| Title: | Analytical and computational solution for the estimation of SNP-heritability in biobank-scale and distributed datasets |
| Journal: | PLOS Computational Biology |
| Published: | 21 Oct 2025 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/41118419/ |
| DOI: | https://doi.org/10.1371/journal.pcbi.1013568 |
Publication 16688
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Abstract
For a complex trait, heritability ([Formula: see text]) gives the genetic determination of its variation. Given the emergence of biobank-scale data, a more powerful method is needed to estimate [Formula: see text]. Based on the framework of Haseman-Elston regression (RHE-reg), we integrate a fast randomization algorithm to estimate [Formula: see text], and RHE-reg can tackle biobank-scale data, such as UK Biobank (UKB), very efficiently. Furthermore, we present an analytical solution that balances computational cost and precision of the estimation, a property that is important in dealing with biobank-scale data. We investigated the performance of the RHE-reg in simulated data and also applied it for 81 UKB quantitative traits; as tested in UKB data of nearly 300,000 unrelated individuals, it took on average about 4.5 hours to complete an estimation when used 10 CPUs. We extended the application of RHE-reg into distributed datasets when privacy is not compromised. As shown in UKB and simulated data the performance of RHE-reg was accurate in estimating [Formula: see text]. The software for estimating SNP-heritability for biobank-scale data is released.</p>
8 Keywords
- Algorithms
- Biological Specimen Banks
- Computational Biology
- Computer Simulation
- Humans
- Models, Genetic
- Polymorphism, Single Nucleotide
- Quantitative Trait, Heritable
9 Authors
- Guo-An Qi
- Qi-Xin Zhang
- Jingyu Kang
- Tianyuan Li
- Xiyun Xu
- Zhe Zhang
- Zhe Fan
- Siyang Liu
- Guo-Bo Chen
1 Application
| Application ID | Title |
|---|---|
| 41376 | Statistical genetics methods for complex traits using large-scale genomic data |
Enabling scientific discoveries that improve human health