Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE
- PMID: 17060360
- DOI: 10.1093/bioinformatics/btl539
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE
Abstract
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
Similar articles
-
Using sex-averaged genetic maps in multipoint linkage analysis when identity-by-descent status is incompletely known.Genet Epidemiol. 2006 Jul;30(5):384-96. doi: 10.1002/gepi.20151. Genet Epidemiol. 2006. PMID: 16685713
-
Inferential testing for linkage with GENEHUNTER-MODSCORE: the impact of the pedigree structure on the null distribution of multipoint MOD scores.Genet Epidemiol. 2008 Jan;32(1):73-83. doi: 10.1002/gepi.20264. Genet Epidemiol. 2008. PMID: 17849490
-
Linkage analysis of alcohol dependence using MOD scores.BMC Genet. 2005 Dec 30;6 Suppl 1(Suppl 1):S162. doi: 10.1186/1471-2156-6-S1-S162. BMC Genet. 2005. PMID: 16451624 Free PMC article.
-
GENEHUNTER: your 'one-stop shop' for statistical genetic analysis?Hum Hered. 2002;53(1):2-7. doi: 10.1159/000048598. Hum Hered. 2002. PMID: 11901265 Review.
-
A survey of current software for linkage analysis.Hum Genomics. 2003 Nov;1(1):63-5. doi: 10.1186/1479-7364-1-1-63. Hum Genomics. 2003. PMID: 15601534 Free PMC article. Review.
Cited by
-
A genome-wide search for linkage to allergic rhinitis in Danish sib-pair families.Eur J Hum Genet. 2012 Sep;20(9):965-72. doi: 10.1038/ejhg.2012.46. Epub 2012 Mar 14. Eur J Hum Genet. 2012. PMID: 22419170 Free PMC article.
-
RAB23 mutations in Carpenter syndrome imply an unexpected role for hedgehog signaling in cranial-suture development and obesity.Am J Hum Genet. 2007 Jun;80(6):1162-70. doi: 10.1086/518047. Epub 2007 Apr 18. Am J Hum Genet. 2007. PMID: 17503333 Free PMC article.
-
MLEP: an R package for exploring the maximum likelihood estimates of penetrance parameters.BMC Res Notes. 2012 Aug 28;5:465. doi: 10.1186/1756-0500-5-465. BMC Res Notes. 2012. PMID: 22929166 Free PMC article.
-
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.PLoS Genet. 2019 Dec 20;15(12):e1007979. doi: 10.1371/journal.pgen.1007979. eCollection 2019 Dec. PLoS Genet. 2019. PMID: 31860654 Free PMC article.
-
Motor sequencing deficit as an endophenotype of speech sound disorder: a genome-wide linkage analysis in a multigenerational family.Psychiatr Genet. 2012 Oct;22(5):226-34. doi: 10.1097/YPG.0b013e328353ae92. Psychiatr Genet. 2012. PMID: 22517379 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources