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Genotype imputation and reference panel: a systematic evaluation on haplotype size and diversity.

Wei-Yang Bai1,2, Xiao-Wei Zhu1,2, Pei-Kuan Cong1,2

  • 1Diseases & Population (DaP) Geninfo Lab, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China.

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|February 1, 2020
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Optimizing genomic imputation requires careful selection of reference panels. Larger, population-specific panels improve accuracy, but optimal diversity varies for common versus rare variants in Han Chinese and European populations.

Keywords:
Chinese populationHRCgenotype imputationreference panel

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Genomic imputation is crucial for inferring ungenotyped single nucleotide polymorphisms.
  • Reference panel composition significantly impacts imputation accuracy.
  • Understanding population-specific requirements for reference panels is essential.

Purpose of the Study:

  • To investigate the impact of reference panel size and diversity on imputation accuracy for Han Chinese and European populations.
  • To identify optimal reference panel strategies for different variant frequencies.
  • To evaluate existing reference panels and propose custom panel compositions.

Main Methods:

  • Conducted 622 imputations using 394 customized reference panels.
  • Varied reference panel size and population diversity.
  • Assessed imputation accuracy for common, low-frequency, and rare variants.
  • Evaluated performance of Haplotype Reference Consortium (HRC) and 1000 Genomes Project panels.

Main Results:

  • Population-specific panels improve imputation accuracy.
  • For fixed panel size, increased diversity decreased accuracy for common variants but improved it for rare variants.
  • Expanding panels benefited European common variant imputation.
  • Han Chinese imputation accuracy peaked with 8-21% diverse samples.
  • HRC panel performed best for Europeans; custom panel ratios proposed for Han Chinese.

Conclusions:

  • Reference panel composition is critical for accurate genomic imputation.
  • Optimal diversity strategies differ between common and rare variants and populations.
  • A high-quality, large-scale Chinese reference panel is still needed.
  • A tool for investigating reference panel reconstruction in other populations was provided.