Abstracts

Malformations of cortical development (MCD) are a common cause of intractable childhood epilepsy. A genetic basis has been established for some bilateral and diffuse MCD, as well as for cortical tubers in tuberous sclerosis complex. However, the role of genetic aberrations in the formation of focal MCD is not clear. We studied DNA from tissue samples from epilepsy surgery resections of focal MCD. Using analysis of data from single nucleotide polymorphism (SNP) arrays, we examined changes in allele copy number to identify regions potentially involved in the formation of these MCD. We obtained 16 samples of flash-frozen brain tissue resected during focal epilepsy surgery. We extracted DNA from frozen tissue using standard methods. DNA was digested, amplified, and hybridized to Affymetrix 100K SNP arrays. Using the software dChipSNP, analysis for copy number change and loss of heterozygosity was performed in 16 samples using 29 related and unrelated germline DNA samples for comparison.
We performed quantitative PCR (qPCR) in cases in which copy number change was detected. In two samples, copy number analysis of the SNP data suggested an increase in copy number from two (normal) to three in a large region of chromosome 1q. Both samples were obtained from hemispherectomy specimens, one from a patient with left hemimegalencephaly and the other with extensive left hemisphere cortical dysplasia. Further analysis with qPCR suggested increased copy number at 1q, with the calculated copy number of 1q ranging from 2.2 to 2.5. Our SNP and qPCR data are consistent with increased allele copy number in a large region of chromosome 1q in two samples of focal MCD. The qPCR-derived calculated copy number is between 2 and 3 in the region of 1q probed, which is consistent with an actual copy number of 3 in the setting of stromal contamination. Further characterization of this copy change should be performed in these samples, for example, using fluorescence in situ hybridization targeting chromosome 1q. Further SNP analysis of DNA derived from LASER-capture microdissected cells would limit stromal contamination of the DNA and allow more precise quantitation of copy number of this region by qPCR. These cases, along with a third case of a child with a focal transmantle heterotopia and germline mosaicism for a translocation involving 1q, suggest that amplification of a gene in the 1q region may be responsible for the formation of some focal MCDs in patients with epilepsy. (Supported by Michelle and Roger Marino Fellowship in Epilepsy (A.P.), The Dana Foundation (P.M.B.), Howard Hughes Medical Institute (C.A.W.).)