Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection
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Abstract
Recent work has hinted at the linkage disequilibrium (LD)-dependent architecture of human complex traits, where SNPs with low levels of LD (LLD) have larger per-SNP heritability. Here we analyzed summary statistics from 56 complex traits (average N = 101,401) by extending stratified LD score regression to continuous annotations. We determined that SNPs with low LLD have significantly larger per-SNP heritability and that roughly half of this effect can be explained by functional annotations negatively correlated with LLD, such as DNase I hypersensitivity sites (DHSs). The remaining signal is largely driven by our finding that more recent common variants tend to have lower LLD and to explain more heritability (P = 2.38 × 10-104); the youngest 20% of common SNPs explain 3.9 times more heritability than the oldest 20%, consistent with the action of negative selection. We also inferred jointly significant effects of other LD-related annotations and confirmed via forward simulations that they jointly predict deleterious effects.
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Heritability enrichment (or depletion) in a set of variants provides evidence of functional relevance for the region to the trait and suggests the action of selection.
“Heritability enrichment (or depletion) in a set of variants provides evidence of functional relevance for the region to the trait and suggests the action of selection51 (see the model in Discussion).”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [51]
The Introduction describes heritability enrichment in functional annotations, and the Discussion links specific LD-related heritability patterns to negative selection. The paper does not establish that enrichment or depletion in any set of variants, by itself, suggests selection; its selection inference depends on the particular patterns and supporting simulations. Page numbers are unavailable in our copy. (LLM, conf=0.84)
Experimental — accuracy not yet measuredBackground selection appears to play a primary role in shaping the highly polygenic architecture of human traits and diseases.
“In particular, background selection (i.e., the selective removal of deleterious alleles across the genome) appears to play a primary role in shaping the highly polygenic architecture of human traits and diseases [1, 7–9].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [9]
The Results (Multiple LD-related annotations impact complex trait architectures; page unavailable) report an association between a background-selection statistic and trait heritability. The Discussion (page unavailable) says negative selection affects complex traits on a polygenic, genome-wide scale and suggests it has a greater impact than positive selection. It does not establish that background selection specifically plays the primary role claimed. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe lack of enrichment of Neandertal associations with psychiatric and neurological diagnostic categories by the present study and McArthur et al. is consistent with previous studies that have shown that many complex traits, and in particular diseases, are targets of purifying selection.
“In general, the lack of an enrichment of Neandertal associations with psychiatric and neurological diagnostic categories by our study and McArthur et al. is consistent with previous studies that have shown that many complex traits, and in particular diseases, are targets of purifying selection [45, 46].”
From Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes (2022) · cites this paper as [45]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredGenomic features related to natural selection are enriched for loci associated with complex traits.
“Genomic features related to natural selection are enriched for loci associated with complex traits [1, 7–9].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [9]
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“• B Statistic [53], nucleotide diversity [54] and recombination rate [54] are mathematical quantities derived from evolutionary models, and are computed directly on the genomic position of the variant.”
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“Second, we employed a stratified LDSC 24,25 with 97 baseline linkage disequilibrium (LD) annotations 26 for our EAS GWAS summary statistics and EUR summary statistics by Lee et al. 14 .”
- Authors
- Gazal, S., Finucane, H. K., Furlotte, N. A., Loh, P.-R., Palamara, P. F., Liu, X., Schoech, A., Bulik-Sullivan, B., Neale, B. M., Gusev, A., & Price, A. L.
- Affiliations
- Broad Institute (US)
- 23andMe (United States) (US)
- Corresponding author
- Gazal, Steven
- Price, Alkes L
- ORCID
- Venue
- Nature Genetics
- Published
- 2017-09-11
- Volume
- 49
- Issue
- 10
- Pages
- 1421-1427
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6133304
- OpenAlex
- W2952882474
- Cited by
- 525
- References
- 97
- Citations by year
- 2026: 72 · 2025: 64 · 2024: 80 · 2023: 62 · 2022: 68 · 2021: 58 · 2020: 46 · 2019: 41 · 2018: 26 · 2017: 6
- FWCI
- 21.55
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-07-04)
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (16549, MH107649)
- National Institute of Mental Health (R01MH107649, R01MH101244)
- National Human Genome Research Institute (U01HG009088)
- 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
- linkage disequilibrium, complex traits, negative selection, common genetic variants, DNase I hypersensitive sites, deleterious mutations, genetic architecture, forward modeling
- MeSH terms
- Alleles, Humans, Models, Genetic, Selection, Genetic, Genetic Variation, Linkage Disequilibrium, Chi-Square Distribution, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Genetic Fitness, Molecular Sequence Annotation, Datasets as Topic
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