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Bioinformatics Advance Access originally published online on October 23, 2006
Bioinformatics 2007 23(1):64-70; doi:10.1093/bioinformatics/btl539
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE

Johannes Dietter 1,*, Manuel Mattheisen 2, Robert Fürst 2, Franz Rüschendorf 3, Thomas F. Wienker 2 and Konstantin Strauch 1

1 Institute of Medical Biometry and Epidemiology, Philipps University Marburg 35032 Marburg, Germany
2 Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn 53105 Bonn, Germany
3 Gene Mapping Center, Max-Delbrück-Center for Molecular Medicine 13092 Berlin, Germany

*To whom correspondence should be addressed.

Motivation: 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.

Availability: The new version of GENEHUNTER-MODSCORE can be downloaded from the following website: http://www.staff.uni-marburg.de/~strauchk/software.html

Contact: dietter{at}med.uni-marburg.de

Received on May 12, 2006; revised on October 13, 2006; accepted on October 16, 2006

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