The team develops new models and statistical methods for data from epidemiological studies and clinical trials, with a strong emphasis on cohort data analysis.
Objectives
Our project aims to develop, evaluate and apply statistical methods for the analysis of any kind of health data (cohorts, case-control studies, medico-administrative and hospital data bases…) with the final objective to answer clinical and public health questions regarding all aspects of diseases: future burden, risk factors, individual prediction, disease progression, understanding underlying pathological mechanisms, and evaluating and understanding treatment effects. We are mainly interested in dynamic models accounting for the time-dimension of pathological processes and incomplete or inaccurate data (selection bias, attrition, censoring, truncation, measurement errors…). Thus, we will continue to develop statistical methods for the analysis of complex survival and longitudinal data, while, for the next 5-year period, we will also tackle two main new challenges: causality and big-data issues.
Causal questions are related to our research about the mechanism underlying pathological processes in chronic diseases, the role of some long-term exposure and the impact of social inequalities in health. We will investigate the causal interpretation of the multivariate models we develop (especially joint models for longitudinal data and time-to-event) and we will propose new methods for studying causality for censored time-to-events and/or time-dependent markers or risk factors.
With the opening of administrative and hospital data bases to research as well as technological progress allowing to collect a very large amount of data (genetics, biology, imaging, IoT data), we face an increasing number of predictors, markers and outcomes of different types. The models we have developed so far are quite complex and the estimation procedures are often time-consuming and thus not suitable for huge data sets or high dimensional time-dependent markers or exposures. We will thus develop new biostatistical models and estimation procedures that tackle high-dimensionality issues with the goals of individual risk prediction or understanding of the interdependencies between multiple (pathological and/or exposure) processes.
While each researcher from the team has one or two favorite domains of applications in which he/she has acquired a high level of expertise (Alzheimer’s disease, HIV, cancer and chronic kidney disease), we will open to new health questions related for instance to the progression of MSA, the prediction of cardiovascular risk or the prognosis in neuro-intensive care unit.
Research area
Our projects can be divided into 6 axes:
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Modeling the progression of chronic diseases
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Modeling time-dependent exposure
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Causality
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Individual dynamic prediction
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Estimation and projection of Public Health indicators
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Methods for clinical research
Software
Find here all our files
R packages :
- FRAILTYPACK: R package for Shared, Joint (Generalized) Frailty Models; Surrogate Endpoints
https://cran.r-project.org/web/packages/frailtypack/index.html
https://github.com/socale/frailtypack
- LCMM : Estimation of various models for longitudinal and time-to-event data based on latent classes and latent processes
https://cran.r-project.org/web/packages/lcmm/index.html
https://github.com/CecileProust-Lima/lcmm
- SmoothHazard: A R package for the estimation of illness-death models for interval-censored data
- CinLPN: Estimation of a dynamic causal model based on a system of latent processes
- marqLevAlg: A Parallelized General-Purpose Optimization Based on Marquardt-Levenberg Algorithm
https://cran.r-project.org/web/packages/marqLevAlg/index.html
https://github.com/VivianePhilipps/marqLevAlgParallel/
- JLPM: estimation of different joint models based on latent processes
- NormPsy: Normalisation of Mini Mental State Examination (MMSE)
- weightQuant: Estimation of observation-specific weights for incomplete longitudinal data with selection by death and bootstrap inference procedure for weighted quantile regressions
- MCSPCD :Monte Carlo Simulation for Projections of epidemiological burden of Chronic Disease and evaluation of impact of changes in risk factor distribution for a given year
- QoLSEM: Estimation of a structural equation model for the global analysis of health-related quality of life data
- BQt: Bayesian estimation of quantile regression mixed models
- JMcuR: Estimation of joint models for repeated measurements and time-to-event data included a cure fraction
Other programs :
- CPMCGLM : correction de la p-valeur après plusieurs codages dans les modèles linéaires généralisés
- R code for sparse conditional logistic regression
- PSPMCM: Macro SAS pour l’estimation de modèles de survie de mélange avec une fraction non à risque (Mixture Cure Models)
- MKVPCI : Programme pour l’estimation des modèles de Markov avec intensités de transition constantes par morceaux et covariables.
- Projection with Semi-Markov Model
Carreer
If you are interested by research in Biostatistics and more generally Statistics applied to health, send a motivated application to sandrine.darmigny@u-bordeaux.fr. Our biostatistics team welcomes interns, PhD students and postdoctoral researchers each year.
Main publications in 2021
2021-1 Acar N, Merle, BMJ, Ajana, S, …, Jacqmin-Gadda H, Bretillon L, Delcourt C for the Biomarkers of LIpid Status And metabolism in Retinal ageing (BLISAR) Study Group. Predicting the retinal content in omega-3 fatty acids for age-related macular-degeneration. Clin Transl Med 2021, 11(7):e404. https://doi.org/10.1002/ctm2.404
2021-2 Ajana S, Cougnard-Grégoire A, Colijn JM, …, Jacqmin-Gadda H*, Klaver C*, Delcourt C*and on behalf of the EYE-RISK Consortium. (*co-last authors). Predicting progression to advanced age-related macular degeneration from clinical, genetic and lifestyle factors using machine learning, Ophtalmology, 2021, 128(4):587-597.
2021-3 Amadou A, Praud D, Coudon T, …, Leffondre K, …, Mancini FR, Fervers B. Risk of breast cancer associated with long-term exposure to Benzo[a]pyrene (BaP) air pollution: Evidence from the French E3N cohort study. Environ Int 2021; 149:106399.
2021-4 Andersen P. K., Pohar Perme M., van Houwelingen H. C., Cook R. J., Joly P., Martinussen T., Taylor J. M. G., Abrahamowicz M. and Therneau T. M., (2021). Analysis of time-to-event for observational studies: Guidance to the use of intensity models. Stat Med. 2021, 40(1): 185-211.
2021-5 Baussard L, Proust-Lima C, Philipps V, Portales F, Ychou M, Mazard T, Cousson-Gélie, F. Determinants of Distinct Trajectories of Fatigue in Patients Undergoing Chemotherapy for a Metastatic Colorectal Cancer: 6-Month Follow-up Using Growth Mixture Modeling. J Pain Symptom Manage. 2021;S0885-3924(21)00398-5.
2021-6 Ben-Hassen, C., Helmer, C., Berr, C., Jacqmin-Gadda, H. 5-year dynamic prediction of dementia using repeated measures of cognitive tests and a dependency scale. Am J Epidemiol, 2021 (online 9/11/2021) https://doi.org/10.1093/aje/kwab269
2021-07 Branchoux S, Ledoux Sofeu C, Gaudin AF, Kurt M, Moshyk A, Italiano A, Bellera C., Rondeau V. Time to next treatment or death as a candidate surrogate end-point for overall survival in advanced melanoma patients treated with immune-checkpoint inhibitors : an insight from the phase iii checkmate 067 trial. ESMO 2021, 7 :100340.
2021-8 Carles, S., Taddé, B. O., Berr, C., Helmer, C., Jacqmin-Gadda, H., Carrière, I., Proust-Lima, C. Dynamic reciprocal relationships between cognitive and functional declines along the Alzheimer’s disease continuum in the prospective COGICARE study. Alz Res Therapy 2021, 13(1), 1-12.
2021-9 Castel C, Sommen C, Le Strat Y, Alioum A. A multi-state Markov model using notification data to estimate HIV incidence, number of undiagnosed individuals living with HIV, and delay between infection and diagnosis : illustration in France, 2008-2018. Stat Methods Med Res. 2021 Nov;30(11):2382-2398.
2021-10 Castel C, Sommen C, Chatignoux E, Le Strat Y, Alioum A. Bayesian multi-response nonlinear mixed-effect model : application of two recent HIV infection biomarkers. Int J Biostat. 2021 Aug 13. doi: 10.1515/ijb-2021-0030
2021-11 Chamberlain, J. D., Rouanet, A., Dubois, B., …., Chene G, Dufouil C.& Memento Study group. Investigating the association between cancer and the risk of dementia: Results from the Memento cohort. Alzheimer’s & Dementia 2021, 17(9):1415-1421
2021-12 Chauvet J. and Rondeau V. A flexible class of generalized joint frailty models for the analysis of survival endpoints. Statistics in Medicine, In press, 2021.
2021-13 Cheradame J, Piscione J, Carling C, Guinoiseau J-P, Dufour B, Jacqmin-Gadda H *, Decq Ph * (*co-last authors). Incidence and risk factors in concussion events: A 5-season study in the French Top 14 Rugby Union Championship. Am J Sports Med 2021, https://doi.org/10.1177%2F03635465211006480.
2021-14 Dartigues J-F, Le Bourdonnec K, Tabue-Teguo M, …, Amieva H, Proust-Lima C. Co-Occurrence of Geriatric Syndromes and Diseases in the General Population:Assessment of the Dimensions of Aging. J Nutr Health Aging. 2021, https://doi.org/10.1093/gerona/glx068.
2021-15 de Courson H, Ferrer L, Barbieri A, Tully PJ, Woodward M, Chalmers J, Tzourio C*, Leffondré K* (*co-last authors). Impact of Model Choice When Studying the Relationship Between Blood Pressure Variability and Risk of Stroke Recurrence. Hypertension. 2021;78(5):1520-1526.
2021-16 Deygas F, Amadou A, Coudon T, …, Leffondré K, Fervers B, Praud D. Long-term atmospheric exposure to PCB153 and breast cancer risk in a case-control study nested in the French E3N cohort. Environment Research 2021; 195:110743. https://doi.org/10.1016/j.envres.2021.110743
2021-17 Dinart D, Bellera C, and Rondeau V. Sample size estimation for cancer randomized trials in the presence of heterogeneous populations,. Biometrics, 2021; DOI: 10.1111/biom.13527
2021-18 Driollet B, Bayer F, Kwon T,…, Harambat J*, Leffondré K* (*co-last authors). Social deprivation is associated with lower access to pre-emptive kidney transplantation and more urgent-start dialysis in the pediatric population. Kidney International Reports 2021; https://doi.org/10.1016/j.ekir.2021.12.015
2021-19 Du Preez A, Lefèvre-Arbogast S, Houghton V, …,Proust-Lima C,…, Samieri C, Thuret, S. The serum metabolome mediates the concert of diet, exercise, and neurogenesis, determining the risk for cognitive decline and dementia. Alzheimers Dement 2021; https://doi.org/10.1002/alz.12428
2021-20 Emura T., Sofeu C., and Rondeau V.. Conditional copula models for correlated sur- vival endpoints : individual patient data meta-analysis of randomized controlled trials. Stat Med Res, 2021, 30(12); https://doi.org/10.1177%2F09622802211046390
2021-21 Faucon A-L, Leffondré K, Flamant M, Metzger M, Boffa J-J, Haymann J-P, Houillier P, Thervet E, Vrtovsnik F, Proust‐Lima C, Stengel B, Vidal-Petiot E, Geri G, and the NephroTest study group. Trajectory of extracellular fluid volume over time and subsequent risks of end-stage kidney disease and mortality in chronic kidney disease: a prospective cohort study. J Intern Med 2021;289(2):193 205.
2021-22 Frison E, Proust-Lima C, Mangin J-F, Habert M-O, Bombois S, Ousset P-J, et al. Diabetes Mellitus and Cognition: Pathway Analysis in the MEMENTO Cohort. Neurology. 2021;97(8):e836 48.
2021-23 Jacqmin-Gadda H, Ferrer L, Proust-Lima C. Joint Models for Longitudinal and Time to Event Data. In Handbook of Statistical Methods for Randomized, Controlled Trials. Edit: K Kim, F Bretz, YK Cheung, LV Hampson, Chapman and Hall/ CRC Press, 2021
2021-24 Kaboré R, Ferrer L, Couchoud C, Hogan J, …, Harambat J*, Leffondré K* (*co-last authors). Dynamic prediction models for graft failure in pediatric kidney transplantation. Nephrol Dial Transplant 2021; 36(5):927-935.
2021-25 Lefèvre-Arbogast S, Hejblum BP, Helmer C, …, Proust-Lima C,…., Korosi A, Samieri C. Early signature in the blood lipidome associated with subsequent cognitive decline in the elderly: A case-control analysis nested within the Three-City cohort study. EBioMedicine 2021; 64:103216.
2021-26 Lenain R, Boucquemont J, Leffondré K, Couchoud C, Lassalle M, Hazzan M, Foucher Y. Clinical trial emulation by matching time-dependent propensity scores: The example of estimating impact of kidney transplantation. Epidemiology 2021; 32(2):220-229.
2021-27 Mathieu C, Joly P, Jacqmin-Gadda H, Wanneveich M, Bégaud B, Pariente A. Patterns of Benzodiazepine Use and Excess Risk of All-Cause Mortality in the Elderly: A Nationwide Cohort Study. Drug Saf. 2021, 44(1):53-62.
2021-28 Philipps V, Hejblum BP, Prague M, Commenges D, Proust-Lima C. Robust and Efficient Optimization Using a Marquardt-Levenberg Algorithm with R Package marqLevAlg. The R journal 2021; http://arxiv.org/abs/2009.03840
2021-29 Prezelin-Reydit M, Madden L, Macher MA, …, Leffondré K*, Harambat J* (*co-last authors). Preemptive kidney transplantation is associated with transplantation outcomes in children: results from the French kidney replacement therapy registry. Transplantation 2021; https://doi.org/10.1097/TP.0000000000003757
2021-30 Raynaud M, Aubert O, Reese PP, …, Proust-Lima C,…,.Lefaucheur C, Loupy A. Trajectories of glomerular filtration rate and progression to end stage kidney disease after kidney transplantation. Kidney Int 2021;99(1):186 97.
2021-31 Rouanet A, Avila-Rieger J, Dugravot A, , Gross A, Proust-Lima C. How selection over time contributes to the inconsistency of the association between sex/gender and cognitive decline across cognitive aging cohorts. Am J Epidemiol 2021; doi: 10.1093/aje/kwab227
2021-32 Thomas A, Proust-Lima C, Baillet M, Helmer C, Delcourt C, Foubert-Samier A, Catheline G, Feart C, Samieri C. Plasma carotenoids and medial temporal lobe atrophy in older adults. Clin Nutr 2021;40(4):2460 3.
2021-33 Wagner M, Grodstein F, Leffondre K, Samieri C*, Proust-Lima C* (*co-last authors). Time-varying associations between an exposure history and a subsequent health outcome: a landmark approach to identify critical windows. BMC Med Res Methodol 2021;21(1):266
PUBLICATIONS PREPRINT
Devaux A, Genuer R, Pérès K, Proust-Lima C. Individual dynamic prediction of clinical endpoint from large dimensional longitudinal biomarker history: a landmark approach. ArXiv:210201466. 2 févr 2021
Available at http://arxiv.org/abs/2102.01466
Valeri L, Proust-Lima C, Fan W, Chen JT, Jacqmin-Gadda H. A multistate approach for mediation analysis in the presence of semi-competing risks with application in cancer survival disparities. arXiv:210213252. 25 févr 2021; Available at http://arxiv.org/abs/2102.13252
Saulnier T, Philipps V, Meissner WG, Rascol O, Pavy-Le-Traon A, Foubert-Samier A, et al. Joint models for the longitudinal analysis of measurement scales in the presence of informative dropout. arXiv:211002612. 6 oct 2021; Available at http://arxiv.org/abs/2110.02612
Proust-Lima C, Philipps V, Perrot B, Blanchin M, Sébille V. Modeling repeated self-reported outcome data: a continuous-time longitudinal Item Response Theory model. arXiv:210913064. 28 déc 2021; Abailable at http://arxiv.org/abs/2109.13064
Munsch G, Goumidi L, van Hylckama Vlieg A, Ibrahim-Kosta M, Bruzelius M, Deleuze JF, Rosendaal FR, Jacqmin-Gadda H, Morange PE, Trégouët DA. Modelling of time-to-events in an ambispective study: illustration with the analysis of ABO blood groups on venous throm-bosis recurrence. Available at https://medrxiv.org/cgi/content/short/2021.11.20.21266583v1
Details
Centre de recherche INSERM U1219
Université de Bordeaux – ISPED
146 rue Léo-Saignat
33076 BORDEAUX cedex
Tél : +33 (0)5 57 57 13 93
Tél : +33 (0)5 57 57 95 68
Fax : +33 (0)5 56 24 00 81
Informations
News
- 12 Feb 2020
Biostatistics Conferences 2020
These events have been organised by Bordeaux Population Health – UMR 1219 and the Public Health Department of…
- 11 Feb 2020
Inserm Workshop 261 – Recent advances in statistical analysis of survival data – May and Sept 2020
Registration deadline: March 6, 2020 Organizers: Hélène JACQMIN-GADDA (Inserm U1219, Bordeaux), Aurélien LATOUCHE (Inserm U900/Cnam, Paris), Virginie RONDEAU…
Members
- Ahmadou Alioum
- Antoine Barbieri
- Ariane Bercu
- Jérémy Chéradame
- Leonie Courcoul
- Sandrine Darmigny
- Hugues de Courson
- Anthony Devaux
- Bénédicte Driollet
- Helene Jacqmin-Gadda
- Pierre Joly
- Johann KUHN
- Kateline Le Bourdonnec
- Quentin Le Coënt
- Lisa Le Gall
- Karen Leffondre
- Gaelle Munsch
- Bessekon Serge NIANGORAN
- Viviane Philipps
- Cécile Proust-Lima
- Manel Rakez
- Virginie Rondeau
- Anaïs Rouanet
- Tiphaine SAULNIER
