Linkage analysis in a familial case of idiopathic epilepsy and its implications in drug development

Abstract

Epilepsy, which affects about 1 % of the population worldwide, is a term that covers a range of heterogeneous disorders of brain function. The only common denominator of this condition is the susceptibility to repeated, unprovoked seizures of various phenotypes. While some epilepsies may be caused by a number of known neurological and metabolic conditions, others have unknown aetiology and are idiopathic. In recent years, significant research has been carried out on the genetics of epilepsy, and a number of mutations, mostly in genes that code for ion channels, have been linked to the epilepsy phenotype. Linkage analysis has played a major role in the discovery of these genes, using large families with several affected individuals. In this study, linkage analysis was used to identify possible novel causative loci in a chromosomal interval that is linked to the epilepsy phenotype in a Maltese family, which has seven affected individuals with epilepsy or febrile seizures, over three generations. The inheritance pattern in the family was found to be autosomal dominant with incomplete penetrance. The syndrome in the family was characteristic of generalized epilepsy with febrile seizures plus (GEFS+) in being idiopathic, and with the affected family members having febrile seizures together with other types of epilepsy. The predominance of febrile seizures that remit before age six could also characterize the phenotype as familial febrile seizures. This study identified other loci beside the main linkage interval on chromosome 20, which may harbour genes that may explain phenotype heterogeneity and reduced penetrances in various family members. Linkage analysis was performed using high-density single nucleotide polymorphisims (SNP) genechips. Analysis of the DNA from affected family members identified a linkage interval of about 20cM on chromosome 20 (20q13.32-33) which gave a parametric LOD score of 2.67. This score is suggestive evidence for linkage. By varying the penetrance and disease inheritance models, two other linkage intervals were observed on cytogenetic bands 3q21.3 and 13q13-14. The linkage interval on chromosome 20 was confirmed using markers for Short Tandem Repeats (STRs). This region harbours several genes. The Zlr score peaked in a region of about 1.2cM, which has 18 genes, two of which have been already linked to other epilepsy syndromes. The best candidate genes in this region were CHRNA4 and KCNQ2 (which both code for ion channels) and STMN3, which is involved in neurite growth. DNA resequencing of the exons and intronlexon junctions of these genes, identified variations between the affected family members and the non-affected members. The affected individuals were found to have a different haplotype from the non-affected individuals. A novel 24bp deletion was, in fact, identified in all the affected individuals. This allele was found to normally occur only at a frequency of 0.04 in the general Maltese population. Analysis of the affected allele, using bioinformatics software predicted an alternative splice site and a different folding pattern of the pre-mRNA, when compared to the reference sequence. cDNA sequencing of the CHRNA4 transcript of an affected individual, did not show any variation from the reference sequence. Copy Number Variation analysis identified regions where the two family members who have the disease haplotype, but do not have epilepsy seizures, differ from the other affected individuals with epilepsy. This project has identified novel genetic loci, which contribute to the phenotype of epilepsy. This could contribute to a better understanding of the cause of this condition. When considering that 30% of people who have epilepsy are pharmacoresistant, and other affected individuals still have a low quality of life in spite of treatment with antiepileptic drugs, it is imperative that the knowledge gained though genetic studies is used in the identification of novel therapeutic targets and the development of new drugs. This study also gives insights on the possible use of such genetic data for innovative drug development.