ArticlePloS one2013
Assessing methods for assigning SNPs to genes in gene-based tests of association using common variants.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 2 of them syntheses that pooled it.
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Who cites it
25 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A gene based combination test using GWAS summary data.BMC bioinformatics · 2023Pooled it
- Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity.Human molecular genetics · 2015Pooled it
- Susceptibility to Childhood Pneumonia: A Genome-Wide Analysis.American journal of respiratory cell and molecular biology · 2017Trial
- Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior.Communications biology · 2024Article
- Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach.Veterinary research communications · 2024Article
- Regulatory elements inGenetics in medicine open · 2024Article
- A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.Nature communications · 2020Article
- ARMC 5 Variants and Risk of Hypertension in Blacks: MH- GRID Study.Journal of the American Heart Association · 2019Article
- An Exome-Wide Association Study Identifies New Susceptibility Loci for Age of Smoking Initiation in African- and European-American Populations.Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco · 2019Article
- Learning the optimal scale for GWAS through hierarchical SNP aggregation.BMC bioinformatics · 2018Article
- Epigenetic dysregulation of naive CD4+ T-cell activation genes in childhood food allergy.Nature communications · 2018Article
- Polymorphic Variations Associated With Doxorubicin-Induced Cardiotoxicity in Breast Cancer Patients.Oncology research · 2017Article
- Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci.British journal of cancer · 2017Article
- Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure.Genetic epidemiology · 2017Article
- PR Interval Associated Genes, Atrial Remodeling and Rhythm Outcome of Catheter Ablation of Atrial Fibrillation-A Gene-Based Analysis of GWAS Data.Frontiers in genetics · 2017Article
- Computational discovery of transcription factors associated with drug response.The pharmacogenomics journal · 2016Article
- Gene-based analysis identified the gene ZNF248 is associated with late-onset asthma in African Americans.Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology · 2016Article
- Adaptive gene- and pathway-trait association testing with GWAS summary statistics.Bioinformatics (Oxford, England) · 2016Article
- A genome-wide screening and SNPs-to-genes approach to identify novel genetic risk factors associated with frontotemporal dementia.Neurobiology of aging · 2015Article
- Proteomic and genomic evidence implicates the postsynaptic density in schizophrenia.Molecular psychiatry · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Gene-based tests of association are frequently applied to common SNPs (MAF>5%) as an alternative to single-marker tests. In this analysis we conduct a variety of simulation studies applied to five popular gene-based tests investigating general trends related to their performance in realistic situations. In particular, we focus on the impact of non-causal SNPs and a variety of LD structures on the behavior of these tests. Ultimately, we find that non-causal SNPs can significantly impact the power of all gene-based tests. On average, we find that the "noise" from 6-12 non-causal SNPs will cancel out the "signal" of one causal SNP across five popular gene-based tests. Furthermore, we find complex and differing behavior of the methods in the presence of LD within and between non-causal and causal SNPs. Ultimately, better approaches for a priori prioritization of potentially causal SNPs (e.g., predicting functionality of non-synonymous SNPs), application of these methods to sequenced or fully imputed datasets, and limited use of window-based methods for assigning inter-genic SNPs to genes will improve power. However, significant power loss from non-causal SNPs may remain unless alternative statistical approaches robust to the inclusion of non-causal SNPs are developed.
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