GeneFinder uses Generalized Estimating Equations (GEE, Liang and Zeger 1986) to estimate the location of a susceptibility gene based on the IBD (identical by descent) sharing of multiple markers of affected sib pairs. GeneFinder naturally continues the analysis of a standard linkage software such as GeneHunter or MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. GeneFinder is highly recommended to follow up a linkage test.

1. Input files
2. Extensions of GeneFinder
3. Download
4. Older versions
5. References

1. INPUT FILES

GeneFinder requires a data file, a pedigree file, and an IBD file. The following command line specifies these three types of input files and performs a GEE analysis:

prompt> gf -d ex.dat -p ex.ped -i ex.ibd --gee

2. EXTENSIONS OF GENEFINDER

GeneFinder has been extended in a number of ways. The following functions have been implemented:

• Localization of disease susceptibility gene using multipoint markers (Liang et al. 2001)

  prompt> gf -d ex.dat -p ex.ped -i ex.ibd --gee
  

• Gene localization incorporating the effect of a covariate (Glidden et al. 2003)

  prompt> gf -d ex.dat -p ex.ped -i ex.ibd --cgee --cov 1 --threshold 18.1

• Gene localization conditional on a gene at another chromosome (Chiu and Liang 2004)

  prompt> gf -d ex.dat -p ex.ped -i ex.ibd -a addition.ibd --cgee --condition 31.4

• Localization of two linked disease genes (Biernacka et al. 2004)

  prompt> gf -d ex.dat -p ex.ped -i ex.ibd --tgee 80

• Gene localization incorporating parent-of-origin effect (Chen et al. unpublished)

  prompt> gf -d ex.dat -p ex.ped -i ex.s15 --pgee

• Gene localization using relative pairs other than sib pairs (Schaid et al. 2005)

  prompt> gf -d ex.dat -p ex.ped -i ex.ibd --gee --relative 16

• Gene localization using pairs such as affected-unaffected pairs in addition to affected pairs (unpublished)

  prompt> gf -d ex.dat -p ex.ped -i ex.ibd --cgee --aff 3

3. DOWNLOAD GENEFINDER 1.2.2

Executables (8/21/2005): Unix/Solaris | Windows | Linux

Examples: ex1.loc |  ex1.ped 

4. DOWNLOAD OLDER VERSIONS

Executables (6/9/2004): Unix | Windows | Linux

Source code: gf119.cpp | public119.cpp

5. REFERENCE

1. Biernacka JM, Sun L, Bull SB (2005) Simultaneous localization of two linked disease susceptibility genes. Genet Epidemiol 28:33-47 [PDF]
2. Chiu YF, Liang KY (2004) Conditional multipoint linkage analysis using affected sib pairs: an alternative approach. Genet Epidemiol 26:108-115 [PDF]
3. 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 [PDF]
4. 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 [PDF]
5. 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 [PDF] 
6. 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 [PDF]
7. Liang KY, Zeger SL (1986) Longitudinal data analysis using generalized linear models. Biometrika 73: 13-22 [PDF]
8. Schaid DJ, Sinnwell JP, Thibodeau SN (2005) Robust multipoint identical-by-descent mapping for affected relative pairs. Am J Hum Genet 76:128-138 [PDF]

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Last updated: Oct 10 2005 by Wei-Min Chen