Details
| Original language | English |
|---|---|
| Article number | 59 |
| Journal | BMC genetics |
| Volume | 13 |
| Publication status | Published - 18 Jul 2012 |
Abstract
Background: Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs).Results: We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcomp.Conclusions: We show that the proposed multiple contrast test of model-specific variance heterogeneity can be used to test for potential interactions between SNPs and unknown alleles, loci or covariates and provide valuable additional information compared with traditional tests. Although the test is statistically valid for severely unbalanced designs, care is needed in interpreting the results at loci with low allele frequencies.
Keywords
- Genetic association study, Interaction, Quantitative traits, Variance heterogeneity
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Genetics
- Medicine(all)
- Genetics(clinical)
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In: BMC genetics, Vol. 13, 59, 18.07.2012.
Research output: Contribution to journal › Article › Research › peer review
}
TY - JOUR
T1 - Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci
AU - Hothorn, Ludwig A.
AU - Libiger, Ondrej
AU - Gerhard, Daniel
N1 - Funding Information: We appreciate the two anonymous reviewers for their insightful and constructive comment. The work for the first author was partly supported by the German Science Foundation grand DfG-HO1687.
PY - 2012/7/18
Y1 - 2012/7/18
N2 - Background: Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs).Results: We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcomp.Conclusions: We show that the proposed multiple contrast test of model-specific variance heterogeneity can be used to test for potential interactions between SNPs and unknown alleles, loci or covariates and provide valuable additional information compared with traditional tests. Although the test is statistically valid for severely unbalanced designs, care is needed in interpreting the results at loci with low allele frequencies.
AB - Background: Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs).Results: We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcomp.Conclusions: We show that the proposed multiple contrast test of model-specific variance heterogeneity can be used to test for potential interactions between SNPs and unknown alleles, loci or covariates and provide valuable additional information compared with traditional tests. Although the test is statistically valid for severely unbalanced designs, care is needed in interpreting the results at loci with low allele frequencies.
KW - Genetic association study
KW - Interaction
KW - Quantitative traits
KW - Variance heterogeneity
UR - http://www.scopus.com/inward/record.url?scp=84872664050&partnerID=8YFLogxK
U2 - 10.1186/1471-2156-13-59
DO - 10.1186/1471-2156-13-59
M3 - Article
C2 - 22808950
AN - SCOPUS:84872664050
VL - 13
JO - BMC genetics
JF - BMC genetics
SN - 1471-2156
M1 - 59
ER -