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A simple correction for multiple comparisons in interval mapping genome scans
Open accessAbstract
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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“Modifications to the Bonferroni correction in the context of QTL mapping have been proposed by Cheverud (2001), and further modifications proposed by Li and Ji (2005).”
From The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis (2013) · cites this paper as Cheverud (2001)
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Metadata
- Authors
- Cheverud, J. M.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Cheverud, James M
- ORCID
- Cheverud, James M
- Venue
- Heredity
- Published
- 2001
- Volume
- 87
- Issue
- 1
- Pages
- 52-58
- ISSN
- 0018-067X (ISSN-L)
- OpenAlex
- W2054881132
- Cited by
- 421
- References
- 21
- Citations by year
- 2026: 8 · 2025: 16 · 2024: 13 · 2023: 10 · 2022: 21 · 2021: 21 · 2020: 18 · 2019: 9 · 2018: 17 · 2017: 10 · 2016: 30 · 2015: 21 · 2014: 14 · 2013: 24 · 2012: 25
- FWCI
- 3.43
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Heredity (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (9726433)
- National Institutes of Health (5r01dk052514-06)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK52514)
- Division of Environmental Biology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- multiple testing correction, interval mapping, genome scan, Bonferroni correction, significance threshold, marker density, chromosome length, QTL mapping
- MeSH terms
- Analysis of Variance, Biometry, Chromosome Mapping, Computer Simulation, Genetic Markers, Genotype, Genetic Linkage, Models, Genetic, Statistics as Topic, Models, Statistical, Quantitative Trait, Heritable
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