Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: environmental covariates, gene-gene and gene-environment interaction.

Statistical Applications in Genetics and Molecular Biology
Mike SchmidtSilke Schmidt

Abstract

We have previously distributed a software package, SIMLA (SIMulation of Linkage and Association), which can be used to generate disease phenotype and marker genotype data in three-generational pedigrees of user-specified structure. To our knowledge, SIMLA is the only publicly available program that can simulate variable levels of both linkage (recombination) and linkage disequilibrium (LD) between marker and disease loci in general pedigrees. While the previous SIMLA version provided flexibility in choosing many parameters relevant for linkage and association mapping of complex human diseases, it did not allow for the segregation of more than one disease locus in a given pedigree and did not incorporate environmental covariates possibly interacting with disease susceptibility genes. Here, we present an extension of the simulation algorithm characterized by a much more general penetrance function, which allows for the joint action of up to two genes and up to two environmental covariates in the simulated pedigrees, with all possible multiplicative interaction effects between them. This makes the program even more useful for comparing the performance of different linkage and association analysis methods applied to complex human p...Continue Reading

Citations

Jan 7, 2010·BMC Bioinformatics·Roberto AmatoSergio Cocozza
May 10, 2008·BMC Proceedings·Xuejun QinElizabeth R Hauser
Mar 27, 2007·PLoS Genetics·Bo PengMarek Kimmel
Aug 6, 2010·PloS One·Francesco Lescai, Claudio Franceschi
Dec 17, 2014·Genetic Epidemiology·Bo PengEric J Feuer
May 14, 2008·Genetic Epidemiology·Ren-Hua ChungElizabeth R Hauser
Apr 6, 2007·Genetic Epidemiology·Silke SchmidtElizabeth R Hauser
Mar 12, 2008·Genetic Epidemiology·Alexandre BureauChantal Mérette
Dec 25, 2010·Autism Research : Official Journal of the International Society for Autism Research·D SalyakinaM A Pericak-Vance
Jun 23, 2010·Genetic Epidemiology·Xuejun QinSilke Schmidt
Apr 28, 2006·American Journal of Human Genetics·Silke SchmidtMargaret A Pericak-Vance
Dec 13, 2006·American Journal of Human Genetics·Ren-Hua ChungEden R Martin
May 24, 2011·Omics : a Journal of Integrative Biology·Cheng-Hong YangHsueh-Wei Chang
Jun 21, 2013·BMC Bioinformatics·Ren-Hua Chung, Chung-Chin Shih
Apr 3, 2008·Human Heredity·E R Martin, M A Schmidt

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