ArticleEuropean journal of human genetics : EJHG2012
Use of the gamma method for self-contained gene-set analysis of SNP data.
Article in European journal of human genetics : EJHG, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis 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
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 29 citations in OpenAlex.
- Statistical genomics in rare cancer.Seminars in cancer biology · 2020Pooled it
- Pharmacogenomics of estrogens on changes in carotid artery intima-medial thickness and coronary arterial calcification: Kronos Early Estrogen Prevention Study.Physiological genomics · 2016Trial
- Review
- DOT: Gene-set analysis by combining decorrelated association statistics.PLoS computational biology · 2020Article
- Ontogeny Related Changes in the Pediatric Liver Metabolome.Frontiers in pediatrics · 2020Article
- Meta-Qtest: meta-analysis of quadratic test for rare variants.BMC medical genomics · 2019Article
- Application of the parametric bootstrap for gene-set analysis of gene-environment interactions.European journal of human genetics : EJHG · 2018Article
- Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2016Article
- The Roles of Genes in the Neuronal Migration and Neurite Outgrowth Network in Developmental Dyslexia: Single- and Multiple-Risk Genetic Variants.Molecular neurobiology · 2016Article
- Adaptive Set-Based Methods for Association Testing.Genetic epidemiology · 2016Article
- Article
- Genetic variants in DNA repair genes as potential predictive markers for oxaliplatin chemotherapy in colorectal cancer.The pharmacogenomics journal · 2015Article
- Gene set analysis: A step-by-step guide.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2015Review
- Relative performance of gene- and pathway-level methods as secondary analyses for genome-wide association studies.BMC genetics · 2015Article
- Functional and genomic context in pathway analysis of GWAS data.Trends in genetics : TIG · 2014Review
- A set-based association test identifies sex-specific gene sets associated with type 2 diabetes.Frontiers in genetics · 2014Article
- Integrative gene set analysis: application to platinum pharmacogenomics.Omics : a journal of integrative biology · 2014Article
- Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study.Scientific reports · 2013Article
- Gene-environment interactions in genome-wide association studies: current approaches and new directions.Journal of child psychology and psychiatry, and allied disciplines · 2013Review
- Genome-wide gene-set analysis for identification of pathways associated with alcohol dependence.The international journal of neuropsychopharmacology · 2013Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Gene-set analysis (GSA) evaluates the overall evidence of association between a phenotype and all genotyped single nucleotide polymorphisms (SNPs) in a set of genes, as opposed to testing for association between a phenotype and each SNP individually. We propose using the Gamma Method (GM) to combine gene-level P-values for assessing the significance of GS association. We performed simulations to compare the GM with several other self-contained GSA strategies, including both one-step and two-step GSA approaches, in a variety of scenarios. We denote a 'one-step' GSA approach to be one in which all SNPs in a GS are used to derive a test of GS association without consideration of gene-level effects, and a 'two-step' approach to be one in which all genotyped SNPs in a gene are first used to evaluate association of the phenotype with all measured variation in the gene and then the gene-level tests of association are aggregated to assess the GS association with the phenotype. The simulations suggest that, overall, two-step methods provide higher power than one-step approaches and that combining gene-level P-values using the GM with a soft truncation threshold between 0.05 and 0.20 is a powerful approach for conducting GSA, relative to the competing approaches assessed. We also applied all of the considered GSA methods to data from a pharmacogenomic study of cisplatin, and obtained evidence suggesting that the glutathione metabolism GS is associated with cisplatin drug response.
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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.