ArticleNature communications2023
Accurate and efficient estimation of local heritability using summary statistics and the linkage disequilibrium matrix.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Improved heritability partitioning and enrichment analyses using summary statistics with graphREML.Nature genetics · 2026Article
- Unravelling the genetic architecture of cerebral small vessel disease in the context of stroke.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2026Review
- When can whole-genome SNP heritability be reliably estimated from summary statistics?bioRxiv : the preprint server for biology · 2026Article
- Decoding Complex Traits in Goats Through Genome-Wide Association Studies: Progress, Challenges, and Perspectives.International journal of molecular sciences · 2026Review
- Estimating the heritability of longitudinal rate-of-change: genetic insights into PSA velocity in prostate cancer-free individuals.Biostatistics (Oxford, England) · 2026Article
- Logica: A likelihood framework for cross-ancestry local genetic correlation estimation using summary statistics.American journal of human genetics · 2025Article
- Genetic risk predictions using deep learning models with summary data.Frontiers in bioinformatics · 2025Article
- Local genetic correlation via knockoffs reduces confounding due to cross-trait assortative mating.American journal of human genetics · 2024Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- A polygenic risk score model for psoriasis based on the protein interactions of psoriasis susceptibility loci.Frontiers in genetics · 2024Article
- Genome-wide association analysis of fleece traits in Northwest Xizang white cashmere goat.Frontiers in veterinary science · 2024Article
- Accurate and efficient estimation of local heritability using summary statistics and the linkage disequilibrium matrix.Nature communications · 2023Article
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Abstract
Existing SNP-heritability estimators that leverage summary statistics from genome-wide association studies (GWAS) are much less efficient (i.e., have larger standard errors) than the restricted maximum likelihood (REML) estimators which require access to individual-level data. We introduce a new method for local heritability estimation-Heritability Estimation with high Efficiency using LD and association Summary Statistics (HEELS)-that significantly improves the statistical efficiency of summary-statistics-based heritability estimator and attains comparable statistical efficiency as REML (with a relative statistical efficiency >92%). Moreover, we propose representing the empirical LD matrix as the sum of a low-rank matrix and a banded matrix. We show that this way of modeling the LD can not only reduce the storage and memory cost, but also improve the computational efficiency of heritability estimation. We demonstrate the statistical efficiency of HEELS and the advantages of our proposed LD approximation strategies both in simulations and through empirical analyses of the UK Biobank data.
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