sensitivity of the promoter cartography, we propose, in addition to automatic adaptation of window size, consideration of the nonconstant frequency of motifs in promoters. Key words: transcription factor binding site, transcription start site, preferential position, sliding window size, motif distribution, topological constraints. Les sites de fixation des facteurs de transcription (TFBS), impliques dans la regulation de l'expression des genes, sont nombreux a etre observes a une distance preferentielle des sites de debuts de transcription. Cette propriete est exploitee dans des approches predictives in silico. Avec une fenetre glissante parcourant les promoteurs, la recherche de surrepresentations locales de motifs a demontre son efficacite. Neanmoins, les consequences du choix de la taille de cette fenetre n'ont jamais ete etudiees. Nous proposons une approche qui adapte automatiquement cette taille de fenetre aux distributions. Cette approche permet de caracteriser avec plus de precision les contraintes topologiques des motifs et des listes de genes les contenant. De plus, l'utilisation de notre approche a mis en evidence que le nombre d'occurrences non fonctionnelles des motifs n'est pas constant et que les motifs pourraient etre contre selectionneesa l'approche de leur region fonctionnelle. Ainsi, pour accroitre l'efficacite des approches in silico recherchant des TFBS, nous proposons d'utiliser une taille de fenetre glissante qui s'adapte a chaque distribution de motif et de considerer la frequence non constante des elements dans les promoteurs. Cela conduit a une cartographie des promoteurs etudies statistiquement plus sensible. Mots-cles: site de fixation des facteurs de transcription, site d'initiation de la transcription, position preferentielle, taille de la fenetre glissante, distribution de motif, contraintes topologiques., Introduction In eukaryotes, many biochemical processes are highly regulated at different levels of gene transcription including initiation, elongation, and termination. Transcription initiation for protein-coding genes requires the formation of the [...]

Published
2010
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44. DNAJC13 mutations in Parkinson disease

Author

Vilariño-Güell, Carles, Rajput, Alex, Milnerwood, Austen J., Shah, Brinda, Szu-Tu, Chelsea, Trinh, Joanne, Yu, Irene, Encarnacion, Mary, Munsie, Lise N., Tapia, Lucia, Gustavsson, Emil K., Chou, Patrick, Tatarnikov, Igor, Evans, Daniel M., Pishotta, Frederick T., Volta, Mattia, Beccano-Kelly, Dayne, Thompson, Christina, Lin, Michelle K., Sherman, Holly E., Han, Heather J., Guenther, Bruce L., Wasserman, Wyeth W., Bernard, Virginie, Ross, Colin J., Appel-Cresswell, Silke, Stoessl, Jon A., Robinson, Christopher A., Dickson, Dennis W., Ross, Owen A., Wszolek, Zbigniew K., Aasly, Jan O., Wu, Ruey-Meei, Hentati, Faycal, Gibson, Rachel A., McPherson, Peter S., Girard, Martine, Rajput, Michele, Rajput, Ali H., and Farrer, Matthew J.

Published
2014
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45. Antagonistic Representations of Space Between the Aboriginal Noongars and the Australian State

Author

Bernard, Virginie, Centre de Recherche et de Documentation sur l'Océanie (CREDO), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Bernard, Virginie

Subjects
[SHS.ANTHRO-SE] Humanities and Social Sciences/Social Anthropology and ethnology, [SHS.DROIT]Humanities and Social Sciences/Law, [SHS.DROIT] Humanities and Social Sciences/Law, Australia (South West), State relations, Representations of space, Social and territorial organisation, Indigenous land claims (Native title), Australian Aborigines (Noongars), [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology
Abstract

International audience; This article seeks to account for the antagonistic representations of space between the Aboriginal Noongars of the South West of Western Australia and the Australian State in the context of the Noongars’ native title claims, both in Courts and through a negotiation process. First, during the trials, the Noongars faced the State of Western Australia and the Federal State around the concept of society, which the native title legislation imposes. The Noongars had to comply with the requirements of the law, but faced with the rigid legal approach of the concept of society defended by their opponents, they sought to soften its definition to reflect the flexibility and dynamism that characterizes their conception of space and their social and territorial organisation.The Noongars then negotiated with the State of Western Australia to resolve their land claims and obtain a comprehensive economic, social, financial and political agreement. The Noongars and the State of Western Australia brought their perspectives closer together during this negotiation process. The Noongars’ conception of space and social and territorial organisation was rationalized through the establishment of a system of governance, the political basis of the Noongar nation in the making. This formalization was asked for by a majority of Noongars as it would allow them to remain united, to function and prosper, but also to be recognized by the State and thus gain a certain amount of autonomy.

Published
2019

46. The need to display 'tradition': Claiming Native Title in southwestern Australia

Author

Bernard, Virginie, Bernard, Virginie, Centre de Recherche et de Documentation sur l'Océanie (CREDO), and École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SHS.ANTHRO-SE] Humanities and Social Sciences/Social Anthropology and ethnology, Australia (South West), State relations, [SHS.HIST] Humanities and Social Sciences/History, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, Australian Aborigines (Noongars), Indigenous land claims (Native title), [SHS.HIST]Humanities and Social Sciences/History, ComputingMilieux_MISCELLANEOUS, Single Noongar Claim, Tradition
Abstract

International audience

Published
2019

47. Comparison of Total Work Inability between Medical Examiners and Emergency Physicians

Author

Fraticelli, Laurie, Claustre, Clément, Boniol, Laurent, Chambost, Marc, Maiello, Ernesto, Bernard, Virginie, Dodane-Loyenet, Antoine, Martinez, Mikaël, El Khoury, Carlos, Des Accidents Et Des Traumatismes de L’ain, Groupe de L’observatoire Régional, Parcours santé systémique (P2S), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Centre hospitalier Lucien Hussel, and Fraticelli, Laurie

Subjects
Medical examiners, [STAT.ME] Statistics [stat]/Methodology [stat.ME], [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Emergency department, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Total work inability, MESH: Total work inability, Medical examiners, Emergency physicians, Emergency department, Agreement, Emergency physicians, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], [STAT.ME]Statistics [stat]/Methodology [stat.ME], [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Agreement
Abstract

International audience; Aim: We aimed to compare the total work incapacity (TTI) durations assigned by the emergency physician at admission, and assigned in hindsight by medical examiners and emergency physicians.Procedure: We included traffic and domestic accidents from the regional observatory for accidents and trauma (ORAT) that led to the allocation of a TTI. Three medical examiners and three emergency physicians allocated TTI durations in number of days, based on information from the ORAT. We reported the intra- and inter-physician quality based on 94 and 376 patients. The concordance was evaluated with the intra-class correlation coefficient (ICC). An agreement was observed between prescribers if the difference between their TTIs was less than or equal to 20% of the average of the assigned TTIs.Results: Concordance between medical examiners was moderate (CCI: 0.67 [0.51; 0.80]), also between emergency physicians (CCI: 0.62 [0.50; 0.72]) and between medical examiners and emergency physicians (CCI: 0.66 [0.59; 0.71]). We observed only 16% situations of agreements. Among the agreements, patients did not share common characteristics. They were usually admitted on the day of the accident and most often had head, face or neck injuries. Among the disagreement situations, patients had more frequent spinal cord injuries and were associated with a disability that did not affect normal function (IIS score 1).Conclusion: We observed a strong heterogeneity in the assessment between medical examiners and emergency physicians, leading to inequity in the judicial treatment of injuries and in the medical follow-up of victims.

Published
2020

49. QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction

Author

Deveau, Paul, Colmet Daage, Leo, Oldridge, Derek, Bernard, Virginie, Bellini, Angela, Chicard, Mathieu, Clement, Nathalie, Lapouble, Eve, Combaret, Valerie, Boland, Anne, Meyer, Vincent, Deleuze, Jean-Francois, Janoueix-Lerosey, Isabelle, Barillot, Emmanuel, Delattre, Olivier, Maris, John M, Schleiermacher, Gudrun, and Boeva, Valentina

Subjects
DNA Copy Number Variations, Whole Genome Sequencing, DNA Mutational Analysis, High-Throughput Nucleotide Sequencing, Genome Analysis, Original Papers, Clonal Evolution, Molecular Typing, Gene Frequency, Neoplasms, Mutation, Cluster Analysis, Humans, Software
Abstract

Motivation In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering [reducing dispersion in variant allele frequency estimates (VAFs)] and using all biologically relevant variants. Results We present a framework for defining cancer clones using most reliable variants of high depth of coverage and assigning functional mutations to the detected clones. The key element of our framework is QuantumClone, a method for variant clustering into clones based on VAFs, genotypes of corresponding regions and information about tumor purity. We validated QuantumClone and our framework on simulated data. We then applied our framework to whole genome sequencing data for 19 neuroblastoma trios each including constitutional, diagnosis and relapse samples. We confirmed an enrichment of damaging variants within such pathways as MAPK (mitogen-activated protein kinases), neuritogenesis, epithelial-mesenchymal transition, cell survival and DNA repair. Most pathways had more damaging variants in the expanding clones compared to shrinking ones, which can be explained by the increased total number of variants between these two populations. Functional mutational rate varied for ancestral clones and clones shrinking or expanding upon treatment, suggesting changes in clone selection mechanisms at different time points of tumor evolution. Availability and implementation Source code and binaries of the QuantumClone R package are freely available for download at https://CRAN.R-project.org/package=QuantumClone. Contact gudrun.schleiermacher@curie.fr or valentina.boeva@inserm.fr Supplementary information Supplementary data are available at Bioinformatics online.

Published
2018

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