A simple correction for multiple comparisons in interval mapping genome scans.
paper
Cited
Public
Unavailable
- Authors
- Cheverud, J M
- Year
- 2001
- Journal
- Heredity
- PMID
- 11678987
- DOI
- 10.1046/j.1365-2540.2001.00901.x
Several approaches have been proposed to correct point-wise significance thresholds used in interval-mapping genome scans. A method for significance threshold correction based on the Bonferroni test is presented. This test involves calculating the effective number of independent comparisons performed in a genome scan from the variance of the eigenvalues of the observed marker correlation matrix. The more highly correlated the markers, the higher the variance of the eigenvalues and the lower the number of independent tests performed on a chromosome. This approach was evaluated by mapping 1000 normally distributed phenotypes along chromosomes of varying length and marker density in a population size of 500. Experiment-wise significance thresholds obtained from the simulation are compared to those calculated using the Bonferroni criterion and the newly developed measure of the effective number of independent tests in a genome scan. The Bonferroni calculation produced significance thresholds very similar to those obtained by simulation. The threshold levels for both Bonferroni and simulation analysis depended strongly on the marker density and size of chromosomes. There was a slight bias of about 1% in the thresholds obtained at the 5% and 10% point-wise significance levels. The method introduced here provides a relatively simple correction for multiple comparisons that can be easily calculated using standard statistics packages.
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| Epistasis and the evolutionary dynamics of measured genotypic values during simulated serial bottlenecks. | Jarvis JP et al. | β | 2009 | β |
| Family-based mitochondrial association study of traits related to type 2 diabetes and the metabolic syndrome in adolescents. | Byrne EM et al. | β | 2009 | β |
| Generation of Gene Ontology benchmark datasets with various types of positive signal. | TΓΆrΓΆnen P et al. | β | 2009 | β |
| Genetic studies of amyotrophic lateral sclerosis: controversies and perspectives. | Beleza-Meireles A et al. | β | 2009 | β |
| Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. | Baranzini SE et al. | β | 2009 | β |
| Quantitative trait loci with effects on feed efficiency traits in Hereford x composite double backcross populations. | MΓ‘rquez GC et al. | β | 2009 | β |
| Rapid and accurate multiple testing correction and power estimation for millions of correlated markers. | Han B et al. | β | 2009 | β |
| Strong evidence for a novel schizophrenia risk locus on chromosome 1p31.1 in homogeneous pedigrees from Tamil Nadu, India. | Holliday EG et al. | β | 2009 | β |
| The largest prospective warfarin-treated cohort supports genetic forecasting. | Wadelius M et al. | β | 2009 | β |
| A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. | Gao X et al. | β | 2008 | β |
| An epistatic genetic basis for physical activity traits in mice. | Leamy LJ et al. | β | 2008 | β |
| Considering dependence among genes and markers for false discovery control in eQTL mapping. | Chen L et al. | β | 2008 | β |
| Genetic architecture of adiposity and organ weight using combined generation QTL analysis. | Fawcett GL et al. | β | 2008 | β |
| Genome-wide significance for dense SNP and resequencing data. | Hoggart CJ et al. | β | 2008 | β |
| HSPA5 promoter polymorphisms and risk of Parkinson's disease in Taiwan. | Chen CM et al. | β | 2008 | β |
| Investigation of phenotypes associated with mood and anxiety among male and female fragile X premutation carriers. | Hunter JE et al. | β | 2008 | β |
| Methods for handling multiple testing. | Rice TK et al. | β | 2008 | β |
| Multi-environment QTL mixed models for drought stress adaptation in wheat. | Mathews KL et al. | β | 2008 | β |
| New correction algorithms for multiple comparisons in case-control multilocus association studies based on haplotypes and diplotype configurations. | Misawa K et al. | β | 2008 | β |
| On multiple-testing correction in genome-wide association studies. | Moskvina V et al. | β | 2008 | β |
| Permutation - based statistical tests for multiple hypotheses. | Camargo A et al. | β | 2008 | β |
| Pleiotropic scaling of gene effects and the 'cost of complexity'. | Wagner GP et al. | β | 2008 | β |
| Polymorphisms in the 5' upstream region of the CXCR1 chemokine receptor gene, and their association with somatic cell score in Holstein cattle in Canada. | Leyva-Baca I et al. | β | 2008 | β |
| Promoter polymorphisms modulating HSPA5 expression may increase susceptibility to Taiwanese Alzheimer's disease. | Hsu WC et al. | β | 2008 | β |
| Quantitative trait loci for physical activity traits in mice. | Lightfoot JT et al. | β | 2008 | β |
| Sex modifies the relationship between age and gait: a population-based study of older adults. | Callisaya ML et al. | β | 2008 | β |
| Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis. | Yu Z et al. | β | 2008 | β |
| What do we know and when do we know it? | Nicholls A | β | 2008 | β |
| 2,3,7,8-Tetrachlorodibenzo-p-dioxin affects fluctuating asymmetry of molar shape in mice, and an epistatic interaction of two genes for molar size. | Keller JM et al. | β | 2007 | β |
| A novel method combining linkage disequilibrium information and imputed functional knowledge for tagSNP selection. | Rochat RH et al. | β | 2007 | β |
| Association analysis of the chromosome 4p15-p16 candidate region for bipolar disorder and schizophrenia. | Christoforou A et al. | β | 2007 | β |
| Association of warfarin dose with genes involved in its action and metabolism. | Wadelius M et al. | β | 2007 | β |
| Identification of promoter variants in baboon endothelial lipase that regulate high-density lipoprotein cholesterol levels. | Cox LA et al. | β | 2007 | β |
| Multiple testing in the genomics era: findings from Genetic Analysis Workshop 15, Group 15. | Martin LJ et al. | β | 2007 | β |
| Quantitative trait loci with additive effects on growth and carcass traits in a Wagyu-Limousin F2 population. | Alexander LJ et al. | β | 2007 | β |
| Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. | Alexander LJ et al. | β | 2007 | β |
| Screening of 134 single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes replicates association with 12 SNPs in nine genes. | Willer CJ et al. | β | 2007 | β |
| So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. | Conneely KN et al. | β | 2007 | β |
| The genetic basis of quantitative variation in susceptibility of Arabidopsis thaliana to Pseudomonas syringae (Pst DC3000): evidence for a new genetic factor of large effect. | Kover PX et al. | β | 2007 | β |
| Tumor necrosis factor-alpha promoter polymorphism is associated with the risk of Parkinson's disease. | Wu YR et al. | β | 2007 | β |
| Data-mining methods as useful tools for predicting individual drug response: application to CYP2D6 data. | Sabbagh A et al. | β | 2006 | β |
| Detecting multiple associations in genome-wide studies. | Dudbridge F et al. | β | 2006 | β |
| Effect of genotype and environment on branching in weedy green millet (Setaria viridis) and domesticated foxtail millet (Setaria italica) (Poaceae). | Doust AN et al. | β | 2006 | β |
| Patterning of geographic variation in Middle Pleistocene Homo frontal bone morphology. | Athreya S | β | 2006 | β |
| Trait components provide tools to dissect the genetic susceptibility of migraine. | Anttila V et al. | β | 2006 | β |
| Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. | Li J et al. | β | 2005 | β |
| An epistatic genetic basis for fluctuating asymmetry of tooth size and shape in mice. | Leamy LJ et al. | β | 2005 | β |
| Evaluation of Nyholt's procedure for multiple testing correction. | Salyakina D et al. | β | 2005 | β |
| Fine-mapping gene-by-diet interactions on chromosome 13 in a LG/J x SM/J murine model of obesity. | Ehrich TH et al. | β | 2005 | β |
| Genetic architecture of Arabidopsis thaliana response to infection by Pseudomonas syringae. | Kover PX et al. | β | 2005 | β |
| Genetic variation in selenoprotein S influences inflammatory response. | Curran JE et al. | β | 2005 | β |
| Genomewide significant linkage to migrainous headache on chromosome 5q21. | Nyholt DR et al. | β | 2005 | β |
| Nonreplication in genetic studies of complex diseases--lessons learned from studies of osteoporosis and tentative remedies. | Shen H et al. | β | 2005 | β |
| p-Value simulation for affected sib pair multiple testing. | Wu X et al. | β | 2005 | β |
| Regional structural characterization of the brain of schizophrenia patients. | Yushkevich P et al. | β | 2005 | β |
| Size as a line of least evolutionary resistance: diet and adaptive morphological radiation in New World monkeys. | Marroig G et al. | β | 2005 | β |
| The genetic basis for inflorescence variation between foxtail and green millet (poaceae). | Doust AN et al. | β | 2005 | β |
| The importance of modelling heterogeneity in complex disease: application to NIMH Schizophrenia Genetics Initiative data. | Holliday E et al. | β | 2005 | β |
| A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. | Nyholt DR | β | 2004 | β |
| Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies. | Dudbridge F et al. | β | 2004 | β |
| Epistasis affecting litter size in mice. | Peripato AC et al. | β | 2004 | β |
| Evidence for nucleolus organizer regions as the units of regulation in nucleolar dominance in Arabidopsis thaliana interecotype hybrids. | Lewis MS et al. | β | 2004 | β |
| Genetic control of branching in foxtail millet. | Doust AN et al. | β | 2004 | β |
| Pleiotropic effects on mandibular morphology II: differential epistasis and genetic variation in morphological integration. | Cheverud JM et al. | β | 2004 | β |
| Quantitative trait loci for obesity- and diabetes-related traits and their dietary responses to high-fat feeding in LGXSM recombinant inbred mouse strains. | Cheverud JM et al. | β | 2004 | β |
| A genome-wide scan for loci predisposing to non-syndromic cleft lip with or without cleft palate in two large Syrian families. | Wyszynski DF et al. | β | 2003 | β |
| Impact of character correlation and variable groupings on modern human population tree resolution. | Athreya S et al. | β | 2003 | β |
| Pleiotropic effects on mandibular morphology I. Developmental morphological integration and differential dominance. | Ehrich TH et al. | β | 2003 | β |
| An epistatic genetic basis for fluctuating asymmetry of mandible size in mice. | Leamy LJ et al. | β | 2002 | β |
| Contribution of maternal effect QTL to genetic architecture of early growth in mice. | Wolf JB et al. | β | 2002 | β |
| Genetic influences on maternal care. | Peripato AC et al. | β | 2002 | β |
| Quantitative trait loci for maternal performance for offspring survival in mice. | Peripato AC et al. | β | 2002 | β |