ArticleHuman heredity2010
Simulating sequences of the human genome with rare variants.
Article in Human heredity, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs.BMC bioinformatics · 2019Article
- Power and sample size calculations for high-throughput sequencing-based experiments.Briefings in bioinformatics · 2018Article
- Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.PloS one · 2017Article
- On Sample Size and Power Calculation for Variant Set-Based Association Tests.Annals of human genetics · 2016Article
- Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits.Bioinformatics (Oxford, England) · 2015Article
- Reproducible simulations of realistic samples for next-generation sequencing studies using Variant Simulation Tools.Genetic epidemiology · 2015Article
- Genetic data simulators and their applications: an overview.Genetic epidemiology · 2015Article
- A C++ template library for efficient forward-time population genetic simulation of large populations.Genetics · 2014Article
- Power analysis and sample size estimation for sequence-based association studies.Bioinformatics (Oxford, England) · 2014Article
- SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies.BMC bioinformatics · 2013Article
- Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect.PLoS genetics · 2013Article
- A fast and noise-resilient approach to detect rare-variant associations with deep sequencing data for complex disorders.Genetic epidemiology · 2012Article
- SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits.Bioinformatics (Oxford, England) · 2012Article
- ALF--a simulation framework for genome evolution.Molecular biology and evolution · 2012Article
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2 authors.
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Abstract
objectiveSimulated samples have been widely used in the development of efficient statistical methods identifying genetic variants that predispose to human genetic diseases. Although it is well known that natural selection has a strong influence on the number and diversity of rare genetic variations in human populations, existing simulation methods are limited in their ability to simulate multi-locus selection models with realistic distributions of the random fitness effects of newly arising mutants.
methodsWe developed a computer program to simulate large populations of gene sequences using a forward-time simulation approach. This program is capable of simulating several multi-locus fitness schemes with arbitrary diploid single-locus selection models with random or locus-specific fitness effects. Arbitrary quantitative trait or disease models can be applied to the simulated populations from which individual- or family-based samples can be drawn and analyzed.
resultsUsing realistic demographic and natural selection models estimated from empirical sequence data, datasets simulated using our method differ significantly in the number and diversity of rare variants from datasets simulated using existing methods that ignore natural selection. Our program thus provides a useful tool to simulate datasets with realistic distributions of rare genetic variants for the study of genetic diseases caused by such variants.
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