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Risk stratification integrating genetic data for factor VIII inhibitor development in patients with severe hemophilia A.

Bachelet D, Albert T, Mbogning C, Hässler S, Zhang Y, Schultze-Strasser S, Repessé Y, Rayes J, Pavlova A, Pezeshkpoor B, Liphardt K, Davidson JE, Hincelin-Méry A, Dönnes P, Lacroix-Desmazes S, Königs C, Oldenburg J, Broët P; ABIRISK consortium.

PLoS One. 2019 Jun 13;14(6):e0218258. doi: 10.1371/journal.pone.0218258. eCollection 2019.


Detection and kinetics of persistent neutralizing anti-interferon-beta antibodies in patients with multiple sclerosis. Results from the ABIRISK prospective cohort study.

Jensen PEH, Warnke C, Ingenhoven K, Piccoli L, Gasis M, Hermanrud C, Fernandez-Rodriguez BM, Ryner M, Kramer D, Link J, Ramanujam R, Auer M, Buck D, Grummel V, Bertotti E, Fissolo N, Oliver-Martos B, Nytrova P, Khalil M, Guger M, Rathmaier S, Sievers-Stober C, Lindberg RLP, Hässler S, Bachelet D, Aktas O, Donnellan N, Lawton A, Hemmer B, Havrdova EK, Kieseier B, Hartung HP, Comabella M, Montalban X, Derfuss T, Sellebjerg F, Dönnes P, Pallardy M, Spindeldreher S, Broët P, Deisenhammer F, Fogdell-Hahn A, Sorensen PS; ABIRISK Consortium.

J Neuroimmunol. 2019 Jan 15;326:19-27. doi: 10.1016/j.jneuroim.2018.11.002. Epub 2018 Nov 7.


Incidence and risk factors for adalimumab and infliximab anti-drug antibodies in rheumatoid arthritis: A European retrospective multicohort analysis.

Quistrebert J, Hässler S, Bachelet D, Mbogning C, Musters A, Tak PP, Wijbrandts CA, Herenius M, Bergstra SA, Akdemir G, Johannesson M, Combe B, Fautrel B, Chollet-Martin S, Gleizes A, Donnellan N, Deisenhammer F, Davidson J, Hincelin-Mery A, Dönnes P, Fogdell-Hahn A, De Vries N, Huizinga T, Abugessaisa I, Saevarsdottir S, Hacein-Bey-Abina S, Pallardy M, Broët P, Mariette X; ABIRISK Consortium.

Semin Arthritis Rheum. 2019 Jun;48(6):967-975. doi: 10.1016/j.semarthrit.2018.10.006. Epub 2018 Oct 12.


Monocyte NOTCH2 expression predicts IFN-β immunogenicity in multiple sclerosis patients.

Adriani M, Nytrova P, Mbogning C, Hässler S, Medek K, Jensen PEH, Creeke P, Warnke C, Ingenhoven K, Hemmer B, Sievers C, Lindberg Gasser RL, Fissolo N, Deisenhammer F, Bocskei Z, Mikol V, Fogdell-Hahn A, Kubala Havrdova E, Broët P, Dönnes P, Mauri C, Jury EC; ABIRISK Consortium.

JCI Insight. 2018 Jun 7;3(11). pii: 99274. doi: 10.1172/jci.insight.99274. eCollection 2018 Jun 7.


A two-stage design for phase II trials with time-to-event endpoint using restricted follow-up.

Belin L, De Rycke Y, Broët P.

Contemp Clin Trials Commun. 2017 Oct 1;8:127-134. doi: 10.1016/j.conctc.2017.09.010. eCollection 2017 Dec.


A test for comparing current status survival data with crossing hazard functions and its application to immunogenicity of biotherapeutics.

Jonas SF, Mbogning C, Broët P.

Stat Med. 2017 Nov 30;36(27):4364-4377. doi: 10.1002/sim.7439. Epub 2017 Aug 30.


Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.

Jusakul A, Cutcutache I, Yong CH, Lim JQ, Huang MN, Padmanabhan N, Nellore V, Kongpetch S, Ng AWT, Ng LM, Choo SP, Myint SS, Thanan R, Nagarajan S, Lim WK, Ng CCY, Boot A, Liu M, Ong CK, Rajasegaran V, Lie S, Lim AST, Lim TH, Tan J, Loh JL, McPherson JR, Khuntikeo N, Bhudhisawasdi V, Yongvanit P, Wongkham S, Totoki Y, Nakamura H, Arai Y, Yamasaki S, Chow PK, Chung AYF, Ooi LLPJ, Lim KH, Dima S, Duda DG, Popescu I, Broet P, Hsieh SY, Yu MC, Scarpa A, Lai J, Luo DX, Carvalho AL, Vettore AL, Rhee H, Park YN, Alexandrov LB, Gordân R, Rozen SG, Shibata T, Pairojkul C, Teh BT, Tan P.

Cancer Discov. 2017 Oct;7(10):1116-1135. doi: 10.1158/2159-8290.CD-17-0368. Epub 2017 Jun 30.


A score test for comparing cross-sectional survival data with a fraction of non-susceptible patients and its application in clinical immunology.

Jonas SF, Mbogning C, Hässler S, Broët P.

PLoS One. 2017 Jun 30;12(6):e0179896. doi: 10.1371/journal.pone.0179896. eCollection 2017.


Clinical practice of analysis of anti-drug antibodies against interferon beta and natalizumab in multiple sclerosis patients in Europe: A descriptive study of test results.

Link J, Ramanujam R, Auer M, Ryner M, Hässler S, Bachelet D, Mbogning C, Warnke C, Buck D, Hyldgaard Jensen PE, Sievers C, Ingenhoven K, Fissolo N, Lindberg R, Grummel V, Donnellan N, Comabella M, Montalban X, Kieseier B, Soelberg Sørensen P, Hartung HP, Derfuss T, Lawton A, Sikkema D, Pallardy M, Hemmer B, Deisenhammer F, Broët P, Dönnes P, Davidson J, Fogdell-Hahn A; ABIRISK Consortium.

PLoS One. 2017 Feb 7;12(2):e0170395. doi: 10.1371/journal.pone.0170395. eCollection 2017.


Occurrence of Anti-Drug Antibodies against Interferon-Beta and Natalizumab in Multiple Sclerosis: A Collaborative Cohort Analysis.

Bachelet D, Hässler S, Mbogning C, Link J, Ryner M, Ramanujam R, Auer M, Hyldgaard Jensen PE, Koch-Henriksen N, Warnke C, Ingenhoven K, Buck D, Grummel V, Lawton A, Donnellan N, Hincelin-Mery A, Sikkema D, Pallardy M, Kieseier B, Hemmer B, Hartung HP, Soelberg Sorensen P, Deisenhammer F, Dönnes P, Davidson J, Fogdell-Hahn A, Broët P; ABIRISK Consortium.

PLoS One. 2016 Nov 2;11(11):e0162752. doi: 10.1371/journal.pone.0162752. eCollection 2016.


Bagging survival tree procedure for variable selection and prediction in the presence of nonsusceptible patients.

Mbogning C, Broët P.

BMC Bioinformatics. 2016 Jun 7;17(1):230. doi: 10.1186/s12859-016-1090-x.


A Rescue Strategy for Handling Unevaluable Patients in Simon's Two Stage Design.

Belin L, Broët P, De Rycke Y.

PLoS One. 2015 Sep 14;10(9):e0137586. doi: 10.1371/journal.pone.0137586. eCollection 2015.


A Bagged, Partially Linear, Tree-Based Regression Procedure for Prediction and Variable Selection.

Mbogning C, Perdry H, Broët P.

Hum Hered. 2015;79(3-4):182-93. doi: 10.1159/000380850. Epub 2015 Jul 28.


Standardizing terms, definitions and concepts for describing and interpreting unwanted immunogenicity of biopharmaceuticals: recommendations of the Innovative Medicines Initiative ABIRISK consortium.

Rup B, Pallardy M, Sikkema D, Albert T, Allez M, Broet P, Carini C, Creeke P, Davidson J, De Vries N, Finco D, Fogdell-Hahn A, Havrdova E, Hincelin-Mery A, C Holland M, H Jensen PE, Jury EC, Kirby H, Kramer D, Lacroix-Desmazes S, Legrand J, Maggi E, Maillère B, Mariette X, Mauri C, Mikol V, Mulleman D, Oldenburg J, Paintaud G, R Pedersen C, Ruperto N, Seitz R, Spindeldreher S, Deisenhammer F; ABIRISK Consortium.

Clin Exp Immunol. 2015 Sep;181(3):385-400. doi: 10.1111/cei.12652. Epub 2015 Jul 2. Review.


Patterns of chromosomal copy-number alterations in intrahepatic cholangiocarcinoma.

Dalmasso C, Carpentier W, Guettier C, Camilleri-Broët S, Borelli WV, Campos Dos Santos CR, Castaing D, Duclos-Vallée JC, Broët P.

BMC Cancer. 2015 Mar 14;15:126. doi: 10.1186/s12885-015-1111-6.


Influence of trial duration on the bias of the estimated treatment effect in clinical trials when individual heterogeneity is ignored.

Cécilia-Joseph E, Auvert B, Broët P, Moreau T.

Biom J. 2015 May;57(3):371-83. doi: 10.1002/bimj.201400046. Epub 2015 Jan 16.


A novel tree-based procedure for deciphering the genomic spectrum of clinical disease entities.

Mbogning C, Perdry H, Toussile W, Broët P.

J Clin Bioinforma. 2014 Apr 16;4:6. doi: 10.1186/2043-9113-4-6. eCollection 2014.


Reduction of microRNA 122 expression in IFNL3 CT/TT carriers and during progression of fibrosis in patients with chronic hepatitis C.

Estrabaud E, Lapalus M, Broët P, Appourchaux K, De Muynck S, Lada O, Martinot-Peignoux M, Bièche I, Valla D, Bedossa P, Marcellin P, Vidaud M, Asselah T.

J Virol. 2014 Jun;88(11):6394-402. doi: 10.1128/JVI.00016-14. Epub 2014 Mar 26.


Intertumor heterogeneity of non-small-cell lung carcinomas revealed by multiplexed mutation profiling and integrative genomics.

Tan DS, Camilleri-Broët S, Tan EH, Alifano M, Lim WT, Bobbio A, Zhang S, Ng QS, Ang MK, Iyer NG, Takano A, Lim KH, Régnard JF, Tan P, Broët P.

Int J Cancer. 2014 Sep 1;135(5):1092-100. doi: 10.1002/ijc.28750. Epub 2014 Apr 3.


A discrimination index for selecting markers of tumor growth dynamic across multiple cancer studies with a cure fraction.

Rouam S, Broët P.

Genomics. 2013 Aug;102(2):102-11. doi: 10.1016/j.ygeno.2013.02.013. Epub 2013 Mar 6.


Thymic carcinomas: clinicopathologic study of 37 cases from a single institution.

Thomas de Montpréville V, Ghigna MR, Lacroix L, Besse B, Broet P, Dartevelle P, Fadel E, Dorfmuller P.

Virchows Arch. 2013 Mar;462(3):307-13. doi: 10.1007/s00428-013-1371-y. Epub 2013 Jan 15.


A model-based statistic for detecting molecular markers associated with complex survival patterns in early-stage cancer.

Broët P, Moreau T.

J Clin Bioinforma. 2012 Aug 6;2(1):14. doi: 10.1186/2043-9113-2-14.


Single-nucleotide polymorphism-defined class I and class III major histocompatibility complex genetic subregions contribute to natural long-term nonprogression in HIV infection.

Guergnon J, Dalmasso C, Broet P, Meyer L, Westrop SJ, Imami N, Vicenzi E, Morsica G, Tinelli M, Zanone Poma B, Goujard C, Potard V, Gotch FM, Casoli C, Cossarizza A, Macciardi F, Debré P, Delfraissy JF, Galli M, Autran B, Costagliola D, Poli G, Theodorou I, Riva A; GISHEAL Consortium.

J Infect Dis. 2012 Mar 1;205(5):718-24. doi: 10.1093/infdis/jir833. Epub 2012 Jan 11.


IL28B polymorphism is associated with treatment response in patients with genotype 4 chronic hepatitis C.

Asselah T, De Muynck S, Broët P, Masliah-Planchon J, Blanluet M, Bièche I, Lapalus M, Martinot-Peignoux M, Lada O, Estrabaud E, Zhang Q, El Ray A, Vidaud D, Ripault MP, Boyer N, Bedossa P, Valla D, Vidaud M, Marcellin P.

J Hepatol. 2012 Mar;56(3):527-32. doi: 10.1016/j.jhep.2011.09.008. Epub 2011 Sep 25.


Detection of chromosomal abnormalities using high resolution arrays in clinical cancer research.

Dalmasso C, Broët P.

J Biomed Inform. 2011 Dec;44(6):936-42. doi: 10.1016/j.jbi.2011.06.003. Epub 2011 Jun 15.


Genomic profiles specific to patient ethnicity in lung adenocarcinoma.

Broët P, Dalmasso C, Tan EH, Alifano M, Zhang S, Wu J, Lee MH, Régnard JF, Lim D, Koong HN, Agasthian T, Miller LD, Lim E, Camilleri-Broët S, Tan P.

Clin Cancer Res. 2011 Jun 1;17(11):3542-50. doi: 10.1158/1078-0432.CCR-10-2185. Epub 2011 Apr 26.


CXCL12 expression by healthy and malignant ovarian epithelial cells.

Machelon V, Gaudin F, Camilleri-Broët S, Nasreddine S, Bouchet-Delbos L, Pujade-Lauraine E, Alexandre J, Gladieff L, Arenzana-Seisdedos F, Emilie D, Prévot S, Broët P, Balabanian K.

BMC Cancer. 2011 Mar 16;11:97. doi: 10.1186/1471-2407-11-97.


A pseudo-R2 measure for selecting genomic markers with crossing hazards functions.

Rouam S, Moreau T, Broët P.

BMC Med Res Methodol. 2011 Mar 15;11:28. doi: 10.1186/1471-2288-11-28.


Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms.

Ruggiero D, Dalmasso C, Nutile T, Sorice R, Dionisi L, Aversano M, Bröet P, Leutenegger AL, Bourgain C, Ciullo M.

PLoS One. 2011 Feb 9;6(2):e16982. doi: 10.1371/journal.pone.0016982.


Genomic aberrations associated with outcome in anaplastic oligodendroglial tumors treated within the EORTC phase III trial 26951.

Idbaih A, Dalmasso C, Kouwenhoven M, Jeuken J, Carpentier C, Gorlia T, Kros JM, French P, Teepen J, Broët P, Delattre O, Mokhtari K, Sanson M, Delattre JY, van den Bent M, Hoang-Xuan K.

J Neurooncol. 2011 Jun;103(2):221-30. doi: 10.1007/s11060-010-0380-9. Epub 2010 Sep 6.


Neurotensin receptor 1 determines the outcome of non-small cell lung cancer.

Alifano M, Souazé F, Dupouy S, Camilleri-Broët S, Younes M, Ahmed-Zaïd SM, Takahashi T, Cancellieri A, Damiani S, Boaron M, Broët P, Miller LD, Gespach C, Regnard JF, Forgez P.

Clin Cancer Res. 2010 Sep 1;16(17):4401-10. doi: 10.1158/1078-0432.CCR-10-0659.


Identifying common prognostic factors in genomic cancer studies: a novel index for censored outcomes.

Rouam S, Moreau T, Broët P.

BMC Bioinformatics. 2010 Mar 24;11:150. doi: 10.1186/1471-2105-11-150.


Finding exclusively deleted or amplified genomic areas in lung adenocarcinomas using a novel chromosomal pattern analysis.

Broët P, Tan P, Alifano M, Camilleri-Broët S, Richardson S.

BMC Med Genomics. 2009 Jul 14;2:43. doi: 10.1186/1755-8794-2-43.


False discovery rate estimation for frequentist pharmacovigilance signal detection methods.

Ahmed I, Dalmasso C, Haramburu F, Thiessard F, Broët P, Tubert-Bitter P.

Biometrics. 2010 Mar;66(1):301-9. doi: 10.1111/j.1541-0420.2009.01262.x. Epub 2009 May 4.


Prediction of clinical outcome in multiple lung cancer cohorts by integrative genomics: implications for chemotherapy selection.

Broët P, Camilleri-Broët S, Zhang S, Alifano M, Bangarusamy D, Battistella M, Wu Y, Tuefferd M, Régnard JF, Lim E, Tan P, Miller LD.

Cancer Res. 2009 Feb 1;69(3):1055-62. doi: 10.1158/0008-5472.CAN-08-1116. Epub 2009 Jan 27.


Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study.

Dalmasso C, Carpentier W, Meyer L, Rouzioux C, Goujard C, Chaix ML, Lambotte O, Avettand-Fenoel V, Le Clerc S, de Senneville LD, Deveau C, Boufassa F, Debré P, Delfraissy JF, Broet P, Theodorou I; ANRS Genome Wide Association 01.

PLoS One. 2008;3(12):e3907. doi: 10.1371/journal.pone.0003907. Epub 2008 Dec 24.


Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays.

Tuefferd M, De Bondt A, Van Den Wyngaert I, Talloen W, Verbeke T, Carvalho B, Clevert DA, Alifano M, Raghavan N, Amaratunga D, Göhlmann H, Broët P, Camilleri-Broët S.

Genes Chromosomes Cancer. 2008 Nov;47(11):957-64. doi: 10.1002/gcc.20599.


Impaired performance of FDR-based strategies in whole-genome association studies when SNPs are excluded prior to the analysis.

Marenne G, Dalmasso C, Perdry H, Génin E, Broët P.

Genet Epidemiol. 2009 Jan;33(1):45-53. doi: 10.1002/gepi.20355.


A mixture model approach to multiple testing for the genetic analysis of gene expression.

Dalmasso C, Pickrell J, Tuefferd M, Génin E, Bourgain C, Broët P.

BMC Proc. 2007;1 Suppl 1:S141. Epub 2007 Dec 18.


Modulation of several waves of gene expression during FGF-1 induced epithelial-mesenchymal transition of carcinoma cells.

Billottet C, Tuefferd M, Gentien D, Rapinat A, Thiery JP, Broët P, Jouanneau J.

J Cell Biochem. 2008 Jun 1;104(3):826-39. doi: 10.1002/jcb.21667.


Multiple testing in the genomics era: findings from Genetic Analysis Workshop 15, Group 15.

Martin LJ, Woo JG, Avery CL, Chen HS, North KE, Au K, Broët P, Dalmasso C, Guedj M, Holmans P, Huang B, Kuo PH, Lam AC, Li H, Manning A, Nikolov I, Sinha R, Shi J, Song K, Tabangin M, Tang R, Yamada R.

Genet Epidemiol. 2007;31 Suppl 1:S124-31. Review.


HER2 status in ovarian carcinomas: a multicenter GINECO study of 320 patients.

Tuefferd M, Couturier J, Penault-Llorca F, Vincent-Salomon A, Broët P, Guastalla JP, Allouache D, Combe M, Weber B, Pujade-Lauraine E, Camilleri-Broët S.

PLoS One. 2007 Nov 7;2(11):e1138.


A constrained polynomial regression procedure for estimating the local False Discovery Rate.

Dalmasso C, Bar-Hen A, Broët P.

BMC Bioinformatics. 2007 Jun 29;8:229.


Constitutive phosphoinositide 3-kinase/Akt activation represents a favorable prognostic factor in de novo acute myelogenous leukemia patients.

Tamburini J, Elie C, Bardet V, Chapuis N, Park S, Broët P, Cornillet-Lefebvre P, Lioure B, Ugo V, Blanchet O, Ifrah N, Witz F, Dreyfus F, Mayeux P, Lacombe C, Bouscary D.

Blood. 2007 Aug 1;110(3):1025-8. Epub 2007 Apr 10.


Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients.

Broët P, Kuznetsov VA, Bergh J, Liu ET, Miller LD.

Bioinformatics. 2006 Jun 15;22(12):1477-85. Epub 2006 Mar 21.


Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model.

Broët P, Richardson S.

Bioinformatics. 2006 Apr 15;22(8):911-8. Epub 2006 Feb 2.


A uniform activated B-cell-like immunophenotype might explain the poor prognosis of primary central nervous system lymphomas: analysis of 83 cases.

Camilleri-Broët S, Crinière E, Broët P, Delwail V, Mokhtari K, Moreau A, Kujas M, Raphaël M, Iraqi W, Sautès-Fridman C, Colombat P, Hoang-Xuan K, Martin A.

Blood. 2006 Jan 1;107(1):190-6. Epub 2005 Sep 8.


Chromosome 1p loss: a favorable prognostic factor in low-grade gliomas.

Kujas M, Lejeune J, Benouaich-Amiel A, Crinière E, Laigle-Donadey F, Marie Y, Mokhtari K, Polivka M, Bernier M, Chretien F, Couvelard A, Capelle L, Duffau H, Cornu P, Broët P, Thillet J, Carpentier AF, Sanson M, Hoang-Xuan K, Delattre JY.

Ann Neurol. 2005 Aug;58(2):322-6.


[Multiple comparison procedures: principles, limits. Applications to microarray phenotype-genotype analysis].

Dalmasso C, Broët P, Moreau T.

Rev Epidemiol Sante Publique. 2004 Dec;52(6):523-37. Review. French.


Correlations between molecular profile and radiologic pattern in oligodendroglial tumors.

Laigle-Donadey F, Martin-Duverneuil N, Lejeune J, Crinière E, Capelle L, Duffau H, Cornu P, Broët P, Kujas M, Mokhtari K, Carpentier A, Sanson M, Hoang-Xuan K, Thillet J, Delattre JY.

Neurology. 2004 Dec 28;63(12):2360-2. Review.


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