Efficient variance components analysis across millions of genomes
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Abstract
While variance components analysis has emerged as a powerful tool in complex trait genetics, existing methods for fitting variance components do not scale well to large-scale datasets of genetic variation. Here, we present a method for variance components analysis that is accurate and efficient: capable of estimating one hundred variance components on a million individuals genotyped at a million SNPs in a few hours. We illustrate the utility of our method in estimating and partitioning variation in a trait explained by genotyped SNPs (SNP-heritability). Analyzing 22 traits with genotypes from 300,000 individuals across about 8 million common and low frequency SNPs, we observe that per-allele squared effect size increases with decreasing minor allele frequency (MAF) and linkage disequilibrium (LD) consistent with the action of negative selection. Partitioning heritability across 28 functional annotations, we observe enrichment of heritability in FANTOM5 enhancers in asthma, eczema, thyroid and autoimmune disorders.
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RHE-mc can partition genetic variance across large sample sizes.
“We use RHE-mc, a method that can partition genetic variance across large sample sizes, to estimate NIM heritability (Pazokitoroudi et al., 2020).”
From The lingering effects of Neanderthal introgression on human complex traits (2023) · cites this paper as Pazokitoroudi et al., 2020
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Jeong, M., Pazokitoroudi, A., Liu, Z., & Sankararaman, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.09.584258
Self-citationJeong, M., Pazokitoroudi, A., Liu, Z., & Sankararaman, S. (2024) · Lecture notes in computer science · doi:10.1007/978-1-0716-3989-4_56
Self-citationPowerful one-dimensional scan to detect heterotic QTLPreprint
Li, G., Schmidt, R., Zhao, Y., Reif, J. C., & Jiang, Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.06.652159
Kinship estimation bias carries over to heritability estimation bias using variance components
Hou, Z., & Ochoa, A. (2025) · Genetics · doi:10.1093/genetics/iyaf238
Highly efficient genotype compression leveraging genealogical relatednessPreprint
Shen, A. Z., Wang, X., Mancuso, N., & O’Connor, L. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.29.721594
Gerussi, A., Caime, C., Wang, H., Cordell, H. J., Mells, G. F., Sandford, R. N., Jones, D. E., Hirschfield, G. M., Siminovitch, K. A., Gershwin, M. E., et al. (2026) · Liver International · doi:10.1111/liv.70868
Self-citation
- Authors
- Pazokitoroudi, A., Wu, Y., Burch, K. S., Hou, K., Zhou, A., Pasaniuc, B., & Sankararaman, S.
- Affiliations
- University of California, Los Angeles (US)
- Corresponding author
- Sankararaman, Sriram
- Venue
- Nature Communications
- Published
- 2020-08-11
- Volume
- 11
- Issue
- 1
- Pages
- 4020-4020
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC7419517
- OpenAlex
- W3048701096
- Cited by
- 55
- References
- 38
- Citations by year
- 2026: 5 · 2025: 15 · 2024: 9 · 2023: 8 · 2022: 6 · 2021: 8 · 2020: 3 · 2019: 1
- FWCI
- 3.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R35GM125055)
- NSF | Directorate for Computer & Information Science & Engineering | Division of Information and Intelligent Systems (III-1705121)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- variance component analysis, SNP heritability, complex trait genetics, minor allele frequency, linkage disequilibrium, negative selection, asthma, atopic dermatitis, autoimmune disease, thyroid dysfunction
- MeSH terms
- Alleles, Gene Frequency, Genotype, Humans, Models, Genetic, Phenotype, Genetic Variation, Linkage Disequilibrium, Genome, Human, Quantitative Trait, Heritable, Multifactorial Inheritance, Polymorphism, Single Nucleotide
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