“Blinders, phenotype, and fashionable genetic analysis”: Setting the record straight for epilepsy! (2011)

To the Editors: Greenberg and Subaran (2011) suggest that progress in epilepsy genetics is blinkered by a preoccupation with ion channels. Yes, relationships between epilepsy and ion channel genes, for example KCNQ2, KCNQ3, CHRNA2, CHRNA4,CHRNB2, SCN1A, SCN2A, SCN1B, GABRA1, and GABRG2, were well established during the pioneering years of epilepsy genetics. However, relationships have surfaced over the last decade also between epilepsy and non–ion channel genes, for example with LGI1, EFHC1, ARX, CDKL5, PCDH19, PRICKLE1, SCARB2, SLC2A1, and TBC1D24. Ignoring epilepsy genes encoding ion channels would have introduced a negative bias and delayed progress. What little that is so far known of genetic mechanisms stems from all of the epilepsy genes identified to date. Due to the nature of the underlying genetic architecture and logistics of experimentally validating minute changes to gene function, extension to the common epilepsies with complex inheritance involving multiple genes is extremely challenging. It would be naive to dismiss genetic variation in ion channels as a likely source for at least part of the genetic susceptibility for periodic conditions such as epilepsy. A clear example of the “archetypal” article referred to by Greenberg and Subaran (2011) as circuitous is one, which we are particularly proud of, implicating SCN1B (Wallace et al., 1998). Incorporating our understanding of the fundamental biology for the condition into the analysis facilitated the timely entrée of sodium channels as agents provocateurs for various kinds of episodic seizures, some even related through a shared mutation segregating within families. The positive aspect of the work of Greenberg and Subaran (2011) is that it provides the opportunity to raise hitherto neglected issues. For epilepsies with complex inheritance, what do observations of small changes in function associated with some of the genetic variants in ion channel genes, CACNA1H for example, really mean? Electrophysiologic interpretation suggests that they may lower the threshold, in concert with other susceptibility genes, to release the seizure (Heron et al., 2007). Some genetic variants in CACNA1H may also contribute to autism spectrum disorders (Splawski et al., 2006). Are the changes to channel properties, perhaps affecting human physiology in a small way, related to epilepsy, to autism spectrum disorders, to both, or entirely to some other as yet unknown condition? Another pertinent issue related to the epilepsies with complex inheritance is phenotype characterization. We agree with Greenberg and Subaran (2011), and Scheffer (2011), of its significance. But we do so for different reasons. Uniformity of phenotype does not necessarily lead to genetic uniformity; conversely, genetic uniformity does not necessarily create phenotypic uniformity (Mulley et al., 2005; Mefford & Mulley, 2010; Mulley et al., 2011). Although clinical diagnoses are essential to broadly categorize cases, we question the depth of endophenotyping required for directing the search for susceptibility genes, because we now realize that it does not necessarily ensure genetic homogeneity, and if it did, we do not know which component(s), or which combination of components, of the clinical phenotype are the relevant ones. The most compelling reason for detailed phenotyping carried out a priori relative to molecular analysis is so that genotype–phenotype relationships can be assessed by molecular indicators without needing additional consents to return to the subjects who initially donated their DNA, and it eliminates any potential for post hoc bias in the clinical data. The report of Gurnett and Hedera (2007) drew attention to all 3,000 genes expressed at the synapse, among others, as epilepsy candidate genes. Unique microchromosomal copy number variants possess the power to disclose new gene families associated with epilepsy (Mefford & Mulley, 2010). Massively parallel sequencing (MPS), as used to identify TBC1D24 underlying a form of monogenic epilepsy, illustrates application of the latest gene discovery approach (Corbett et al., 2010). For the case of epilepsies with complex genetics, statistical theory is under development (Price et al., 2010) to analyze results that will flow from MPS (Mardis, 2008) for the analysis of next generation genome-wide association studies (GWAS) (Kryukov et al., 2007). Maybe these research directions, which have been a feature of the past half decade, are fashionable in the context of human molecular genetics. But as applied to epilepsy, they are timely, progressive, and effective internationally driven approaches directed at further removing epilepsy from the shadows. As laboratory based medical scientists, heavily and directly involved in the processes of gene discovery, our message to Greenberg and Subaran (2011), and to other like-minded commentators, is simple. The primary technologies dating from the first application of linkage analysis to families with epilepsy, and GWAS to affected individuals in populations, right through to modern MPS applied to monogenic or complex epilepsies, have a common thread—they all represent unbiased approaches directed at the discovery of epilepsy genes. In some cases the gene we are hunting will be revealed to encode an ion channel, and in some cases not. We thank the National Health and Medical Research Council of Australia, SA Pathology, and MS McLeod Trustees for support. None of the authors has any conflict of interest to disclose. We confirm that we have read the Journal’s position on issues involved in ethical publication and affirm that this report is consistent with those guidelines.