Predicting Treatment Effect from Surrogate Endpoints and Historical Trials

By Stuart G. Baker, 2017

Introduction

This software fits a zero-intercept random effects linear model to data on surrogate and true endpoints in previous trials.

Requirement:  Mathematica Version 11 or later.

To run the program

copy all files into some folder called "FOLDER"
start a new Mathematica session
type SetDirectory["FOLDER"]
type << sfit.m
type SFit[data,options]


Key Function: SFit[data, options] where

Option Default Explanation
SizeNewTrial Automatic (median size of previous trials) Size of new trial with only surrogate endpoint
ShowCalc False Show intermediate calculations


dataset={xvec,yvec,nvec,wvec,name},

xvec lists of differences in surrogate endpoints over all trials
yvec lists of differences in true endpoints over all trials
nvec list of sample sizes over all trials
wvec lists of estimated variances of true endpoint over all trials
name name of data set

File Contents

Download All (ZIP, 25 KB)

Media Folder: 

File name Description
sfit.m main packages
sfitplot.m core plotting program
sfitsimplot.m plotting hypothetical data
sfitsim.m simulations
sfitlik.m fitting model with simple estimates and MLE’s
sfitdata.m generates data examples from the literature

As an example, type SFit[dataMANU]

Disclaimer

This code is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and non-infringement. In no event shall the NCI or the individual developers be liable for any claim, damages or other liability of any kind. Use of this code by recipient is at recipient's own risk. NCI makes no representations that the use of the code will not infringe any patent or proprietary rights of third parties.

The data were obtained from the following studies:

Sargent, DJ, Wieand, S, Haller, DG, Gray, R, Benedetti, J, Buyse, M, Labianca, R, Seitz, J F, Callaghan, C J O, Francini, G, Grothey, A, O'Connell, M, Catalano, PJ, Blanke, CD, Kerr D, Green, E, Wolmark, N, Andre, T, Goldberg, RM, and De Gramont A (2005) Disease-free survival (DFS) vs overall survival (OS) as a primary endpoint for adjuvant colon cancer studies: Individual patient data from 20,898 patients on 18 randomized trials J Clin Oncol 23, 8664-8670

Meta-Analysis Group in Cancer (2004) Modulation of fluorouracil by leucovorin in patients with advanced colorectal cancer: an updated meta-analysis J Clin Oncol 22, 3766-3775

Buyse, M, Burzykowski, T, Carroll, K, Michiels, S, Sargent, D, Miller, LL, Elfring, GL, Pignon, JP, and Piedbois, P (2007) Progression-free survival is a surrogate for survival in advanced colorectal cancer J Clin Oncol 25, 5218-5224

Last updated: May 03, 2017