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Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty

View ORCID ProfileDavid Gerard
doi: https://doi.org/10.1101/2021.02.08.430270
David Gerard
Department of Mathematics and Statistics, American University, Washington, DC, 20016, USA
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  • For correspondence: gerard.1787@gmail.com
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Abstract

Linkage disequilibrium (LD) estimates are often calculated genome-wide for use in many tasks, such as SNP pruning and LD decay estimation. However, in the presence of genotype uncertainty, naive approaches to calculating LD have extreme attenuation biases, incorrectly suggesting that SNPs are less dependent than in reality. These biases are particularly strong in polyploid organisms, which often exhibit greater levels of genotype uncertainty than diploids. A principled approach using maximum likelihood estimation with genotype likelihoods can reduce this bias, but is prohibitively slow for genome-wide applications. Here, we present scalable moment-based adjustments to LD estimates based on the marginal posterior distributions of the genotypes. We demonstrate, on both simulated and real data, that these moment-based estimators are as accurate as maximum likelihood estimators, and are almost as fast as naive approaches based only on posterior mean genotypes. This opens up bias-corrected LD estimation to genome-wide applications. Additionally, we provide standard errors for these moment-based estimators. All methods are implemented in the ldsep package on the Comprehensive R Archive Network https://cran.r-project.org/package=ldsep.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://cran.r-project.org/package=ldsep

  • https://doi.org/10.5281/zenodo.4543473

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 22, 2021.
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Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty
David Gerard
bioRxiv 2021.02.08.430270; doi: https://doi.org/10.1101/2021.02.08.430270
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Scalable Bias-corrected Linkage Disequilibrium Estimation Under Genotype Uncertainty
David Gerard
bioRxiv 2021.02.08.430270; doi: https://doi.org/10.1101/2021.02.08.430270

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