Sequence-Level Population Simulations Over Large Genomic Regions

Simulation is an invaluable tool for investigating the effects of various population genetics modeling assumptions on resulting patterns of genetic diversity, and for assessing the performance of statistical techniques, for example those designed to detect and measure the genomic effects of selectio...

Full description

Saved in:
Bibliographic Details
Published in:Genetics (Austin) 2007-11, Vol.177 (3), p.1725-1731
Main Authors: Hoggart, Clive J, Chadeau-Hyam, Marc, Clark, Taane G, Lampariello, Riccardo, Whittaker, John C, De Iorio, Maria, Balding, David J
Format: Article
Language:English
Subjects:
Alleles
Computer Simulation
Evolution, Molecular
Genetics, Population
Genomics
Genomics - statistics & numerical data
Investigations
Models, Genetic
Polymorphism, Single Nucleotide
Population genetics
Recombination, Genetic
Selection, Genetic
Software
Studies
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Simulation is an invaluable tool for investigating the effects of various population genetics modeling assumptions on resulting patterns of genetic diversity, and for assessing the performance of statistical techniques, for example those designed to detect and measure the genomic effects of selection. It is also used to investigate the effectiveness of various design options for genetic association studies. Backward-in-time simulation methods are computationally efficient and have become widely used since their introduction in the 1980s. The forward-in-time approach has substantial advantages in terms of accuracy and modeling flexibility, but at greater computational cost. We have developed flexible and efficient simulation software and a rescaling technique to aid computational efficiency that together allow the simulation of sequence-level data over large genomic regions in entire diploid populations under various scenarios for demography, mutation, selection, and recombination, the latter including hotspots and gene conversion. Our forward evolution of genomic regions (FREGENE) software is freely available from www.ebi.ac.uk/projects/BARGEN together with an ancillary program to generate phenotype labels, either binary or quantitative. In this article we discuss limitations of coalescent-based simulation, introduce the rescaling technique that makes large-scale forward-in-time simulation feasible, and demonstrate the utility of various features of FREGENE, many not previously available.
ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1534/genetics.106.069088