An R package

BMC Genetics

Yurii S Aulchenko³  Cornelia M van Duijn²  Paul HC Eilers¹  Najaf Amin²  Maksim V Struchalin² 

[1] Department of Biostatistics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands;Department of Epidemiology, Erasmus MC, Rotterdam, 3000 CA, The Netherlands;Recombination and Segregation laboratory, Institute of Cytology and Genetics SD RAS, Novosibirsk, 630090, Russia

关键词: the GenABEL project;    VariABEL;    environmental sensitivity;    variance heterogeneity;    gene-gene interactions (GxG);    gene-environment interactions (GxE);    genome-wide association (GWA);    single-nucleotide polymorphisms (SNPs);   

Others  :  1122535
DOI  :  10.1186/1471-2156-13-4

 received in 2011-06-28, accepted in 2012-01-24,  发布年份 2012

【 摘 要 】

Background

Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our understanding of the genetic background underlying complex traits. Genome-wide testing of complex genetic models is a computationally demanding task. Moreover, testing of such models leads to multiple comparison problems that reduce the probability of new findings. Assuming that the genetic model underlying a complex trait can include hundreds of genes and environmental factors, testing of these models in genome-wide association studies represent substantial difficulties.

We and Pare with colleagues (2010) developed a method allowing to overcome such difficulties. The method is based on the fact that loci which are involved in interactions can show genotypic variance heterogeneity of a trait. Genome-wide testing of such heterogeneity can be a fast scanning approach which can point to the interacting genetic variants.

Results

In this work we present a new method, SVLM, allowing for variance heterogeneity analysis of imputed genetic variation. Type I error and power of this test are investigated and contracted with these of the Levene's test. We also present an R package, VariABEL, implementing existing and newly developed tests.

Conclusions

Variance heterogeneity analysis is a promising method for detection of potentially interacting loci. New method and software package developed in this work will facilitate such analysis in genome-wide context.

【 授权许可】

   
2012 Struchalin et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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