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Population Replacement Strategies for Controlling Vector Populations and the Use of Wolbachia pipientis for Genetic Drive
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Strategies for phasing and imputation in a population isolate.

Anthony Francis Herzig1,2, Teresa Nutile3, Marie-Claude Babron1,2

  • 1Université Paris-Diderot, Sorbonne Paris Cité, U946, Paris, France.

Genetic Epidemiology
|January 11, 2018
PubMed
Summary

This study compared genetic phasing and imputation software for population isolates. SHAPEIT2, SHAPEIT3, and EAGLE2 excelled at phasing, while MINIMAC3, IMPUTE4, and IMPUTE2 showed strong imputation performance.

Keywords:
founder effectgenotyping errorsidentity by descentlinkage disequilibriumstudy specific panel

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Area of Science:

  • Genetics
  • Population Genetics
  • Bioinformatics

Background:

  • Population isolates offer reduced heterogeneity for genetic association studies.
  • Cost-efficient sequencing and imputation are key for large-scale genetic studies in these populations.
  • Accurate genetic phasing and imputation are crucial for gene mapping in isolates.

Purpose of the Study:

  • To compare the performance of various genetic phasing and imputation software.
  • To identify optimal study designs for genetic association studies in population isolates.
  • To evaluate the impact of genotyping errors and missing data on software performance.

Main Methods:

  • Simulated 1,115,604 variants on chromosome 10 for 477 individuals from the Campora isolate.
  • Assessed phasing software: ALPHAPHASE, SLRP, SHAPEIT2, SHAPEIT3, BEAGLE, EAGLE.
  • Evaluated imputation software: IMPUTE2, IMPUTE4, MINIMAC3, BEAGLE, PBWT.
  • Introduced simulated genotyping errors and missing data to assess robustness.

Main Results:

  • SHAPEIT2, SHAPEIT3, and EAGLE2 demonstrated highly accurate phasing performance.
  • MINIMAC3, IMPUTE4, and IMPUTE2 were strong performers for genetic imputation.
  • A population-specific reference panel significantly improved imputation accuracy.

Conclusions:

  • Specific software like SHAPEIT2/3 and EAGLE2 are recommended for accurate phasing in population isolates.
  • MINIMAC3, IMPUTE4, and IMPUTE2 are reliable choices for imputation in such studies.
  • Utilizing population-specific reference panels is vital for maximizing imputation accuracy in isolate studies.