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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)
          G3 (Bethesda, Md.)
          Genetics Society of America
          2160-1836
          2160-1836
          Apr 2012
          : 2
          : 4
          Article
          GGG_001297
          10.1534/g3.111.001297
          3337470
          22540033
          6ab6ce3b-ee4e-486a-a34a-17b087326788
          History

          GenPred,genome-wide association studies (GWAS),pedigrees,quantitative trait loci (QTL),shared data resources,simulation method

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