GeneFinder
by Wei-Min Chen, Kung-Yee Liang, Yen-Feng Chiu
Copyright (C) Johns Hopkins University
Bloomberg School of Public Health Department of Biostatistics
Most of conventional linkage analysis based on multiple testing (including GeneHunter, SAGE, MERLIN etc.) focus on hypothesis testing, i.e., they are good at answering question that within a certain genomic region whether or not susceptibility genes exist. A 95% confidence interval for the gene location is usually approximated by a 1.5-LOD interval. This is NOT a genuine asymptotic 95% confidence interval. Disadvantages of conventional linkage analysis as an estimation procedure are discussed in associated papers.
GeneFinder uses Generalized Estimating Equations (GEE) to estimate the location of a susceptibility gene based on the IBD (identical by descent) sharing of multiple markers of affected sib pairs. GeneFinder can further the analysis of a standard linkage software such as GeneHunter by providing a more reasonable gene location estimation and the corresponding confidence interval. Once a gene is confirmed, GeneFinder is highly recommended for the purpose of estimating its position.
For further questions and comments, you are welcome to contact Wei-Min Chen at wechen@umich.edu.
GeneFinder 1.1.9 (June 9, 2004)
Download GeneFinder for UNIX/Solaris
Download GeneFinder for Windows & DOS
Download Software Manual and Example files: ex1.loc ex1.ped ( ex1.in ex1.gf )
A simple example to run GeneFinder (NEW function):
1. Make sure you can run MERLIN in the working directory. Otherwise replace line "ibd" by "ibd merlin.ibd" if IBD file exists.
2. Type following lines in GeneFinder:
mar ex1.loc
ped ex1.ped
ibd
gee
gee 20
plot ex1.ps
กก
Acknowledgements:
The current GeneFinder software is written in C++, basing on a previous Fortran program and several script programs written by Dr. Yen-Feng Chiu. This work is supported by National Institutes of Health grant GM49909. Many thanks to Dr. Karl Broman for his helpful comments and to Ms. Virginia K. Lasseter, Dr. Fang-Chi Hsu and Mingyao Li for bug reporting.
1. Liang KY, Zeger SL (1986) Longitudinal data analysis using generalized linear models. Biometrika 73: 13-22 [324KB, in PDF format]
2. Liang KY, Chiu YF, Beaty TH (2001) A robust identity by descent procedure using affected sib pairs: a multipoint approach for complex diseases. Hum Hered 51: 64-78 [346KB, in PDF format]
3. Liang KY, Chiu YF, Beaty TH, Wjst M (2001) A multipoint analysis using affected sib pairs: incorporation of linkage evidence from unlinked regions. Genetic Epidemiology 21: 105-122 [160KB, in PDF format]
4. Liang KY, Huang CY, Beaty TH (2000) A unified sampling approach for multipoint analysis of qualitative and quantitative traits in sib pairs. Am J Hum Genet 66: 1631-1641 [233KB, in PDF format]
5. Glidden DV, Liang KY, Chiu YF, Pulver AE (2003) Multipoint affected sibpair linkage methods for localizing susceptibility genes of complex diseases. Genet Epidemiol 24:107-117 [185KB, in PDF format]
Genetic
Analysis Software | Program TDT Power Calculator | Return
to My Home Page
You are visitor