Skip to main content
Top
Published in: BMC Medical Informatics and Decision Making 1/2018

Open Access 01-12-2018 | Technical advance

Development and evaluating multimarker models for guiding treatment decisions

Authors: Parvin Tajik, Mohammad Hadi Zafarmand, Aeilko H. Zwinderman, Ben W. Mol, Patrick M. Bossuyt

Published in: BMC Medical Informatics and Decision Making | Issue 1/2018

Login to get access

Abstract

Background

Despite the growing interest in developing markers for predicting treatment response and optimizing treatment decisions, an appropriate methodology to identify, combine and evaluate such markers has been slow to develop. We propose a step-by-step strategy for analysing data from existing randomised trials with the aim of identifying a multi-marker model for guiding decisions about treatment.

Methods

We start with formulating the treatment selection problem, continue with defining the treatment threshold, prepare a list of candidate markers, develop the model, apply the model to estimate individual treatment effects, and evaluate model performance in the study group of patients who meet the trial eligibility criteria. In this process, we rely on some well-known techniques for multivariable prediction modelling, but focus on predicting benefit from treatment, rather than outcome itself. We present our approach using data from a randomised trial in which 808 women with multiple pregnancy were assigned to cervical pessary or control, to prevent adverse perinatal outcomes. Overall, cervical pessary did not reduce the risk of adverse perinatal outcomes.

Results

The treatment threshold was zero. We had a preselected list of 5 potential markers and developed a logistic model including the markers, treatment and all marker-by-treatment interaction terms. The model was well calibrated and identified 35% (95% confidence interval (CI) 32 to 39%) of the trial participants as benefitting from pessary insertion. We estimated that the risk of adverse outcome could be reduced from 13.5 to 8.1% (5.4% risk reduction; 95% CI 2.1 to 8.6%) through model-based selective pessary insertion. The next step is external validation upon existence of independent trial data.

Conclusions

We suggest revisiting existing trials data to explore whether differences in treatment benefit can be explained by differences in baseline characteristics of patients. This could lead to treatment selection tools which, after validation in comparable existing trials, can be introduced into clinical practice for guiding treatment decisions in future patients.
Literature
1.
go back to reference Spear BB, Heath-Chiozzi M, Huff J. Clinical application of pharmacogenetics. Trends Mol Med. 2001;7(5):201–4.CrossRefPubMed Spear BB, Heath-Chiozzi M, Huff J. Clinical application of pharmacogenetics. Trends Mol Med. 2001;7(5):201–4.CrossRefPubMed
2.
go back to reference Sun X, Briel M, Busse JW, You JJ, Akl EA, Mejza F, Bala MM, Bassler D, Mertz D, Diaz-Granados N, et al. Credibility of claims of subgroup effects in randomised controlled trials: systematic review. BMJ. 2012;344:e1553.CrossRefPubMed Sun X, Briel M, Busse JW, You JJ, Akl EA, Mejza F, Bala MM, Bassler D, Mertz D, Diaz-Granados N, et al. Credibility of claims of subgroup effects in randomised controlled trials: systematic review. BMJ. 2012;344:e1553.CrossRefPubMed
3.
go back to reference Kent DM, Rothwell PM, Ioannidis JP, Altman DG, Hayward RA. Assessing and reporting heterogeneity in treatment effects in clinical trials: a proposal. Trials. 2010;11:85.CrossRefPubMedPubMedCentral Kent DM, Rothwell PM, Ioannidis JP, Altman DG, Hayward RA. Assessing and reporting heterogeneity in treatment effects in clinical trials: a proposal. Trials. 2010;11:85.CrossRefPubMedPubMedCentral
4.
go back to reference Roberts WE, Morrison JC, Hamer C, Wiser WL. The incidence of preterm labor and specific risk factors. Obstet Gynecol. 1990;76(1 Suppl):85S–9S.PubMed Roberts WE, Morrison JC, Hamer C, Wiser WL. The incidence of preterm labor and specific risk factors. Obstet Gynecol. 1990;76(1 Suppl):85S–9S.PubMed
5.
go back to reference Spellacy WN, Handler A, Ferre CD. A case-control study of 1253 twin pregnancies from a 1982-1987 perinatal data base. Obstet Gynecol. 1990;75(2):168–71.PubMed Spellacy WN, Handler A, Ferre CD. A case-control study of 1253 twin pregnancies from a 1982-1987 perinatal data base. Obstet Gynecol. 1990;75(2):168–71.PubMed
6.
go back to reference Liem S, Schuit E, Hegeman M, Bais J, de Boer K, Bloemenkamp K, Brons J, Duvekot H, Bijvank BN, Franssen M, et al. Cervical pessaries for prevention of preterm birth in women with a multiple pregnancy (ProTWIN): a multicentre, open-label randomised controlled trial. Lancet. 2013;382(9901):1341–9.CrossRefPubMed Liem S, Schuit E, Hegeman M, Bais J, de Boer K, Bloemenkamp K, Brons J, Duvekot H, Bijvank BN, Franssen M, et al. Cervical pessaries for prevention of preterm birth in women with a multiple pregnancy (ProTWIN): a multicentre, open-label randomised controlled trial. Lancet. 2013;382(9901):1341–9.CrossRefPubMed
7.
go back to reference Tajik P, Monfrance M, van 't Hooft J, Liem SM, Schuit E, Bloemenkamp KW, Duvekot JJ, Nij Bijvank B, Franssen MT, Oudijk MA, et al. A multivariable model to guide the decision for pessary placement to prevent preterm birth in women with a multiple pregnancy: a secondary analysis of the ProTWIN trial. Ultrasound Obstet Gynecol. 2016;48(1):48–55.CrossRefPubMed Tajik P, Monfrance M, van 't Hooft J, Liem SM, Schuit E, Bloemenkamp KW, Duvekot JJ, Nij Bijvank B, Franssen MT, Oudijk MA, et al. A multivariable model to guide the decision for pessary placement to prevent preterm birth in women with a multiple pregnancy: a secondary analysis of the ProTWIN trial. Ultrasound Obstet Gynecol. 2016;48(1):48–55.CrossRefPubMed
8.
go back to reference Janes H, Brown MD, Huang Y, Pepe MS. An approach to evaluating and comparing biomarkers for patient treatment selection. Int J Biostat. 2014;10(1):99–121.CrossRefPubMedPubMedCentral Janes H, Brown MD, Huang Y, Pepe MS. An approach to evaluating and comparing biomarkers for patient treatment selection. Int J Biostat. 2014;10(1):99–121.CrossRefPubMedPubMedCentral
9.
go back to reference Steyerberg EW. Clinical prediction models: a practical approach to development, validation, and updating. New York: Springer; 2009.CrossRef Steyerberg EW. Clinical prediction models: a practical approach to development, validation, and updating. New York: Springer; 2009.CrossRef
10.
go back to reference Harrell FE. Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis. New York: Springer; 2001.CrossRef Harrell FE. Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis. New York: Springer; 2001.CrossRef
11.
go back to reference Zhao Y, Zeng D, Rush AJ, Kosorok MR. Estimating individualized treatment rules using outcome weighted learning. J Am Stat Assoc. 2012;107(449):1106–18.CrossRefPubMedPubMedCentral Zhao Y, Zeng D, Rush AJ, Kosorok MR. Estimating individualized treatment rules using outcome weighted learning. J Am Stat Assoc. 2012;107(449):1106–18.CrossRefPubMedPubMedCentral
15.
go back to reference Gunter L, Zhu J, Murphy S. Variable selection for qualitative interactions in personalized medicine while controlling the family-wise error rate. J Biopharm Stat. 2011;21(6):1063–78.CrossRefPubMedPubMedCentral Gunter L, Zhu J, Murphy S. Variable selection for qualitative interactions in personalized medicine while controlling the family-wise error rate. J Biopharm Stat. 2011;21(6):1063–78.CrossRefPubMedPubMedCentral
16.
go back to reference Gunter L, Zhu J. Efficient computation and model selection for the support vector regression. Neural Comput. 2007;19(6):1633–55.CrossRefPubMed Gunter L, Zhu J. Efficient computation and model selection for the support vector regression. Neural Comput. 2007;19(6):1633–55.CrossRefPubMed
17.
go back to reference Foster JC, Taylor JM, Ruberg SJ. Subgroup identification from randomized clinical trial data. Stat Med. 2011;30(24):2867–80.CrossRefPubMed Foster JC, Taylor JM, Ruberg SJ. Subgroup identification from randomized clinical trial data. Stat Med. 2011;30(24):2867–80.CrossRefPubMed
18.
go back to reference Foster JC, Taylor JM, Kaciroti N, Nan B. Simple subgroup approximations to optimal treatment regimes from randomized clinical trial data. Biostatistics. 2015;16(2):368–82.CrossRefPubMed Foster JC, Taylor JM, Kaciroti N, Nan B. Simple subgroup approximations to optimal treatment regimes from randomized clinical trial data. Biostatistics. 2015;16(2):368–82.CrossRefPubMed
19.
go back to reference Cai T, Tian L, Wong PH, Wei LJ. Analysis of randomized comparative clinical trial data for personalized treatment selections. Biostatistics. 2011;12(2):270–82.CrossRefPubMed Cai T, Tian L, Wong PH, Wei LJ. Analysis of randomized comparative clinical trial data for personalized treatment selections. Biostatistics. 2011;12(2):270–82.CrossRefPubMed
20.
go back to reference Brinkley J, Tsiatis A, Anstrom KJ. A generalized estimator of the attributable benefit of an optimal treatment regime. Biometrics. 2010;66(2):512–22.CrossRefPubMed Brinkley J, Tsiatis A, Anstrom KJ. A generalized estimator of the attributable benefit of an optimal treatment regime. Biometrics. 2010;66(2):512–22.CrossRefPubMed
21.
go back to reference Dusseldorp E, Van Mechelen I. Qualitative interaction trees: a tool to identify qualitative treatment-subgroup interactions. Stat Med. 2014;33(2):219–37.CrossRefPubMed Dusseldorp E, Van Mechelen I. Qualitative interaction trees: a tool to identify qualitative treatment-subgroup interactions. Stat Med. 2014;33(2):219–37.CrossRefPubMed
22.
go back to reference Pepe MS, Cai T, Longton G. Combining predictors for classification using the area under the receiver operating characteristic curve. Biometrics. 2006;62(1):221–9.CrossRefPubMed Pepe MS, Cai T, Longton G. Combining predictors for classification using the area under the receiver operating characteristic curve. Biometrics. 2006;62(1):221–9.CrossRefPubMed
23.
go back to reference Steyerberg EW, Vergouwe Y. Towards better clinical prediction models: seven steps for development and an ABCD for validation. Eur Heart J. 2014;35(29):1925–31.CrossRefPubMedPubMedCentral Steyerberg EW, Vergouwe Y. Towards better clinical prediction models: seven steps for development and an ABCD for validation. Eur Heart J. 2014;35(29):1925–31.CrossRefPubMedPubMedCentral
24.
go back to reference Steyerberg EW, Moons KG, van der Windt DA, Hayden JA, Perel P, Schroter S, Riley RD, Hemingway H, Altman DG, Group P. Prognosis research strategy (PROGRESS) 3: prognostic model research. PLoS Med. 2013;10(2):e1001381.CrossRefPubMedPubMedCentral Steyerberg EW, Moons KG, van der Windt DA, Hayden JA, Perel P, Schroter S, Riley RD, Hemingway H, Altman DG, Group P. Prognosis research strategy (PROGRESS) 3: prognostic model research. PLoS Med. 2013;10(2):e1001381.CrossRefPubMedPubMedCentral
25.
go back to reference Moons KG, Royston P, Vergouwe Y, Grobbee DE, Altman DG. Prognosis and prognostic research: what, why, and how? BMJ. 2009;338:b375.CrossRefPubMed Moons KG, Royston P, Vergouwe Y, Grobbee DE, Altman DG. Prognosis and prognostic research: what, why, and how? BMJ. 2009;338:b375.CrossRefPubMed
26.
go back to reference Moons KG, Kengne AP, Woodward M, Royston P, Vergouwe Y, Altman DG, Grobbee DE. Risk prediction models: I. Development, internal validation, and assessing the incremental value of a new (bio)marker. Heart. 2012;98(9):683–90.CrossRefPubMed Moons KG, Kengne AP, Woodward M, Royston P, Vergouwe Y, Altman DG, Grobbee DE. Risk prediction models: I. Development, internal validation, and assessing the incremental value of a new (bio)marker. Heart. 2012;98(9):683–90.CrossRefPubMed
27.
go back to reference Moons KG, Kengne AP, Grobbee DE, Royston P, Vergouwe Y, Altman DG, Woodward M. Risk prediction models: II. External validation, model updating, and impact assessment. Heart. 2012;98(9):691–8.CrossRefPubMed Moons KG, Kengne AP, Grobbee DE, Royston P, Vergouwe Y, Altman DG, Woodward M. Risk prediction models: II. External validation, model updating, and impact assessment. Heart. 2012;98(9):691–8.CrossRefPubMed
28.
go back to reference Royston P, Moons KG, Altman DG, Vergouwe Y. Prognosis and prognostic research: developing a prognostic model. BMJ. 2009;338:b604.CrossRefPubMed Royston P, Moons KG, Altman DG, Vergouwe Y. Prognosis and prognostic research: developing a prognostic model. BMJ. 2009;338:b604.CrossRefPubMed
29.
go back to reference Tibshirani R. Regresssion and shrinkage via the Lasso. J R Stat Soc Ser B. 1996;58:267–88. Tibshirani R. Regresssion and shrinkage via the Lasso. J R Stat Soc Ser B. 1996;58:267–88.
31.
go back to reference van der Leeuw J, Ridker PM, van der Graaf Y, Visseren FL. Personalized cardiovascular disease prevention by applying individualized prediction of treatment effects. Eur Heart J. 2014;35(13):837–43.CrossRefPubMed van der Leeuw J, Ridker PM, van der Graaf Y, Visseren FL. Personalized cardiovascular disease prevention by applying individualized prediction of treatment effects. Eur Heart J. 2014;35(13):837–43.CrossRefPubMed
32.
33.
go back to reference Song X, Pepe MS. Evaluating markers for selecting a patient’s treatment. Biometrics. 2004;60(4):874–83.CrossRefPubMed Song X, Pepe MS. Evaluating markers for selecting a patient’s treatment. Biometrics. 2004;60(4):874–83.CrossRefPubMed
35.
go back to reference Rouse DJ, Caritis SN, Peaceman AM, Sciscione A, Thom EA, Spong CY, Varner M, Malone F, Iams JD, Mercer BM, et al. A trial of 17 alpha-hydroxyprogesterone caproate to prevent prematurity in twins. N Engl J Med. 2007;357(5):454–61.CrossRefPubMed Rouse DJ, Caritis SN, Peaceman AM, Sciscione A, Thom EA, Spong CY, Varner M, Malone F, Iams JD, Mercer BM, et al. A trial of 17 alpha-hydroxyprogesterone caproate to prevent prematurity in twins. N Engl J Med. 2007;357(5):454–61.CrossRefPubMed
36.
go back to reference Roman AS, Rebarber A, Pereira L, Sfakianaki AK, Mulholland J, Berghella V. The efficacy of sonographically indicated cerclage in multiple gestations. J Ultrasound Med. 2005;24(6):763–8. quiz 770-761CrossRefPubMed Roman AS, Rebarber A, Pereira L, Sfakianaki AK, Mulholland J, Berghella V. The efficacy of sonographically indicated cerclage in multiple gestations. J Ultrasound Med. 2005;24(6):763–8. quiz 770-761CrossRefPubMed
37.
go back to reference Norman JE, Mackenzie F, Owen P, Mactier H, Hanretty K, Cooper S, Calder A, Mires G, Danielian P, Sturgiss S, et al. Progesterone for the prevention of preterm birth in twin pregnancy (STOPPIT): a randomised, double-blind, placebo-controlled study and meta-analysis. Lancet. 2009;373(9680):2034–40.CrossRefPubMed Norman JE, Mackenzie F, Owen P, Mactier H, Hanretty K, Cooper S, Calder A, Mires G, Danielian P, Sturgiss S, et al. Progesterone for the prevention of preterm birth in twin pregnancy (STOPPIT): a randomised, double-blind, placebo-controlled study and meta-analysis. Lancet. 2009;373(9680):2034–40.CrossRefPubMed
38.
go back to reference Lim AC, Schuit E, Bloemenkamp K, Bernardus RE, Duvekot JJ, Erwich JJ, van Eyck J, Groenwold RH, Hasaart TH, Hummel P, et al. 17alpha-hydroxyprogesterone caproate for the prevention of adverse neonatal outcome in multiple pregnancies: a randomized controlled trial. Obstet Gynecol. 2011;118(3):513–20.CrossRefPubMed Lim AC, Schuit E, Bloemenkamp K, Bernardus RE, Duvekot JJ, Erwich JJ, van Eyck J, Groenwold RH, Hasaart TH, Hummel P, et al. 17alpha-hydroxyprogesterone caproate for the prevention of adverse neonatal outcome in multiple pregnancies: a randomized controlled trial. Obstet Gynecol. 2011;118(3):513–20.CrossRefPubMed
39.
go back to reference Crowther CA. Hospitalisation and bed rest for multiple pregnancy. Cochrane Database Syst Rev. 2000;2:CD000110. Crowther CA. Hospitalisation and bed rest for multiple pregnancy. Cochrane Database Syst Rev. 2000;2:CD000110.
40.
go back to reference Schaaf JM, Hof MH, Mol BW, Abu-Hanna A, Ravelli AC. Recurrence risk of preterm birth in subsequent twin pregnancy after preterm singleton delivery. BJOG. 2012;119(13):1624–9.CrossRefPubMed Schaaf JM, Hof MH, Mol BW, Abu-Hanna A, Ravelli AC. Recurrence risk of preterm birth in subsequent twin pregnancy after preterm singleton delivery. BJOG. 2012;119(13):1624–9.CrossRefPubMed
41.
go back to reference Esplin MS, O'Brien E, Fraser A, Kerber RA, Clark E, Simonsen SE, Holmgren C, Mineau GP, Varner MW. Estimating recurrence of spontaneous preterm delivery. Obstet Gynecol. 2008;112(3):516–23.CrossRefPubMed Esplin MS, O'Brien E, Fraser A, Kerber RA, Clark E, Simonsen SE, Holmgren C, Mineau GP, Varner MW. Estimating recurrence of spontaneous preterm delivery. Obstet Gynecol. 2008;112(3):516–23.CrossRefPubMed
42.
go back to reference Sperling L, Kiil C, Larsen LU, Qvist I, Schwartz M, Jorgensen C, Skajaa K, Bang J, Tabor A. Naturally conceived twins with monochorionic placentation have the highest risk of fetal loss. Ultrasound Obstet Gynecol. 2006;28(5):644–52.CrossRefPubMed Sperling L, Kiil C, Larsen LU, Qvist I, Schwartz M, Jorgensen C, Skajaa K, Bang J, Tabor A. Naturally conceived twins with monochorionic placentation have the highest risk of fetal loss. Ultrasound Obstet Gynecol. 2006;28(5):644–52.CrossRefPubMed
43.
go back to reference American College of O, Gynecologists committee on practice B-O, Society for Maternal-Fetal M, committee AJE. ACOG practice bulletin #56: multiple gestation: complicated twin, triplet, and high-order multifetal pregnancy. Obstet Gynecol. 2004;104(4):869–83.CrossRef American College of O, Gynecologists committee on practice B-O, Society for Maternal-Fetal M, committee AJE. ACOG practice bulletin #56: multiple gestation: complicated twin, triplet, and high-order multifetal pregnancy. Obstet Gynecol. 2004;104(4):869–83.CrossRef
44.
go back to reference Claggett B, Zhao L, Tian L, Castagno D, Wei LJ. Estimating subject-specific treatment differences for risk-benefit assessment with operating risk event-time data. In: Harvard University Working Paper Series, vol. 125; 2011. Claggett B, Zhao L, Tian L, Castagno D, Wei LJ. Estimating subject-specific treatment differences for risk-benefit assessment with operating risk event-time data. In: Harvard University Working Paper Series, vol. 125; 2011.
46.
go back to reference Dorresteijn JA, Visseren FL, Ridker PM, Wassink AM, Paynter NP, Steyerberg EW, van der Graaf Y, Cook NR. Estimating treatment effects for individual patients based on the results of randomised clinical trials. BMJ. 2011;343:d5888.CrossRefPubMedPubMedCentral Dorresteijn JA, Visseren FL, Ridker PM, Wassink AM, Paynter NP, Steyerberg EW, van der Graaf Y, Cook NR. Estimating treatment effects for individual patients based on the results of randomised clinical trials. BMJ. 2011;343:d5888.CrossRefPubMedPubMedCentral
47.
go back to reference Vickers AJ, Kattan MW, Daniel S. Method for evaluating prediction models that apply the results of randomized trials to individual patients. Trials. 2007;8:14.CrossRefPubMedPubMedCentral Vickers AJ, Kattan MW, Daniel S. Method for evaluating prediction models that apply the results of randomized trials to individual patients. Trials. 2007;8:14.CrossRefPubMedPubMedCentral
48.
go back to reference Vickers AJ, Van Calster B, Steyerberg EW. Net benefit approaches to the evaluation of prediction models, molecular markers, and diagnostic tests. BMJ. 2016;352:i6.CrossRefPubMedPubMedCentral Vickers AJ, Van Calster B, Steyerberg EW. Net benefit approaches to the evaluation of prediction models, molecular markers, and diagnostic tests. BMJ. 2016;352:i6.CrossRefPubMedPubMedCentral
49.
go back to reference Vickers AJ. Incorporating clinical considerations into statistical analyses of markers: a quiet revolution in how we think about data. Clin Chem. 2016;62(5):671–2.CrossRefPubMed Vickers AJ. Incorporating clinical considerations into statistical analyses of markers: a quiet revolution in how we think about data. Clin Chem. 2016;62(5):671–2.CrossRefPubMed
50.
go back to reference Kovalchik SA, Varadhan R, Weiss CO. Assessing heterogeneity of treatment effect in a clinical trial with the proportional interactions model. Stat Med. 2013;32(28):4906–23.CrossRefPubMed Kovalchik SA, Varadhan R, Weiss CO. Assessing heterogeneity of treatment effect in a clinical trial with the proportional interactions model. Stat Med. 2013;32(28):4906–23.CrossRefPubMed
Metadata
Title
Development and evaluating multimarker models for guiding treatment decisions
Authors
Parvin Tajik
Mohammad Hadi Zafarmand
Aeilko H. Zwinderman
Ben W. Mol
Patrick M. Bossuyt
Publication date
01-12-2018
Publisher
BioMed Central
Published in
BMC Medical Informatics and Decision Making / Issue 1/2018
Electronic ISSN: 1472-6947
DOI
https://doi.org/10.1186/s12911-018-0619-5

Other articles of this Issue 1/2018

BMC Medical Informatics and Decision Making 1/2018 Go to the issue