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Biometry Research Group

Statistical Software

Predicting Treatment Effect from Surrogate Endpoints and Historical Trials: An Extrapolation Involving Probabilities of a Binary Outcome or Survival to a Specific Time


Stuart G. Baker* (wrote software)
Daniel J. Sargent
Marc Buyse
Tomasz Burzykowski

The program requires Mathematica 8.01.0 Exit Disclaimer

The key function is Surr[data] where

data={data1x,data2x,data3x,...}
datax={x,infovec}
x = matrix of counts:
rows are trials
columns are cells (000,001,010,011,100,101,110,111)
infovec={control,name0,name1,surrtime,truetime,units,datatype}

control is a list that relates control assigment (based on surrogate) in data to original control assigment in raw data files, 1 if agree, 0 if not,
name0 a list of names for arm 0 (control)
name1 a list of names for arm 1 (experimental)
surrtime is time surrogate observed
truetime is time true observed
units is units of time
datatype is indicator for surrogate, either binary or survival*)

To reproduce results in article, type Surr[data1] and SurrSim[data1,MaxSim->1000]

Downloads

Download All (ZIP, 27KB)

These files were updated 05/24/2011

File name / sizeDescription
surrogate.m (M File, 18KB) basic packages calls the others
surrogatecore.m (M File, 5KB) combination of fitting algorithms
surrogatemix.m (M File, 3KB) fit mixture model
surrogatelin.m (M File, 14KB) fit linear model (basic and transformed)
surrogatepsm.m (M File, 6KB) fit principal stratification model
surrogatedata.m (M File, 9KB) estimated counts from survival data
surrogatesim.m (M File, 4KB) simulation to compute coverage with function
surrogatesimmix.m (M File, 5KB) generate simulation based on mixture model
surrogatesimlin.m (M File, 5KB) generate simulation based on linear model with extra
surrogatesimpsm.m (M File, 5KB) generate simulation based on principal stratification model
surrogatesimsup.m (M File, 13KB) support functions for simulation


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 noninfringement. 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

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Last updated: May 24, 2011