Model-Based Linkage Analysis of a Quantitative Trait
- PMID: 28980251
- DOI: 10.1007/978-1-4939-7274-6_14
Model-Based Linkage Analysis of a Quantitative Trait
Abstract
Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.
Keywords: LOD score; Linkage analysis; Model-based; Pedigree likelihood; Quantitative trait; Recombination fraction; Segregation analysis; Statistical analysis for genetic epidemiology (S.A.G.E.).
Similar articles
-
Model-based linkage analysis of a quantitative trait.Methods Mol Biol. 2012;850:263-83. doi: 10.1007/978-1-61779-555-8_14. Methods Mol Biol. 2012. PMID: 22307703
-
Model-Based Linkage Analysis of a Binary Trait.Methods Mol Biol. 2017;1666:311-326. doi: 10.1007/978-1-4939-7274-6_15. Methods Mol Biol. 2017. PMID: 28980252
-
Model-based linkage analysis of a binary trait.Methods Mol Biol. 2012;850:285-300. doi: 10.1007/978-1-61779-555-8_15. Methods Mol Biol. 2012. PMID: 22307704
-
Genetic linkage methods for quantitative traits.Stat Methods Med Res. 2001 Feb;10(1):3-25. doi: 10.1177/096228020101000102. Stat Methods Med Res. 2001. PMID: 11329691 Review.
-
Gene finding strategies.Biol Psychol. 2002 Oct;61(1-2):53-71. doi: 10.1016/s0301-0511(02)00052-2. Biol Psychol. 2002. PMID: 12385669 Review.
Cited by
-
Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Flowering Time in Brassica napus L.Front Plant Sci. 2021 Feb 3;11:626205. doi: 10.3389/fpls.2020.626205. eCollection 2020. Front Plant Sci. 2021. PMID: 33613591 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources