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2. How does the degree of novelty impacts semi-supervised representation learning for novel class retrieval?

Author

Leroy, Quentin, Buisson, Olivier, and Joly, Alexis

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence
Abstract

Supervised representation learning with deep networks tends to overfit the training classes and the generalization to novel classes is a challenging question. It is common to evaluate a learned embedding on held-out images of the same training classes. In real applications however, data comes from new sources and novel classes are likely to arise. We hypothesize that incorporating unlabelled images of novel classes in the training set in a semi-supervised fashion would be beneficial for the efficient retrieval of novel-class images compared to a vanilla supervised representation. To verify this hypothesis in a comprehensive way, we propose an original evaluation methodology that varies the degree of novelty of novel classes by partitioning the dataset category-wise either randomly, or semantically, i.e. by minimizing the shared semantics between base and novel classes. This evaluation procedure allows to train a representation blindly to any novel-class labels and evaluate the frozen representation on the retrieval of base or novel classes. We find that a vanilla supervised representation falls short on the retrieval of novel classes even more so when the semantics gap is higher. Semi-supervised algorithms allow to partially bridge this performance gap but there is still much room for improvement.

Published
2022

3. 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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4. 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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5. 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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6. 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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7. 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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8. 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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9. 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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10. 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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11. 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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14. 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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15. 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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21. Etude de la population française de Petit Lévrier Italien : origine, description, évolution, situation actuelle et état de santé

Author

Leroy, Quentin, Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), and Institut National Polytechnique de Toulouse - INPT (FRANCE)

Subjects
Médecine vétérinaire et santé animal, Race, Enquête, Etat de santé, Petit Lévrier Italien, France, Chien
Abstract

Le Petit Lévrier Italien est une race de chien très ancienne. Elle est actuellement la seconde race la plus représentée de lévriers en France et sa population est toujours en augmentation. Peu de données sont tout de même disponibles à l’heure actuelle à son sujet. Ce travail a pour but de rassembler les différentes informations disponibles sur la race (importance en termes d’effectifs, données générales, populations de PLI et pathologies présentes en son sein). Par la suite, les différents acteurs de la filière ont été interrogés au moyen d’un questionnaire en ligne : une synthèse de leurs réponses est présentée et discutée.

Published
2018

22. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

Author

Audic Stéphane, Parola Philippe, Socolovschi Cristina, Renesto Patricia, Giumelli Bernadette, Robert Catherine, Leroy Quentin, El Karkouri Khalid, Fournier Pierre-Edouard, and Raoult Didier

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector. Results We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a tra operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to R. prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii have, respectively, the less and most decayed genomes. Eighteen genes are present only in R. africae including one with a putative protease domain upregulated at 37°C. Conclusion Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in Rickettsia species virulence is mostly associated with gene loss. The genome sequence was deposited in GenBank under accession number [GenBank: NZ_AAUY01000001].

Published
2009
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23. Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities

Author

Bechah, Yassina, Karkouri, Khalid El, Mediannikov, Oleg, Leroy, Quentin, Pelletier, Nicolas, Robert, Catherine, Medigue, Claudine, Mege, Jean-Louis, and Raoult, Didier

Subjects
Rickettsia -- Genetic aspects, Proteomics -- Usage, Virulence (Microbiology) -- Research, Gene mutations -- Analysis, Genetic transcription -- Research, Health
Published
2010

24. Deep Sequencing Reveals Occurrence of Subclonal ALK Mutations in Neuroblastoma at Diagnosis

Author

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

Published
2015
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25. Development and Validation of a Microarray for the Investigation of the CAZymes Encoded by the Human Gut Microbiome

Author

Kaoutari, Abdessamad El, Armougom, Fabrice, Leroy, Quentin, Vialettes, Bernard, Million, Matthieu, Raoult, Didier, Henrissat, Bernard, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Nutrition, obésité et risque thrombotique (NORT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Mediterranean Infection Foundation, and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
Adult, DNA, Bacterial, Male, Glycoside Hydrolases, Microarrays, Glycobiology, Carbohydrates, lcsh:Medicine, Real-Time Polymerase Chain Reaction, Biochemistry, Microbiology, Feces, Young Adult, Thinness, Polysaccharides, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Obesity, Gut bacteria, lcsh:Science, Biology, Aged, Oligonucleotide Array Sequence Analysis, Polysaccharide-Lyases, Microbial Metabolism, Bacteria, Gene Expression Profiling, lcsh:R, Computational Biology, Bacteriology, Middle Aged, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Probe hybridization, Anorexia, Bacterial Biochemistry, Polymerase chain reaction, Enzymes, Gastrointestinal Tract, Metabolism, Case-Control Studies, Metagenome, Carbohydrate Metabolism, Female, lcsh:Q, Microbiome, Metagenomics, Biomarkers, Research Article
Abstract

International audience; Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals. Citation: El Kaoutari A, Armougom F, Leroy Q, Vialettes B, Million M, et al. (2013) Development and Validation of a Microarray for the Investigation of the CAZymes Encoded by the Human Gut Microbiome.

Published
2013

26. Development and validation of a microarray for the investigation of the CAZymes encoded by the human gut microbiome

Author

Armougom, Fabrice, Leroy, Quentin, Vialettes, Bernard, Million, Matthieu, Raoult, Didier, Henrissat, Bernard, and El Kaoutari, Abdessamad

Abstract

Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.

Published
2013

27. Correction to: Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.

Author

Kokcha, Sahare, Mishra, Ajay Kumar, Lagier, Jean-Christophe, Million, Matthieu, Leroy, Quentin, Raoult, Didier, and Fournier, Pierre-Edouard

Subjects
BACILLUS (Bacteria)
Abstract

The online version of the original article can be found at https://doi.org/10.4056/sigs.2776064. References 1 Kokcha, S, Mishra, A.K, Lagier, J.C. et al non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov. Following publication of the original article [[1]], the authors flagged the following errors: The original version of this article unfortunately contained two mistakes: (1) the authors had omitted to mention 10403188T as type strain name of the new species I Bacillus timonensis i (MM10403188T had been written instead), and (2) in the last paragraph of the protologue, DSM 253720 had been written in place of DSM 25372. [Extracted from the article]

Published
2023
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28. Abstract 2400: Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for targeted sequencing in a prospective randomized trial for personalized treatment in all tumor type: The SHIVA study

Author

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

Published
2015
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29. PIK3CA Pathway Mutations Predictive of Poor Response Following Standard Radiochemotherapy ± Cetuximab in Cervical Cancer Patients

Author

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

Published
2015
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30. Abstract PD3-8: Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients

Author

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

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

Published
2014
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32. Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients

Author

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

Published
2014
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33. Emergence of New ALK Mutations at Relapse of Neuroblastoma

Author

Schleiermacher, Gudrun, primary, Javanmardi, Niloufar, additional, Bernard, Virginie, additional, Leroy, Quentin, additional, Cappo, Julie, additional, Rio Frio, Thomas, additional, Pierron, Gaelle, additional, Lapouble, Eve, additional, Combaret, Valérie, additional, Speleman, Frank, additional, de Wilde, Bram, additional, Djos, Anna, additional, Øra, Ingrid, additional, Hedborg, Fredrik, additional, Träger, Catarina, additional, Holmqvist, Britt-Marie, additional, Abrahamsson, Jonas, additional, Peuchmaur, Michel, additional, Michon, Jean, additional, Janoueix-Lerosey, Isabelle, additional, Kogner, Per, additional, Delattre, Olivier, additional, and Martinsson, Tommy, additional

Published
2014
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34. Monitoring of circulating tumor DNA in metastatic triple-negative breast cancer patients undergoing chemotherapy.

Author

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

Published
2014
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36. Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model

Author

Tarabeux, Julien, primary, Zeitouni, Bruno, additional, Moncoutier, Virginie, additional, Tenreiro, Henrique, additional, Abidallah, Khadija, additional, Lair, Séverine, additional, Legoix-Né, Patricia, additional, Leroy, Quentin, additional, Rouleau, Etienne, additional, Golmard, Lisa, additional, Barillot, Emmanuel, additional, Stern, Marc-Henri, additional, Rio-Frio, Thomas, additional, Stoppa-Lyonnet, Dominique, additional, and Houdayer, Claude, additional

Published
2013
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40. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

Author

Fournier, Pierre-Edouard, primary, El Karkouri, Khalid, additional, Leroy, Quentin, additional, Robert, Catherine, additional, Giumelli, Bernadette, additional, Renesto, Patricia, additional, Socolovschi, Cristina, additional, Parola, Philippe, additional, Audic, Stéphane, additional, and Raoult, Didier, additional

Published
2009
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42. Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model.

Author

Tarabeux, Julien, Zeitouni, Bruno, Moncoutier, Virginie, Tenreiro, Henrique, Abidallah, Khadija, Lair, Séverine, Legoix-Né, Patricia, Leroy, Quentin, Rouleau, Etienne, Golmard, Lisa, Barillot, Emmanuel, Stern, Marc-Henri, Rio-Frio, Thomas, Stoppa-Lyonnet, Dominique, and Houdayer, Claude

Subjects
BRCA genes, CLINICAL pathology, GENETIC mutation, BIOINFORMATICS, ELECTROPHORESIS, BLOOD sampling
Abstract

To meet challenges in terms of throughput and turnaround time, many diagnostic laboratories are shifting from Sanger sequencing to higher throughput next-generation sequencing (NGS) platforms. Bearing in mind that the performance and quality criteria expected from NGS in diagnostic or research settings are strikingly different, we have developed an Ion Torrent's PGM-based routine diagnostic procedure for BRCA1/2 sequencing. The procedure was first tested on a training set of 62 control samples, and then blindly validated on 77 samples in parallel with our routine technique. The training set was composed of difficult cases, for example, insertions and/or deletions of various sizes, large-scale rearrangements and, obviously, mutations occurring in homopolymer regions. We also compared two bioinformatic solutions in this diagnostic context, an in-house academic pipeline and the commercially available NextGene software (Softgenetics). NextGene analysis provided higher sensitivity, as four previously undetected single-nucleotide variations were found. Regarding specificity, an average of 1.5 confirmatory Sanger sequencings per patient was needed for complete BRCA1/2 screening. Large-scale rearrangements were identified by two distinct analyses, that is, bioinformatics and fragment analysis with electrophoresis profile comparison. Turnaround time was enhanced, as a series of 30 patients were sequenced by one technician, making the results available for the clinician in 10 working days following blood sampling. BRCA1/2 genes are a good model, representative of the difficulties commonly encountered in diagnostic settings, which is why we believe our findings are of interest for the whole community, and the pipeline described can be adapted by any user of PGM for diagnostic purposes. [ABSTRACT FROM AUTHOR]

Published
2014
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