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Accuracy of genotype imputation in Labrador Retrievers.

J Friedrich1, R Antolín1, S M Edwards1

  • 1Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.

Animal Genetics
|July 6, 2018
PubMed
Summary

Genotype imputation in Labrador Retrievers, using high-density (HighD) or low-density (LowD) arrays, accurately predicts genotypes. This method is valuable for reducing costs and increasing sample size in genetic studies.

Keywords:
genome-wide association studiesgenomic predictionimputation accuracylow-density array designpedigree informationreference set

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Area of Science:

  • Veterinary Genetics
  • Animal Genomics

Background:

  • Dogs are valuable models for complex trait genetic analysis.
  • Genotype imputation is crucial for future canine genetic studies, considering breed-specific genetic and pedigree structures.

Purpose of the Study:

  • To evaluate the accuracy of genotype imputation in Labrador Retrievers under various genotyping strategies.
  • To assess the impact of single nucleotide polymorphism (SNP) density and dog relatedness on imputation accuracy.
  • To determine the utility of genotype imputation in genome-wide association analysis and genomic prediction.

Main Methods:

  • Simulated genotyping strategies using data from 1179 Labrador Retrievers.
  • Compared high-density (HighD) and low-density (LowD) arrays with varying SNP masking levels (up to 87.5%).
  • Assessed imputation accuracy through correlations between true and imputed genotypes, with and without pedigree information.

Main Results:

  • Correlations between true and imputed genotypes ranged from 0.92 to 0.97 at 87.5% masking.
  • A likely scenario (10% HighD, 87.5% masked SNPs) yielded a correlation of 0.92.
  • Successful imputation was achieved even without pedigree data and with low dog relatedness.

Conclusions:

  • Genotype imputation is a valuable tool for Labrador Retriever genetic studies, offering cost reduction and increased sample size.
  • Imputation accuracy is high even with reduced SNP density and minimal relatedness.
  • The study supports the application of genotype imputation in genome-wide association studies and genomic prediction in dogs.