Open Access Methodology article

Variance heterogeneity analysis for detection of potentially interacting genetic loci: method and its limitations

Maksim V Struchalin1, Abbas Dehghan1, Jacqueline CM Witteman1, Cornelia van Duijn1 and Yurii S Aulchenko12*

Author Affiliations

1 Department of Epidemiology, Erasmus MC, Rotterdam, 3000 CA, The Netherlands

2 Quantitative Integrative Genomics Group, Institute of Cytology and Genetics SD RAS, Novosibirsk, 630090, Russia

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BMC Genetics 2010, 11:92  doi:10.1186/1471-2156-11-92

Published: 13 October 2010

Additional files

Additional file 1:

Supplementary figures. The file contains the following figures: Figure S1: Distribution of a trait for each genotypic groups and for all groups together before transformation to normality of a trait and after transformation. Figure S2: Dependence of power on interaction effect for direct test and different variance homogeneity tests. Figure S3: Dependence of non-centrality parameter of variance homogeneity test on effect of a factor for a case when group AA is tested against AB and BB. Figure S4: Dependence of non-centrality parameter of variance homogeneity test on effect of a factor for a case when group AB is tested against AA and BB. Figure S5: Dependence of non-centrality parameter of variance homogeneity test on effect of a factor for a case when group BB is tested against AA and AB. Figure S6: Dependence of power of variance homogeneity test on interaction effect for threshold α corresponding to 5·10-8 and 0.01. Figure S7: Genome-wide -log10(pvalue) and Q-Q plot for Levene's variance homogeneity test applied for the Rotterdam Study.

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Additional file 2:

Type I error for a case when all three genotypes are tested against each other. Type I error for variance homogeneity tests when there is effect of SNP which explains 0%, 1%, and 5% of total trait's variance for different frequency of interacting allele (5%, 10%, 25% and 50%) and for different distribution of residual error (normal, three types of t and chi square distribution).

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Additional file 3:

Type I error for a case when genotype AA is tested against AB and BB. Type I error for 1df variance homogeneity tests when AA is tested against AB and BB when there is effect of SNP which explains 0%, 1%, and 5% of total trait's variance for different frequency of interacting allele (5%, 10%, 25% and 50%) and for different distribution of residual error (normal, three types of t and chi square distribution ).

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Additional file 4:

Type I error for a case when genotype AB is tested against AA and BB. Type I error for 1df variance homogeneity tests when AB is tested against AA and BB when there is effect of SNP which explains 0%, 1%, and 5% of total trait's variance for different frequency of interacting allele (5%, 10%, 25% and 50%) and for different distribution of residual error (normal, three types of t and chi square distribution ).

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Additional file 5:

Type I error for a case when genotype BB is tested against AB and AA. Type I error for 1df variance homogeneity tests when BB is tested against AA and AB when there is effect of SNP which explains 0%, 1%, and 5% of total trait's variance for different frequency of interacting allele (5%, 10%, 25% and 50%) and for different distribution of residual error (normal, three types of t and chi square distribution ).

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