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SPREG : Regression Analysis of Secondary Phenotype Data in Case-Control Association Studies

SPREG is a computer program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods, as described in Lin DY, Zeng D. 2009, Proper analysis of secondary phenotype data in case-control association studies, Genetic Epidemiology, 33:256-265.


The software is written in C and built under 64-bit x86-based Linux. The current release performs linear regression analysis of quantitative traits and logistic regression of binary traits under the additive mode of inheritance with or without environmental factors.


spreg   infile   outfile   rate   nenv

All four program parameters are required and must be entered in the same order as specified above.



Parameter Description
infile Name of the input file
outfile Name of the output file
rate Disease rate
nenv Number of environmental variables; 0 or a positive integer



The program requires one input file. The input file contains text data in a matrix format. Suppose there are n study subjects, k genes, and d environmental variables. The input file is a (k + d + 2) by n matrix, with columns representing study subjects, and rows conforming to this format:

  1. Row 1 contains the primary phenotype of the study subjects. This should be the case-control status (1=case; 0=control). Missing values are represented by NA.
  2. Row 2 contains the secondary phenotype values of the study subjects. Their values must be numerical, and can be either binary or continuous. Binary values must be coded as 0 and 1; otherwise they will be treated as continuous. Missing values are represented by NA.
  3. If one or more environmental variables are to be included in the analysis, they must be row 3 through row (d + 2), with each row representing one environmental variable, where d is the total number of environmental variables. Values of environmental variables must be numerical. Missing values are represented by NA.
  4. All subsequent rows are genotypes of genes. Suppose there are k genes while the number of environmental variables is d, noting that d can be 0. Row (d + 3) corresponds to gene 1; row (d + 4) corresponds gene 2; … ; and row (d + k + 2) corresponds to gene k. Values of genotypes must be numerical. Genotype values other than 0, 1, and 2 are accepted. Missing values are represented by NA.

If the disease is rare, enter any number less than 0.01 for the disease rate.


Computational results are written to the output file specified by the user. For each gene, the output shows the maximum likelihood estimate of the genetic effect (i.e., slope parameter in the linear model or log odds ratio in the logistic model), its standard error, the standard-normal test statistic and the (two-sided) p-value.


The example files (can be downloaded in the DOWNLOAD section below) includes an input file demo.dat and an output file demo.out. The input file demo.dat contains the case-control status of 3000 individuals, a continuous secondary phenotype, two environmental variables, and genotypes of 10 genes. The disease rate is 0.08.

Enter the command

spreg demo.dat demo.out 0.08 2

to obtain the output file as given in demo.out. Its contents are


Gene_number    Estimate   Std_Error      Z_stat     p_value
1   5.203e-03   8.509e-03   6.114e-01   5.409e-01
2  -1.275e-03   5.514e-03  -2.312e-01   8.172e-01
3  -3.067e-03   5.713e-03  -5.368e-01   5.914e-01
4   8.081e-04   5.651e-03   1.430e-01   8.863e-01
5  -1.198e-04   8.013e-03  -1.495e-02   9.881e-01
6   2.148e-03   6.575e-03   3.267e-01   7.439e-01
7   2.517e-03   7.245e-03   3.474e-01   7.283e-01
8  -2.308e-03   5.975e-03  -3.864e-01   6.992e-01
9  -2.384e-02   6.004e-03  -3.970e+00   7.178e-05
10  -1.665e-02   6.257e-03  -2.661e+00   7.781e-03



SPREG 2.0 for 64-bit x86 based Linux [updated May 18, 2011]

executable (zip archive) »

Example files [updated May 18, 2011]


Lin DY, Zeng D. 2009. Proper analysis of secondary phenotype data in case-control association studies. Genetic Epidemiology, 33:256-265.



Version Date Description
1.0 April 22, 2008 First version released
2.0 May 18, 2011
  • New Features:
    • 1) Allowing environmental factors in the model
    • 2) Allowing genotype values to be other than 0, 1,
      and 2
    • 3) New input file format
    • 4) New command-line parameters
    • 5) New example data