Genomes and Genes
- Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patientsPhilippe Broet
Faculté de Médecine Université Paris XI, IFR69, 16 Avenue Paul Vaillant Couturier 94807 Villejuif Cedex, France
Bioinformatics 22:1477-85. 2006..In this context, we propose a simple and an efficient method for identifying gene expression changes that characterize early and late recurrence for uncured patients...
- Unobserved covariates in the two-sample comparison of survival times: a maximum efficiency robust testP Broet
INSERM U472, 16 Ave Paul Vaillant Couturier, 94807 Villejuif Cedex, France
Stat Med 18:1791-800; discussion 1801. 1999..A breast cancer clinical trial is analysed as an example. The proposed test might be recommended rather than the logrank for practical situations in which one expects heterogeneity related to omitted covariates...
- Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture modelPhilippe Broet
Faculte de Medecine, Université Paris XI IFR69, 16 Avenue Paul Vaillant Couturier 94807 Villejuif Cedex, France
Bioinformatics 22:911-8. 2006..Inference is performed in a Bayesian framework. From the output, posterior probabilities of belonging to each of the three states are estimated for each genomic sequence and used to classify them...
- Two-sample statistics for testing the equality of survival functions against improper semi-parametric accelerated failure time alternatives: an application to the analysis of a breast cancer clinical trialPhilippe Broet
Department of Public Health and National Institute for Health and Medical Research INSERM U472 Paul Brousse Hospital, Villejuif, France and Institut Curie, 26 Rue d Ulm, Paris, France
Lifetime Data Anal 10:103-20. 2004..As a consequence, the proposed tests can be very easily implemented using widely available software. A breast cancer clinical trial is presented as an example to demonstrate the utility of the proposed tests...
- A mixture model-based strategy for selecting sets of genes in multiclass response microarray experimentsPhilippe Broet
INSERM U472, 16 Avenue Paul Vaillant Couturier, 94807 Villejuif Cedex, France
Bioinformatics 20:2562-71. 2004..Moreover, the method proposed allows calculation of these rates for any predefined subset of genes...
- A semiparametric approach for the two-sample comparison of survival times with long-term survivorsP Broet
National Institute for Health and Medical Research and Department of Public Health, Hopital Paul Brousse, Villejuif, France
Biometrics 57:844-52. 2001..An example investigating the impact of progesterone receptors status on local tumor relapse for patients with early breast cancer illustrates the use of the proposed tests...
- Bayesian hierarchical model for identifying changes in gene expression from microarray experimentsPhilippe Broet
Faculte de Medecine, Université Paris XI and INSERM U472, Hopital Paul Brousse, 16 Avenue Paul Vaillant Couturier, 94807 Villejuif Cedex, France
J Comput Biol 9:671-83. 2002..A case study that investigated those genes that were differentially expressed in two cell lines (normal and modified by a gene transfection) is provided to illustrate the performance and usefulness of this approach...
- Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02)Sophie Limou
Conservatoire National des Arts et Metiers, Universite Paris 7, Paris, France
J Infect Dis 199:419-26. 2009..The present study, the first GWAS of HIV-1 nonprogressors, underscores the potential for some HLA genes to control disease progression soon after infection...
- A simple procedure for estimating the false discovery rateCyril Dalmasso
INSERM U472, Faculté de Médecine Paris Sud 16 Avenue Paul Vaillant Couturier, 94807 Villejuif Cedex, France
Bioinformatics 21:660-8. 2005..Indeed, only an upper bound estimate can be obtained for the key quantity pi0, which is the probability for a gene to be unmodified. In this paper, we propose a novel family of estimators for pi0 that allows the calculation of FDR...
- A constrained polynomial regression procedure for estimating the local False Discovery RateCyril Dalmasso
JE 2492 Univ Paris Sud, Villejuif, France
BMC Bioinformatics 8:229. 2007..The lFDR not only allows an inference to be made for each gene through its specific value, but also an estimate of Benjamini-Hochberg's False Discovery Rate (FDR) for subsets of genes...
- Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03)Sigrid Le Clerc
Conservatoire National des Arts et Metiers, Paris, France
J Infect Dis 200:1194-201. 2009..The discovery of genetic factors that predispose individuals to rapid progression to AIDS should also reveal new insights into the molecular etiology of the pathology...
- Reduction of microRNA 122 expression in IFNL3 CT/TT carriers and during progression of fibrosis in patients with chronic hepatitis CEmilie Estrabaud
INSERM, UMR1149, Team Physiopathology and Treatment of Viral Hepatitis, Centre de Recherche sur l Inflammation, BP 416, Paris, France
J Virol 88:6394-402. 2014..The association between miR-122 and IFNL3 was stronger than the association between miR-122 and response to treatment. miR-122 may play a role in the early viral decline that is dependent on IFNL3 and the innate immune response...
- Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arraysMarianne Tuefferd
JE2492 Department, Faculte de Medecine Paris Sud, IFR69, Villejuif, France
Genes Chromosomes Cancer 47:957-64. 2008..We observed better results using SNP probes than CNV probes for copy number analysis of FFPE material. This is the first report on the detection of copy number alterations in FFPE samples using Affymetrix GeneChip SNP6.0...
- Modulation of several waves of gene expression during FGF-1 induced epithelial-mesenchymal transition of carcinoma cellsClotilde Billottet
CNRS UMR 144 Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
J Cell Biochem 104:826-39. 2008....
- Identifying common prognostic factors in genomic cancer studies: a novel index for censored outcomesSigrid Rouam
Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
BMC Bioinformatics 11:150. 2010....
- A pseudo-R2 measure for selecting genomic markers with crossing hazards functionsSigrid Rouam
Genome Institute of Singapore, Biopolis, Singapore
BMC Med Res Methodol 11:28. 2011..Selection usually relies on statistical univariate indices based on the Cox model. Such model assumes proportional hazards (PH) which is unlikely to hold for each genomic marker...
- Prediction of clinical outcome in multiple lung cancer cohorts by integrative genomics: implications for chemotherapy selectionPhilippe Broet
JE2492, Faculty of Medicine Paris Sud, Bicetre, France
Cancer Res 69:1055-62. 2009..The utility of the IS in identifying early-stage NSCLC patients as candidates for adjuvant treatment should be further evaluated in a clinical trial...
- A mixture model approach to multiple testing for the genetic analysis of gene expressionCyril Dalmasso
JE 2492 Universite Paris Sud, Hôpital Paul Brousse Batiment 15 16, 16 Avenue Paul Vaillant Couturier, Villejuif Cedex 94807, France
BMC Proc 1:S141. 2007..The contribution of our model to estimation of FDR and related criteria is illustrated on the microarray expression profiles data set provided by the Genetic Analysis Workshop 15 Problem 1...
- Genomic aberrations associated with outcome in anaplastic oligodendroglial tumors treated within the EORTC phase III trial 26951Ahmed Idbaih
INSERM, U975, Université Pierre and Marie Curie Paris VI, Faculté de Médecine Pitié Salpêtrière, CNRS UMR 7225, Paris, France
J Neurooncol 103:221-30. 2011..Whole genome analysis appears useful to screen the numerous genomic abnormalities observed in AOTs and to propose new biomarkers particularly in the non-1p/19q codeleted AOTs...
- Impaired performance of FDR-based strategies in whole-genome association studies when SNPs are excluded prior to the analysisGaëlle Marenne
INSERM, UMR S0535, Villejuif, France
Genet Epidemiol 33:45-53. 2009..Based on our findings, excluding markers with high prior probability of being associated cannot be recommended for the analysis of WGA data with FDR-based strategies...
- Neurotensin receptor 1 determines the outcome of non-small cell lung cancerMarco Alifano
Service de Chirurgie Thoracique, Hotel Dieu, Paris, France
Clin Cancer Res 16:4401-10. 2010..This study aimed to investigate the role of the neurotensin/neurotensin receptor I (NTSR1) complex in non-small cell lung cancer (NSCLC) progression...
- Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 studyCyril Dalmasso
JE2492, Faculty of Medicine Paris Sud, Univ Paris Sud, Villejuif, France
PLoS ONE 3:e3907. 2008..Our data provide evidence that the MHC controls both HIV replication and HIV reservoir. They also indicate that two additional genomic loci may influence the HIV reservoir...
- Spatial normalization of array-CGH dataPierre Neuvial
Institut Curie, Service de Bioinformatique, 26, rue d Ulm, Paris, 75248 Cedex 05, France
BMC Bioinformatics 7:264. 2006..Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments...
- Bagging survival tree procedure for variable selection and prediction in the presence of nonsusceptible patientsCyprien Mbogning
Université Paris Saclay, Univ Paris Sud, UVSQ, CESP, INSERM, 14 16 Avenue Paul Vaillant Couturier, Villejuif, 94807, France
BMC Bioinformatics 17:230. 2016..However, the presence of a fraction of nonsusceptible patients in the studied population advocates for considering a criterion tailored to this peculiar situation...
- A Rescue Strategy for Handling Unevaluable Patients in Simon's Two Stage DesignLisa Belin
Biostatistics Department, Hopital, Institut Curie, Paris, France UMR 1178, INSERM, Villejuif, France
PLoS ONE 10:e0137586. 2015..Our rescue strategy is nevertheless the one which best approaches the target error rates requirement. A re-analysis of one real phase II clinical trials on metastatic cancer illustrates the use of the proposed strategy. ..
- A Bagged, Partially Linear, Tree-Based Regression Procedure for Prediction and Variable SelectionCyprien Mbogning
Abirisk Consortium, Villejuif, France
Hum Hered 79:182-93. 2015..In this work, we use bagging to address a classical concern of tree-based methods: their instability...
- Influence of trial duration on the bias of the estimated treatment effect in clinical trials when individual heterogeneity is ignoredElsa Cécilia-Joseph
Inserm U1018, CESP Centre for research in Epidemiology and Population Health, Villejuif, France Faculté de Médecine, University Paris Sud, Le Kremlin Bicetre, France
Biom J 57:371-83. 2015..The possibility of interpreting the long-term decrease in treatment effects as a bias induced by heterogeneity and trial duration is illustrated by a trial in oncology where adjuvant chemotherapy in stage 1B NSCLC was investigated. ..
- HER2 status in ovarian carcinomas: a multicenter GINECO study of 320 patientsMarianne Tuefferd
JE2492, Universite Paris Sud, IFR69, Villejuif, France
PLoS ONE 2:e1138. 2007....
- Characterization of the recurrent 8p11-12 amplicon identifies PPAPDC1B, a phosphatase protein, as a new therapeutic target in breast cancerIsabelle Bernard-Pierrot
UMR 144, Centre National de la Recherche Scientifique, Institut Curie, Paris, France
Cancer Res 68:7165-75. 2008..PPAPDC1B may also potentiate the estrogen receptor pathway by down-regulating DUSP22...
- Analysis of array CGH data: from signal ratio to gain and loss of DNA regionsPhilippe Hupe
Service Bioinformatique, UMR 144 CNRS Institut Curie, 26, rue d Ulm, Paris, 75248 Cedex 05, France
Bioinformatics 20:3413-22. 2004..The achievement of these goals requires a methodology for detecting the breakpoints delimiting altered regions in genomic patterns and assigning a status (normal, gained or lost) to each chromosomal region...
- Visualizing chromosomes as transcriptome correlation maps: evidence of chromosomal domains containing co-expressed genes--a study of 130 invasive ductal breast carcinomasFabien Reyal
Unite Mixte de Recherche 144, Centre National de la Recherche Scientifique, Paris, France
Cancer Res 65:1376-83. 2005..Transcription correlation maps are a new way of visualizing transcriptome data. They will help to identify new genes involved in tumor progression and new mechanisms of gene regulation in tumors...
- Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breastAnne Vincent-Salomon
Institut Curie, Department of Tumor Biology, Paris, France
Clin Cancer Res 14:1956-65. 2008..To gain insight into genomic and transcriptomic subtypes of ductal carcinomas in situ of the breast (DCIS)...
- FcgammaRIIB is differentially expressed during B cell maturation and in B-cell lymphomasSophie Camilleri-Broet
Service d Anatomie Pathologique, Hotel Dieu, AP HP, Universite Paris VI, Paris, France
Br J Haematol 124:55-62. 2004..01). Thus these results challenge the potential role of FcgammaRIIB during B-cell selection in GC, and suggest a prognostic value of FcgammaRIIB expression in DLBCL...
- A uniform activated B-cell-like immunophenotype might explain the poor prognosis of primary central nervous system lymphomas: analysis of 83 casesSophie Camilleri-Broet
Universite Paris Descartes, Faculte de Medecine, Groupe Hospitalier Pitie Salpetriere, AP HP, Paris, France
Blood 107:190-6. 2006..We postulate assigning PCNSL a histogenetic "time-slot," overlapping late GC and early post-GC, that could explain the predominant ABC phenotype observed...
- ITTACA: a new database for integrated tumor transcriptome array and clinical data analysisAdil Elfilali
Institut Curie, Service Bioinformatique, 26 Rue d Ulm, Paris, 75248 Cedex 05, France
Nucleic Acids Res 34:D613-6. 2006..This added flexibility and the user-friendly web interface makes ITTACA especially useful for comparing personal results with the results in the existing literature. ITTACA is accessible online at http://bioinfo.curie.fr/ittaca...