Short communicationEvaluation of multiple putative risk alleles within the 15q13.3 region for genetic generalized epilepsy
Introduction
CHRNA7, at chromosome 15q13.3, encodes the alpha7 subunit of the neuronal nicotinic acetylcholine receptor and has long been a candidate gene for neuropsychiatric disorders. Linkage analyses and neurophysiological studies initially associated the CHRNA7 region with schizophrenia (Freedman et al., 1997). Definitive evidence for involvement of this region in epilepsy and neuropsychiatric disorders emerged with robust demonstration of association between the 15q13.3 microdeletion (del15q13.3) and intellectual disability (ID) in 2008 (Sharp et al., 2008); then subsequently with autism spectrum disorder (ASD), schizophrenia and genetic generalized epilepsy (GGE) (Helbig et al., 2009, Miller et al., 2009, Shinawi et al., 2009, Stefansson et al., 2009). Among the associated heterogeneous phenotypes, GGE is most frequent with over 1% of patients carrying del15q13.3 (Dibbens et al., 2009, Helbig et al., 2009). In those with both intellectual disability and epilepsy consistent with GGE (ID-GGE) over 5% carry del15q13.3 (Mullen et al., 2013). Despite these remarkable carriage rates, particularly in “dual-phenotype” cases, del15q13.3 acts as a risk allele rather than a Mendelian cause of disease (Dibbens et al., 2009).
CHRNA7 and its partial duplication CHRFAM7A, lie within the common 15q13.3 microdeletion. As other neuronal nicotinic acetylcholine receptor subunits are known monogenic causes of epilepsy (CHRNA4, CHRNA2 and CHRNA2), interest focused on CHRNA7 as the likely critical gene in the 15q13.3 region (Taske et al., 2002). This was reinforced by the description of small 15q13.3 deletions encompassing CHRNA7 and CHRFAM7A associated with ID (Liao et al., 2011). This is a complex region, however. The partially duplicated gene alongside CHRNA7, CHRFAM7A, comprises exons 5–10 of CHRNA7 fused to the FAM7A gene. Although previously thought non-functional, more recent evidence suggests CHRFAM7A may affect CHRNA7 currents by regulating surface expression of the channel (de Lucas-Cerrillo et al., 2011).
A number of studies have examined sequence variation in this region. One study in 2002, seeking molecular variation responsible for a putative linkage signal at 15q13-14 in GGE, reported three rare variants, although no significant association was found (Flomen et al., 2006). Variation in CHRNA7 and CHRFAM7A in schizophrenia has also been reported but its significance remains unclear (Flomen et al., 2006, Gault et al., 2003). These studies have been limited by the sequence homology between CHRNA7 and CHRFAM7A. With conventional PCR it is not possible to determine, for the duplicated exons at least, the gene in which variants are located.
In addition, the contribution of a common 2-base pair (bp) deletion in CHRFAM7A to psychiatric disease has been suggested. This deletion is a marker of inversion of CHRFAM7A. An association has been claimed in some cohorts (Gault et al., 2003) but not in others (Flomen et al., 2006, Raux et al., 2002). An association with GGE has also been reported (Rozycka et al., 2013).
Here we examine sequence variation in CHRNA7 and CHRFAM7A in the phenotypes most strongly associated with del15q13.3. We selected probands with either GGE alone or a “dual phenotype” including GGE and a second del15q13.3 phenotype such as ASD, schizophrenia or ID. We hypothesized that sequence variation would act either as a risk allele in a similar manner to del15q13.3 or modify the expression of a co-existing deletion of the other chromosome 15 allele. We utilized long-range PCR to reliably define in which gene variants reside. In addition, we sought to confirm the association of the common 2 bp deletion in CHRFAM7A with GGE.
Section snippets
Subjects
We recruited 174 GGE probands: 77 had GGE alone while 97 had GGE-plus with at least one additional phenotype of ID (77), psychosis (17) or ASD (6). This included 4 previously reported GGE cases and 4 previously reported GGE-plus cases shown to carry the 15q13.3 microdeletion (Dibbens et al., 2009, Mullen et al., 2013). The breakdown in epileptic syndrome diagnosis of this cohort is shown in Table 1. We also genotyped 182 Caucasian controls for rare variants identified in this study.
Genomic DNA
Single nucleotide variants in CHRNA7 and CHRFAM7A
We detected two novel variants and one reported rare variant (Table 2). Three samples failed long range PCR.
In CHRFAM7A one novel missense variant (p.V161L) was detected in a proband with juvenile absence epilepsy that was absent from our controls and approximately 63,000 individuals on the Exome Aggregation Consortium (ExAC) (http://exac.broadinstitute.org) database, and is predicted to be probably damaging by PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/) (Fig. 1, Table 2).
In CHRNA7 we
Discussion
Copy number variants (CNVs), particularly recurrent CNVs, are well established as important risk factors for neurodevelopmental phenotypes such as ID, ASD, schizophrenia and epilepsy. Such CNVs often contain a critical gene or genes in which sequence variation confers similar risk in other cases. For the recurrent 15q13.3 deletion, the likely candidate genes are CHRNA7 and possibly CHRFAM7A.
Due to the structure of this region and the partial duplication of CHRNA7, high throughput sequencing
Conclusion
Our data suggest that in addition to CNVs at the 15q13.3 locus conferring risk for GGE, rare variants within CHRNA7 may also contribute. Our sequencing data is consistent with the earlier investigation of juvenile myoclonic epilepsy by Taske and colleagues (Taske et al., 2002) but the low frequency of variants discovered in both studies suggests that the attributable risk of rare variants in CHRNA7 is quite low. Functional studies or large case–control studies are needed to confirm a pathogenic
Contributors
J.A.D., and S.F.B. initiated and directed the project. J.A.D., M.S.H., T.A., L.D., H.M., H-H.M.D., H.C.M., and B.W.D. performed molecular genetics experiments. S.A.M., S.T.B., K.M.L., I.E.S., and S.F.B. conducted clinical phenotyping. J.A.D., S.A.M., M.S.H., and S.F.B. wrote the paper. All authors discussed the results and commented on the manuscript.
Competing interests
Authors report grant funds that contributed to this project as outlined in the Acknowledgements section. I.E.S. discloses payments from UCB Pharma, Athena Diagnostics and Transgenomics for lectures and educational presentations. S.F.B. discloses payments from UCB Pharma, Novartis Pharmaceuticals, Sanofi-Aventis, and Jansen Cilag for lectures and educational presentations, and a patent for SCN1A testing held by Bionomics Inc and licensed to various diagnostic companies.
Acknowledgements
We thank the patients and families for participating in our research program. Elena Aleksoska (Epilepsy Research Centre, University of Melbourne) is acknowledged for performing genomic DNA extractions. This study was supported by National Health and Medical Research Council Program Grant (628952) to S.F.B and I.E.S, an Australia Fellowship (466671) to S.F.B, a Practitioner Fellowship (1006110) to I.E.S and a Career Development Fellowship (1063799) to M.S.H. We confirm that we have read the
References (15)
- et al.
Function of partially duplicated human alpha77 nicotinic receptor subunit CHRFAM7A gene: potential implications for the cholinergic anti-inflammatory response
J. Biol. Chem.
(2011) - et al.
Evaluation of the positional candidate gene CHRNA7 at the juvenile myoclonic epilepsy locus (EJM2) on chromosome 15q13-14
Epilepsy Res.
(2002) - et al.
Familial and sporadic 15q13.3 microdeletions in idiopathic generalized epilepsy: precedent for disorders with complex inheritance
Hum. Mol. Genet.
(2009) - et al.
Association study of CHRFAM7A copy number and 2 bp deletion polymorphisms with schizophrenia and bipolar affective disorder
Am. J. Med. Genet. B: Neuropsychiatr. Genet.
(2006) - et al.
Linkage of a neurophysiological deficit in schizophrenia to a chromosome 15 locus
Proc. Natl. Acad. Sci. U. S. A.
(1997) - et al.
Comparison of polymorphisms in the alpha7 nicotinic receptor gene and its partial duplication in schizophrenic and control subjects
Am. J. Med. Genet. B: Neuropsychiatr. Genet.
(2003) - et al.
15q13.3 microdeletions increase risk of idiopathic generalized epilepsy
Nat. Genet.
(2009)
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