Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
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Abstract
We introduce an approach to identify disease-relevant tissues and cell types by analyzing gene expression data together with genome-wide association study (GWAS) summary statistics. Our approach uses stratified linkage disequilibrium (LD) score regression to test whether disease heritability is enriched in regions surrounding genes with the highest specific expression in a given tissue. We applied our approach to gene expression data from several sources together with GWAS summary statistics for 48 diseases and traits (average N = 169,331) and found significant tissue-specific enrichments (false discovery rate (FDR) < 5%) for 34 traits. In our analysis of multiple tissues, we detected a broad range of enrichments that recapitulated known biology. In our brain-specific analysis, significant enrichments included an enrichment of inhibitory over excitatory neurons for bipolar disorder, and excitatory over inhibitory neurons for schizophrenia and body mass index. Our results demonstrate that our polygenic approach is a powerful way to leverage gene expression data for interpreting GWAS signals. A new method tests whether disease heritability is enriched near genes with high tissue-specific expression. The authors use gene expression data together with GWAS summary statistics for 48 diseases and traits to identify disease-relevant tissues.
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Partitioned heritability and LDSC-SEG analyses showed similar results for both EAS and EUR populations.
“our partitioned heritability and LDSC-SEG analyses24,25 showed similar results for both populations.”
From Shared genetic architectures of educational attainment in East Asian and European populations (2024) · cites this paper as [25]
Genes with the highest specific expression in brain regions showed the strongest enrichment of risk URVs, most significantly in the human frontal cortex (P = 1.63 x 10 -8 ) and with limited signal in the other tissue types.
“Following earlier reports studying heritability enrichment in GTEx tissues 5,30 , we found that genes with the highest specific expression in brain regions showed the strongest enrichment of risk URVs, most significantly in the human frontal cortex (P = 1.63 x 10 -8 ) and with limited signal in the other tissue types (Figure S19, Table S8, S9).”
From Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia (2020) · cites this paper as [30]
Pathway analyses of common variants have prioritized disease-relevant tissues and cell types and sometimes recapitulated known biology.
“Pathway analyses of common variants have prioritized disease-relevant tissues and cell types, and in some cases, independently recapitulating known biology8,30,31.”
From Rare coding variants in ten genes confer substantial risk for schizophrenia (2022) · cites this paper as [30]
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Self-citationDetecting genome-wide directional effects of transcription factor binding on polygenic disease risk
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Self-citationThe 22q11.2 region regulates presynaptic gene-products linked to schizophrenia
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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 .”
Influential
- Authors
- Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P.-R., Lareau, C., Shoresh, N., Genovese, G., Saunders, A., Macosko, E., Pollack, S., The Brainstorm Consortium, Perry, J. R. B., Buenrostro, J. D., Bernstein, B. E., Raychaudhuri, S., McCarroll, S., Neale, B. M., & Price, A. L.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- University of Cambridge (GB)
- Corresponding author
- Finucane, Hilary K.
- Price, Alkes L.
- ORCID
- Venue
- Nature Genetics
- Published
- 2018-04
- Volume
- 50
- Issue
- 4
- Pages
- 621-629
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5896795
- OpenAlex
- W2953357410
- Cited by
- 1,097
- References
- 97
- Citations by year
- 2026: 117 · 2025: 156 · 2024: 150 · 2023: 152 · 2022: 138 · 2021: 149 · 2020: 110 · 2019: 80 · 2018: 35 · 2017: 8 · 2016: 1
- FWCI
- 62.11
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Yale University
- Hertz Foundation
- Lieber Institute for Brain Development
- Novo Nordisk Fonden (NNF 16OC0022018)
- National Institutes of Health (5r01ar063759-07, 16549, 5r01mh094714-04, CA194393, MH107649)
- Medical Research Council (MC_UU_12015/2)
- National Institute of Mental Health (R01MH107649, U01MH103339, R01-MH094714, R21MH105881, U01MH103365, R01MH109978, U01MH103340, R21MH102791, R01MH105472, P50MH106934, U01MH103392, R01MH105898, R21MH103877, U01MH103346)
- National Human Genome Research Institute (U01HG009379, T32HG002295)
- National Cancer Institute (U01CA194393, R01CA194393)
- National Institute of General Medical Sciences (T32GM007753)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (UH2AR067677, R01-AR063759)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- tissue-specific gene expression, disease heritability, linkage disequilibrium score regression, polygenic risk, GWAS summary statistics, gene expression data, brain cell types, excitatory and inhibitory neurons, bipolar disorder, schizophrenia, body mass index
- MeSH terms
- Bipolar Disorder, Brain, Chromatin, Humans, Immune System Diseases, Models, Genetic, Neurons, Schizophrenia, Tissue Distribution, Linkage Disequilibrium, Gene Expression, Body Mass Index, Genetic Predisposition to Disease, Multifactorial Inheritance, Gene Expression Profiling, Epigenesis, Genetic, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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