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bioRxiv · 10.1101/2024.09.20.614017

Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets

Qi, G.-A.·Zhang, Q.-X.·Kang, J.·Li, T.·Xu, X.·Zhang, Z.·Fan, Z.·Liu, S.·Chen, G.-B.
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Abstract

Estimation of heritability has been a routine in statistical genetics, in particular with the increasing sample size such as biobank-scale data and distributed datasets, the latter of which has increasing concerns of privacy. Recently a randomized Haseman-Elston regression (RHE-reg) has been proposed to estimate SNP-heritability, and given sufficient iteration (B) RHE-reg can tackle biobank-scale data, such as UK Biobank (UKB), very efficiently. In this study, we present an analytical solution that balances iteration B and RHE-reg estimation, which resolves the convergence of the proposed RHE-reg in high precision. We applied the method for 81 UKB quantitative traits and estimated their SNP-heritability and test statistics precisely. Furthermore, we extended RHE-reg into distributed datasets and demonstrated their utility in real data application and simulated data. The software for estimating SNP-heritability for biobank-scale data is released: https://github.com/gc5k/gear2.

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Qi, G.-A., Zhang, Q.-X., Kang, J., Li, T., Xu, X., Zhang, Z., Fan, Z., Liu, S., Chen, G.-B.. 2024-09-24. Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets. https://doi.org/10.1101/2024.09.20.614017

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