ArticlePLoS genetics2013
All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers, 5 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
191 citing papers in PubMed, 5 syntheses or guidelines pooled it, 307 citations in OpenAlex.
- Phenotypic and Genetic Links between Body Fat Measurements and Primary Open-Angle Glaucoma.International journal of molecular sciences · 2023Pooled it
- Hypothesis-driven genome-wide association studies provide novel insights into genetics of reading disabilities.Translational psychiatry · 2022Pooled it
- Identifying Risk Genes and Interpreting Pathogenesis for Parkinson's Disease by a Multiomics Analysis.Genes · 2020Pooled it
- Low-frequency and common genetic variation in ischemic stroke: The METASTROKE collaboration.Neurology · 2016Pooled it
- Glutamate Networks Implicate Cognitive Impairments in Schizophrenia: Genome-Wide Association Studies of 52 Cognitive Phenotypes.Schizophrenia bulletin · 2015Pooled it
- Identifying key transcription factors for pharmacogenetic studies of antipsychotics induced extrapyramidal symptoms.Psychopharmacology · 2020Trial
- Genome-Wide Prioritization and Transcriptomics Reveal Novel Signatures Associated With Thiazide Diuretics Blood Pressure Response.Circulation. Cardiovascular genetics · 2017Trial
- Beyond Exons: Linking Noncoding Heritability and Polygenicity across Complex Human Traits and Disorders.bioRxiv : the preprint server for biology · 2026Article
- Whole genome resequencing dataset ofData in brief · 2026Article
- Uniqueness of Heilongjiang Mandarin Fish (Veterinary sciences · 2026Article
- Interaction of early life stress and NAD + /SIRT1 pathway genetic risk promotes depression.Translational psychiatry · 2025Article
- Human genetic variation reveals FCRL3 is a lymphocyte receptor for Yersinia pestis.Cell genomics · 2025Article
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- Preeclampsia prediction and diagnosis: a comprehensive historical review from clinical insights to omics perspectives.Frontiers in medicine · 2025Review
- How Real-World Data Can Facilitate the Development of Precision Medicine Treatment in Psychiatry.Biological psychiatry · 2024Review
- HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications.BMC genomics · 2024Article
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- Data-Driven Characterization of Genetic Variability in Disease Pathways and Pesticide-Induced Nervous System Disease in the United States Population.Environmental health perspectives · 2024Article
- Olfactory genes affect major depression in highly educated, emotionally stable, lean women: a bridge between animal models and precision medicine.Translational psychiatry · 2024Article
- Abundant pleiotropy across neuroimaging modalities identified through a multivariate genome-wide association study.Nature communications · 2024Article
131 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 6 institutions in 3 countries.
Funding
Abstract
Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1-FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.