Statistical Analysis Plan for Stage 1 EMBARC (Establishing Moderators and Biosignatures of Antidepressant Response for Clinical Care) Study

Eva Petkova, R Todd Ogden, Thaddeus Tarpey, Adam Ciarleglio, Bei Jiang, Zhe Su, Thomas Carmody, Philip Adams, Helena C Kraemer, Bruce D Grannemann, Maria A Oquendo, Ramin Parsey, Myrna Weissman, Patrick J McGrath, Maurizio Fava, Madhukar H Trivedi, Eva Petkova, R Todd Ogden, Thaddeus Tarpey, Adam Ciarleglio, Bei Jiang, Zhe Su, Thomas Carmody, Philip Adams, Helena C Kraemer, Bruce D Grannemann, Maria A Oquendo, Ramin Parsey, Myrna Weissman, Patrick J McGrath, Maurizio Fava, Madhukar H Trivedi

Abstract

Antidepressant medications are commonly used to treat depression, but only about 30% of patients reach remission with any single first-step antidepressant. If the first-step treatment fails, response and remission rates at subsequent steps are even more limited. The literature on biomarkers for treatment response is largely based on secondary analyses of studies designed to answer primary questions of efficacy, rather than on a planned systematic evaluation of biomarkers for treatment decision. The lack of evidence-based knowledge to guide treatment decisions for patients with depression has lead to the recognition that specially designed studies with the primary objective being to discover biosignatures for optimizing treatment decisions are necessary. Establishing Moderators and Biosignatures of Antidepressant Response in Clinical Care (EMBARC) is one such discovery study. Stage 1 of EMBARC is a randomized placebo controlled clinical trial of 8 week duration. A wide array of patient characteristics is collected at baseline, including assessments of brain structure, function and connectivity along with electrophysiological, biological, behavioral and clinical features. This paper reports on the data analytic strategy for discovering biosignatures for treatment response based on Stage 1 of EMBARC.

Keywords: combining biomarkers; differential treatment response index; moderator; optimizing treatment decisions; precision medicine.

References

    1. Abayomi K., Gelman A., Levy M. Diagnostics for multiple imputations. Appl. Stat. 2008;57:273–291.
    1. Anderson K., Odell P., Wilson P., Kannel W. Cardiovascular disease risk profiles. Am. Heart J. 1991;121:293–298.
    1. Breiman L., Friedman J.H., Alshen R.A., Stone C.J. Wadsworth; Belmont, CA: 1983. CART: Classification and Regression Trees.
    1. Cattaneo A., Gennerelli M., Uher R., Breen G., Farmer A., Aitchison K., Craig I., Anacker C., Zunsztain P., McGuffin P., Pariante C. Candidate genes expression profile associated with antidepressants response in the GENDEP study: differentiating between baseline ‘predictors’ and longitudinal ‘targets’. Neuropsychopharmacology. 2013;38:377–385.
    1. Chakraborty B., Laber E., Zhao Y. Inference for optimal treatment regimes using adaptive m-Out-of-n bootstrap scheme. Biometrics. 2013;69:714–723.
    1. Chen W., Ghosh D., Raghunatan T., Norkin M., Sargent D., Bepler G. On Bayesian methods of exploring qualitative interactions for targeted treatment. Stat. Med. 2012;31:3693–3707.
    1. Ciarleglio A., Petkova E., Tarpey T., Ogden R.T. Treatment decisions based on scalar and functional baseline covariates. Biometrics. 2015;71:884–894.
    1. Ciarleglio A., Petkova E., Tarpey T., Ogden R.T. Flexible functional regression methods for estimating individualized treatment regimes. STAT. 2016;5:185–199.
    1. Ciarleglio A., Petkova E., Tarpey T., Ogden R.T. Variable selection for treatment decision rules with scalar and functional predictors. Stat. Med. (In revision) 2017
    1. Cloitre M., Petkova E., Su Z., Weiss B. Patient characteristics as a moderator of PTSD treatment outcome: combining symptom burden and strengths. Br. J. Psychiat. Open. 2016;2:101–106.
    1. Cortes C., Vapnik V. Support-vector networks. Mach. Learn. 1995;20:273–297.
    1. Fan J., Lv J. Sure independence screening for ultra-high dimensional feature space. J. of the R. Stat. Soc. Ser. B. 2008;70:849–911.
    1. Fava M., Rush A.J., Trivedi M., Nierenberg A.A., Thase M.E., Sackheim H.A., Quitkin F.M., Wisniewski S.R., Lavori P.W., Rosenbaum J.F., Kupfer D.J. Background and rationale for the sequenced treatment alternatives to relieve depression (STAR*D) study. Psychiat. Clinics of N. Am. 2003;26:457–494.
    1. Gunter L., Zhu J., Murphy S. Variable selection for qualitative interactions in pres- onalized medicine while controlling the family-wise error rate. J. Biopharm. Stat. 2011;21:1063–1078.
    1. Hennings J., Uhr M., Klengel T., Webber P., Pütz B., Czamara D., Ising M., Holsboer F., Lucae S. RNA expression profiling in depressed patients suggests retinoid-related orphan receptor alpha as a biomarker for antidepressant response. Translat. Psychiat. 2015;5:e538.
    1. Korgaonkar M., Williams L., Song Y., Usherwood T., Grieve S. Diffusion ten- sor imaging predictors of treatment outcomes in major depressive disorder. Br. J. Psychiat. 2014;205:321–328.
    1. Kraemer H.C. Discovering, comparing, and combining moderators of treatment on outcome after randomized clinical trials: a parametric approach. Stat. Med. 2013;32:1964–1973.
    1. Krishnan V., Nestler E. The molecular neurobiology of depression. Nature. 2008;455:894–902.
    1. Laber E., Lizotte D., Qian M., Pelham W., Murphy S. Dynamic treatment regimes: technical challenges and applications. Electronic J. Stat. 2014;8:1225–1272.
    1. Laber E., Zhao Y.-Q. Tree-based methods for individualized treatment regimes. Biometrika. 2015;102:501–514.
    1. Leuchter A., Cook I., Marangell L., Gilmer W., Burgoyne K., Howland R., Trivedi M., Zisook S., Jain R., McCracken T., Fava M., Iosifescu D., Greenwald S. Comparative effectiveness of biomarkers and clinical indicators for predicting outcomes of SSRI treatment in major depressive disorder: results of the BRITE-MD study. Psychiat. Res. 2009;169:124–131.
    1. Li J., Chan I. Detecting qualitative interactions in clinical trials: an extension of range test. J. Biopharm. Stat. 2006;16:831–841.
    1. Liu Y., Wang Y., Kosorok M., Zhao Y.-Q., Zeng D. Robust hybrid learning for estimating personalized dynamic treatment regimens. J. Am. Stat. Assoc. (Under Review) 2016
    1. Lu W., Zhang H., Zeng D. Variable selection for optimal treatment decision. Stat. Meth. Med. Res. 2011;22:493–504.
    1. McGrath C., Kelley M., Dunlop B., Holtzheimer P., Craighead W., Mayberg H. Pretreatment brain states identifying likely nonresponse to standard treatments for depression. Biol. Psychiat. 2014;76:527–535.
    1. Mundt J., Vogel A., Feltner D., Lenderking W. Vocal acoustic biomarkers of depres- sion severity and treatment response. Biol. Psychiat. 2012;72:580–587.
    1. Murphy S. Optimal dynamic treatment regimes (with discussion) J. R. Stat. Soc. Ser. B. 2003;58:331–366.
    1. Petkova E., Tarpey T. Partitioning of functional data for understanding heterogeneity in psychiatric conditions. Stat. Interface. 2009;2:413–424.
    1. Petkova E., Tarpey T., Ciarleglio A., Ogden R.T. Deriving a scalar measure from a longitudinal trajectory with applications to placebo response. Stat. Med. 2016 (Submitted for publication)
    1. Petkova E., Tarpey T., Ogden R., Su Z. Generated effect modifiers (GEMs) in randomized clinical trials. Biostatistics. 2017;18(1):105–118.
    1. Qian M., Murphy S. Performance guarantees for individualized treatment rules. Ann. Stat. 2011;39:1180–1210.
    1. Ramsay J.O., Silverman B.W. second ed. Springer; New York: 2005. Functional Data Analysis.
    1. Robins J. Optimal structured nested models for optimal sequential decisions. In: Lin D., Heagerty P.J., editors. Proceedings of the Second Seattle Symposium on Biostatistics. Springer; New York: 2004. pp. 189–326.
    1. Rubin D. Estimating causal effects of treatments in randomized and nonrandomized studies. J. Edu. Psychol. 1974;66:688–701.
    1. Rush A.J., Trivedi M.H., Wisniewski S.R., Nierenberg A.A., Stewart J.W., Warden D., Niederehe G., Thase M.E., Lavory P.W., Lebowitz B.D., McGrath P.J., Rosenbaum J.F., Sackeim H.A., Kupfer D.J., Luther J., Fava M. Acute and longer-term outcomes in depressed outpatients requiring one or several treatment steps: a STAR*D report. Am. J. Psychiat. 2006;163:1905–1917.
    1. Schafer J.L. Chapmen and Hall; New York: 1997. Analysis of Incomplete Multivariate Data.
    1. Schafer J.L. Multiple imputation: a primer. Stat. Meth. Med. Res. 1999;8:3–15.
    1. Song R., Kosorok M., Zeng D., Zhao Y., Laber E.B., Yuan M. On sparse representation for optimal individualized treatment selection with penalized outcome weighted learning. STAT. 2015;4:59–68.
    1. Song X., Pepe M. Evaluating markers for selecting a patient's treatment. Biometrics. 2004;60:874–883.
    1. Su Y.-S., Gelman A., Hill J., Yajima M. Multiple imputation with diagnostics (mi) in R: opening windows into the black box. J. Stat. Softw. 2011;45(1):1–31.
    1. Tarpey T., Petkova E., Lu Y., Govindarajulu U. Optimal partitioning for linear mixed effects models: applications to identifying placebo responders. J. American Statistical Association. 2010;105:968–977.
    1. Tarpey T., Petkova E., Ogden R.T. Profiling placebo responders by self-consistent partitioning of functional data. J. Am. Stat. Assoc. 2003;98:850–858.
    1. Tarpey T., Petkova E., Zhu L. A new approach to stratified psychiatry via convexity-based clustering with applications towards moderator analysis. Stat Interface. 2016;9:255–266.
    1. Tian L., Alizadeh A., Gentles A., Tibshirani R. A simple method for estimating interactions between a treatment and a large number of covariates. J. Am. Stat. Assoc. 2014;109:1517–1532.
    1. Tibshirani R. Regression shrinkage and selection via the LASSO. J. R. Stat. Soc. Ser. B. 1996;58:267–288.
    1. Trivedi M.H., McGrath P., Fava M., Parsey R.V., Kurian B., Phillips M.L., Oquendo M.A., Bruder G., Pizzagalli D., Toups M., Cooper C., Adams P., Weyandt S., Morris D., Grannemann B., Ogden R.T., Buckner R., McInnis M., Kraemer H.C., Petkova E., Carmody T., Weissman M. Establishing Moderators and Biosignatures of Antidepressant Response in Clinical care (EMBARC): rationale and design. J. Psychiat. Res. 2016;78:11–23.
    1. Trivedi M.H., Rush A.J., Wisniewski S.R., Nierenberg A.A., Warden D., Ritz L., Norquist G., Howland R.H., Lebowitz B., McGrath P.J., Shores-Wilson K., Biggs M.M., Balasub- ramani G.K., Fava M. Evaluation of outcomes with citalopram for depression using measurement-based care in STAR*D: implications for clinical practice. Am. J. Psychiat. 2006;163:28–40.
    1. Uher R., Tansey K., Dew T., Maier W., Mors O., Hauser J., Dernovsek M., Heingsburg N., Souery D., A.F, McGuffin P. An inflammatory biomarker as a differential predictor of outcome of depression treatment with escitalopram and nortriptyline. Am. J. Psychiat. 2014;171:1278–1286.
    1. Wang R., Ware J. Detecting moderator effects using subgroup analyses. Prev. Sci. 2013;14:111–120.
    1. Wellek S. Testing for absence of qualitative interactions between risk factors and treatment effect. Biometric. J. 1997;39:809–821.
    1. Wolkowitz O.M., Mellon S.H., Epel E.S., Lin J., Reus V.I., Dhabhar F.S., Blackburn E.H. Resting leukocyte telomerase activity is elevated in major depression and predicts treatment response. Mol. Psychiat. 2012;17:164–172.
    1. Zhang B., Tsiatis A.A., Davidian M., Zhang M., Laber E. Estimating optimal treatment regimes from classification perspective. STAT. 2012;1:103–114.
    1. Zhao Y., Zeng D., Rush A.J., Kosorok M.P. Estimating individualized treatment rules using outcome weighted learning. J. Am. Stat. Assoc. 2012;107:1106–1118.

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