Epilepsy and the new cytogenetics

Abstract

We set out to review the extent to which molecular karyotyping has overtaken conventional cytogenetics in applications related to epilepsy. Multiplex ligase-dependent probe amplification (MLPA) targeted to predetermined regions such as SCN1A and KCNQ2 has been effectively applied over the last half a decade, and oligonucleotide array comparative genome hybridization (array CGH) is now well established for genome-wide exploration of microchromosomal variation. Array CGH is applicable to the characterization of lesions present in both sporadic and familial epilepsy, especially where clinical features of affected cases depart from established syndromes. Copy number variants (CNVs) associated with epilepsy and a range of other syndromes and conditions can be recurrent due to nonallelic homologous recombination in regions of segmental duplication. The most common of the recurrent microdeletions associated with generalized epilepsy are typically seen at a frequency of ∼ 1% at 15q13.3, 16p13.11, and 15q11.2, sites that also confer susceptibility for intellectual disability, autism, and schizophrenia. Incomplete penetrance and variable expressivity confound the established rules of cytogenetics for determining the pathogenicity for novel CNVs; however, as knowledge is gained for each of the recurrent CNVs, this is translated to genetic counseling. CNVs play a significant role in the susceptibility profile for epilepsies, with complex genetics and their comorbidities both from the "hotspots" defined by segmental duplication and elsewhere in the genome where their location and size are often novel.

Figure 1

The conventional G-banded karyotype showing 23 pairs of normal chromosomes as seen under light microscopy.

Figure 2

MLPA analysis showing KCNQ2 exons within the normal range (green), control probes from elsewhere in the genome (blue) and deleted exons (red). The display is generated using GeneMarker software. The points represent comparative peak height ratios for each MLPA probe compared with normal samples.

Figure 3

Signal from Nimblegen chromosome 2-specific oligonucleotide array-CGH. Hybridization data were analysed using SignalMap™ software. A: The familial 1.57 Mb duplication involving 8 contiguous genes including SCN2A, SCN3A and part of SCN1A as reported by Heron et al (2010). B: Three of the Dravet syndrome deletions with excision of SCN1A as reported by Marini et al (2009). Deletion sizes from top to bottom are 1.64 Mb (deleting SCN1A – XIRP2 and all genes between), 1.49 Mb (deleting FAM130A2 – XIRP2 and all genes between) and 588 kb (deleting GALNT3 – SCN9A), respectively.

Figure 4

Microdeletions associated with breakpoint (BP) “hotspots” in the 15q11-q13 region associated with Prader-Willi and Angelman syndromes, autism and genetic generalized epilepsy as described in the text. Blocks of semental duplications, in which the breakpoints lie, are represented at the top by orange/yellow/grey blocks. Red bars represent the unique sequence deleted (or duplicated) between blocks of segmental duplications. Deletions between BP1-BP2 and BP4-BP5, marked with an asterisk, have been associated with generalized epilepsy. The clinical significance of deletions between BP3-BP4 is unknown.