title: SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure.
abstract: Simulation tools that simulate sequence data in unrelated cases and controls or in families with quantitative traits or disease status are important for genetic studies. The simulation tools can be used to evaluate the statistical power for detecting the causal variants when planning a genetic epidemiology study, or to evaluate the statistical properties for new methods. We previously developed SeqSIMLA version 1 (SeqSIMLA1), which simulates family or case-control data with a disease or quantitative trait model. SeqSIMLA1, and several other tools that simulate quantitative traits, do not specifically model the shared environmental effects among relatives on a trait. However, shared environmental effects are commonly observed for some traits in families, such as body mass index. SeqSIMLA1 simulates a fixed three-generation family structure. However, it would be ideal to simulate prespecified pedigree structures for studies involving large pedigrees. Thus, we extended SeqSIMLA1 to create SeqSIMLA2, which can simulate correlated traits and considers the shared environmental effects. SeqSIMLA2 can also simulate prespecified large pedigree structures. There are no restrictions on the number of individuals that can be simulated in a pedigree. We used a blood pressure example to demonstrate that SeqSIMLA2 can simulate realistic correlation structures between the systolic and diastolic blood pressure among relatives. We also showed that SeqSIMLA2 can simulate large pedigrees with large chromosomal regions in a reasonable time frame.
authors.affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
authors.forename: Ren-Hua
authors.initials: RH
authors.lastname: Chung
authors.forename: Wei-Yun
authors.initials: WY
authors.lastname: Tsai
authors.forename: Chang-Hsun
authors.initials: CH
authors.lastname: Hsieh
authors.forename: Kuan-Yi
authors.initials: KY
authors.lastname: Hung
authors.forename: Chao A
authors.initials: CA
authors.lastname: Hsiung
authors.forename: Elizabeth R
authors.initials: ER
authors.lastname: Hauser
mesh_terms: D005828:Genetics, Population; D006801:Humans; D008957:Models, Genetic; D010375:Pedigree; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA; D012984:Software
keywords: extended pedigree; genetic simulation tools; quantitative trait; sequencing