J Korean Med Sci.  2009 Feb;24(1):62-68. 10.3346/jkms.2009.24.1.62.

Gene-to-Gene Interaction between Sodium Channel-Related Genes in Determining the Risk of Antiepileptic Drug Resistance

• Jang SY
• Kim MK
• Lee KR
• Park MS
• Kim BC
• Cho KH
• Lee MC
• Kim YS

• KMID: 1794408
• DOI: http://doi.org/10.3346/jkms.2009.24.1.62

Abstract

The pathogenesis of antiepileptic drug (AED) resistance is multifactorial. However, most candidate gene association studies typically assess the effects of candidate genes independently of each other, which is partly because of the limitations of the parametric-statistical methods for detecting the gene-to-gene interactions. A total of 200 patients with drug-resistant epilepsy and 200 patients with drug-responsive epilepsy were genotyped for 3 representative the single nucleotide polymorphisms (SNPs) of the voltage-gated sodium channel genes (SCN1A, SCN1B, and SCN2A) by polymerase chain reaction and direct sequencing analysis. Besides the typical parametric statistical method, a new statistical method (multifactor dimensionality reduction [MDR]) was used to determine whether gene-to-gene interactions increase the risk of AED resistance. None of the individual genotypes or alleles tested in the present study showed a significant association with AED resistance, regardless of their theoretical functional value. With the MDR method, of three possible 2-locus genotype combinations, the combination of SCN2A-PM with SCN1B-PM was the best model for predicting susceptibility to AED resistance, with a p value of 0.0547. MDR, as an analysis paradigm for investigating multi-locus effects in complex disorders, may be a useful statistical method for determining the role of gene-to-gene interactions in the pathogenesis of AED resistance.

Keyword

Epilepsy; Drug Resistance; Pharmacogenetics; Sodium Channels

MeSH Terms

Adolescent
Adult
Alleles
Anticonvulsants/*therapeutic use
Case-Control Studies
Child
Child, Preschool
Data Interpretation, Statistical
Drug Resistance
Epilepsy/drug therapy/*genetics
Female
Genetic Predisposition to Disease
Genotype
Humans
Infant
Male
Polymorphism, Single Nucleotide
Sodium Channels/*genetics

Figure

• 

  Fig. 1 A comparative analysis for estimating relative allele frequencies in a pool of DNA. Allele frequency in pooled DNA={[Reference Peak Height (Individual)/Reference Peak Height (Pool)]/[Heterozygote Peak Height (Individual)/Heterozygote Peak Height (Pool)]}×0.5. Black arrows indicate heterozygote peaks and red arrows indicate reference peaks.

• 

  Fig. 2 The four general steps involved in using the MDR method for case-control studies (adapted from Ritchie et al., 2001). In step 1, a set of n genetic factors is selected from the pool of all factors. In step 2, the n factors and their possible multifactor classes or cells are represented in n dimensional space. For example, for three loci with three genotypes each, there are 27 three-locus-genotype combinations. The ratio of the number of cases is then estimated within each multifactor class. In step 3, each multifactor cell in n-dimensional space is labeled either as "high-risk," if the cases:control ratio meets or exceeds the given threshold (e.g., ≥1.0), or as "low-risk," if that threshold is not exceeded. This reduces the n-dimensional model to a one-dimensional model. Finally, in step 4, the prediction error of each model is estimated by 10-fold cross-validation. Here, the data (i.e., subjects) are randomly divided into 10 equal parts. Each possible 9/10 of the subjects is used to make predictions regarding the disease status of each possible 1/10 of the subjects excluded. To reduce the possibility of poor prediction error estimates due to the chance division of the data set, the 10-fold cross-validation is repeated 10 times, and the prediction errors are averaged.

• 

  Fig. 3 Best multi-locus model for susceptibility to AED resistance. High-risk genotypes as revealed by MDR are in dark shading and the low-risk genotypes are in light shading. The numbers of individuals with refractory epilepsy are represented within each cell as the left-hand bar of the histogram and the number of individuals with responsive epilepsy are in the right-hand bar.

• 

  Fig. 4 The dendrogram demonstrates the nature of the interactions between SNPs. The colors used in the dendrogram comprise a spectrum of colors representing a continuum from synergy to redundancy.

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