Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE.
BACKGROUND
Sex-specific marker maps have become increasingly available. We have implemented the usage of sex-specific recombination frequencies in the GENEHUNTER-MODSCORE program that performs multipoint linkage analysis. Furthermore, we have devised a consistent method to choose the combinations of male and female genetic positions at which linkage scores should be calculated. Marker coordinates can be read automatically from publicly available genetic maps.


RESULTS
In a MOD-score analysis of the COGA dataset provided for Genetic Analysis Workshop 14, the highest linkage peak on chromosome 1 further increases when using sex-specific maps, while some smaller peaks are decreased. Simulations confirm that the MOD score can be biased when a sex-averaged instead of the correct sex-specific map is employed. This shows that an adequate modeling of the female:male ratio of genetic distances is important, especially for complex traits.


BACKGROUND
The new version of GENEHUNTER-MODSCORE can be downloaded from the following website: http://www.staff.uni-marburg.de/~strauchk/software.html
Dietter
Johannes
J
Institute of Medical Biometry and Epidemiology, Philipps University Marburg, 35032 Marburg, Germany. dietter@med.uni-marburg.de
Mattheisen
Manuel
M
Fürst
Robert
R
Rüschendorf
Franz
F
Wienker
Thomas F
TF
Strauch
Konstantin
K
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D005260:Female; D005787:Gene Frequency; D006801:Humans; D008126:Lod Score; D008297:Male; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic / Q000235:genetics*; D012737:Sex Factors; D012984:Software