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Performance of Genotype Imputation for Low Frequency and Rare Variants from the 1000 Genomes

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  • Hou-Feng Zheng
  • Jing-Jing Rong
  • Ming Liu
  • Fang Han
  • Xing-Wei Zhang
  • J Brent Richards
  • Li Wang

Abstract

Genotype imputation is now routinely applied in genome-wide association studies (GWAS) and meta-analyses. However, most of the imputations have been run using HapMap samples as reference, imputation of low frequency and rare variants (minor allele frequency (MAF) 0.4) and higher mean info score in each MAF bin. Similarly, 1M chip array outperformed 610K and 317K. However for very rare variants (MAF≤0.3%), only 0–1% of the variants were well imputed. We conclude that the imputation of low frequency and rare variants improves with larger reference panels and higher density of genome-wide genotyping arrays. Yet, despite a large reference panel size and dense genotyping density, very rare variants remain difficult to impute.

Suggested Citation

  • Hou-Feng Zheng & Jing-Jing Rong & Ming Liu & Fang Han & Xing-Wei Zhang & J Brent Richards & Li Wang, 2015. "Performance of Genotype Imputation for Low Frequency and Rare Variants from the 1000 Genomes," PLOS ONE, Public Library of Science, vol. 10(1), pages 1-10, January.
    • Handle: RePEc:plo:pone00:0116487
    DOI: 10.1371/journal.pone.0116487
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    References listed on IDEAS

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    1. Martin Ladouceur & Zari Dastani & Yurii S Aulchenko & Celia M T Greenwood & J Brent Richards, 2012. "The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals," PLOS Genetics, Public Library of Science, vol. 8(2), pages 1-11, February.
    2. Brendan Maher, 2008. "Personal genomes: The case of the missing heritability," Nature, Nature, vol. 456(7218), pages 18-21, November.
    3. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
    4. Yu-Fang Pei & Jian Li & Lei Zhang & Christopher J Papasian & Hong-Wen Deng, 2008. "Analyses and Comparison of Accuracy of Different Genotype Imputation Methods," PLOS ONE, Public Library of Science, vol. 3(10), pages 1-7, October.
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    1. Paul S de Vries & Maria Sabater-Lleal & Daniel I Chasman & Stella Trompet & Tarunveer S Ahluwalia & Alexander Teumer & Marcus E Kleber & Ming-Huei Chen & Jie Jin Wang & John R Attia & Riccardo E Mario, 2017. "Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-22, January.

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