ArticleGenetic epidemiology2008
Analysis of multiple SNPs in a candidate gene or region.
Article in Genetic epidemiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
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Who cites it
61 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A method for gene-based pathway analysis using genomewide association study summary statistics reveals nine new type 1 diabetes associations.Genetic epidemiology · 2014Pooled it
- Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies.Genetic epidemiology · 2012Trial
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.PLoS computational biology · 2023Article
- A Comparison of Methods for Gene-Based Testing That Account for Linkage Disequilibrium.Frontiers in genetics · 2022Article
- Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel.Food and energy security · 2021Article
- Polygenic risk score in postmortem diagnosed sporadic early-onset Alzheimer's disease.Neurobiology of aging · 2018Article
- Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure.Genetic epidemiology · 2017Article
- Targeted deep resequencing ofExperimental and therapeutic medicine · 2016Article
- Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level.PLoS computational biology · 2016Article
- Identifying Prognostic SNPs in Clinical Cohorts: Complementing Univariate Analyses by Resampling and Multivariable Modeling.PloS one · 2016Article
- Multiple SNP Set Analysis for Genome-Wide Association Studies Through Bayesian Latent Variable Selection.Genetic epidemiology · 2015Article
- Testing for polygenic effects in genome-wide association studies.Genetic epidemiology · 2015Article
- Rare-Variant Kernel Machine Test for Longitudinal Data from Population and Family Samples.Human heredity · 2015Article
- Identifying rare and common disease associated variants in genomic data using Parkinson's disease as a model.Journal of biomedical science · 2014Article
- Genome-wide investigation of regional blood-based DNA methylation adjusted for complete blood counts implicates BNC2 in ovarian cancer.Genetic epidemiology · 2014Article
- Valid Monte Carlo permutation tests for genetic case-control studies with missing genotypes.Genetic epidemiology · 2014Article
- Introduction to deep sequencing and its application to drug addiction research with a focus on rare variants.Molecular neurobiology · 2014Review
- Penalized regression approaches to testing for quantitative trait-rare variant association.Frontiers in genetics · 2014Article
- A Comparison of Combined P-value Methods for Gene Differential Expression Using RNA-Seq Data.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2014Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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Abstract
We consider the analysis of multiple single nucleotide polymorphisms (SNPs) within a gene or region. The simplest analysis of such data is based on a series of single SNP hypothesis tests, followed by correction for multiple testing, but it is intuitively plausible that a joint analysis of the SNPs will have higher power, particularly when the causal locus may not have been observed. However, standard tests, such as a likelihood ratio test based on an unrestricted alternative hypothesis, tend to have large numbers of degrees of freedom and hence low power. This has motivated a number of alternative test statistics. Here we compare several of the competing methods, including the multivariate score test (Hotelling's test) of Chapman et al. ([2003] Hum. Hered. 56:18-31), Fisher's method for combining P-values, the minimum P-value approach, a Fourier-transform-based approach recently suggested by Wang and Elston ([2007] Am. J. Human Genet. 80:353-360) and a Bayesian score statistic proposed for microarray data by Goeman et al. ([2005] J. R. Stat. Soc. B 68:477-493). Some relationships between these methods are pointed out, and simulation results given to show that the minimum P-value and the Goeman et al. ([2005] J. R. Stat. Soc. B 68:477-493) approaches work well over a range of scenarios. The Wang and Elston approach often performs poorly; we explain why, and show how its performance can be substantially improved.
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