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      Simulated Data for Genomic Selection and Genome-Wide Association Studies Using a Combination of Coalescent and Gene Drop Methods

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          Abstract

          An approach is described for simulating data sequence, genotype, and phenotype data to study genomic selection and genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used to simulate genomic data and phenotypes with flexibility in terms of the historical population structure, recent pedigree structure, distribution of quantitative trait loci effects, and with sequence and single nucleotide polymorphism-phased alleles and genotypes. Ten replicates of a representative scenario used to study genomic selection in livestock were generated and have been made publically available. The simulated data sets were structured to encompass a spectrum of additive quantitative trait loci effect distributions, relationship structures, and single nucleotide polymorphism chip densities.

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          Author and article information

          Journal
          G3 (Bethesda)
          Genetics
          ggg
          ggg
          ggg
          G3: Genes|Genomes|Genetics
          Genetics Society of America
          2160-1836
          1 April 2012
          April 2012
          : 2
          : 4
          : 425-427
          Affiliations
          [* ]School of Environmental and Rural Science, University of New England, Armidale, 2351 New South Wales, Australia
          []Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1230 Domžale, Slovenia
          Author notes

          Supporting information is available online at http://www.g3journal.org/lookup/suppl/doi:10.1534/g3.111.001297/-/DC1

          [1 ]Corresponding author: School of Environmental and Rural Science, University of New England, Armidale, 2351 New South Wales, Australia E-mail: john.hickey@ 123456une.edu.au
          Article
          GGG_001297
          10.1534/g3.111.001297
          3337470
          22540033
          6ab6ce3b-ee4e-486a-a34a-17b087326788
          Copyright © 2012 Hickey, Gorjanc

          This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License ( http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

          History
          : 30 September 2011
          : 09 November 2011
          Categories
          Investigations
          Custom metadata
          v1

          Genetics
          simulation method,genpred,pedigrees,shared data resources,quantitative trait loci (qtl),genome-wide association studies (gwas)

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