使用性别特异性重组率与GENEHUNTER-MODSCORE进行连锁分析。
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE.
作者信息
Dietter Johannes, Mattheisen Manuel, Fürst Robert, Rüschendorf Franz, Wienker Thomas F, Strauch Konstantin
机构信息
Institute of Medical Biometry and Epidemiology, Philipps University Marburg, 35032 Marburg, Germany.
出版信息
Bioinformatics. 2007 Jan 1;23(1):64-70. doi: 10.1093/bioinformatics/btl539. Epub 2006 Oct 23.
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
动机
性别特异性标记图谱越来越容易获得。我们在执行多点连锁分析的GENEHUNTER-MODSCORE程序中实现了性别特异性重组频率的应用。此外，我们设计了一种一致的方法来选择应计算连锁分数的男性和女性遗传位置的组合。标记坐标可以从公开可用的遗传图谱中自动读取。
结果
在为遗传分析研讨会14提供的COGA数据集的MOD分数分析中，使用性别特异性图谱时，1号染色体上的最高连锁峰进一步增加，而一些较小的峰则降低。模拟证实，当使用性别平均而非正确的性别特异性图谱时，MOD分数可能会有偏差。这表明对遗传距离的雌雄比例进行适当建模很重要，尤其是对于复杂性状。
可用性
新版GENEHUNTER-MODSCORE可从以下网站下载：http://www.staff.uni-marburg.de/~strauchk/software.html
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