SCN1A duplications and deletions detected in Dravet syndrome: implications for molecular diagnosis.
OBJECTIVE
We aimed to determine the type, frequency, and size of microchromosomal copy number variations (CNVs) affecting the neuronal sodium channel α 1 subunit gene (SCN1A) in Dravet syndrome (DS), other epileptic encephalopathies, and generalized epilepsy with febrile seizures plus (GEFS+).


METHODS
Multiplex ligation-dependent probe amplification (MLPA) was applied to detect SCN1A CNVs among 289 cases (126 DS, 97 GEFS+, and 66 with other phenotypes). CNVs extending beyond SCN1A were further characterized by comparative genome hybridization (array CGH).


RESULTS
Novel SCN1A CNVs were found in 12.5% of DS patients where sequence-based mutations had been excluded. We identified the first partial SCN1A duplications in two siblings with typical DS and in a patient with early-onset symptomatic generalized epilepsy. In addition, a patient with DS had a partial SCN1A amplification of 5-6 copies. The remaining CNVs abnormalities were four partial and nine whole SCN1A deletions involving contiguous genes. Two CNVs (a partial SCN1A deletion and a duplication) were inherited from a parent, in whom there was mosaicism. Array CGH showed intragenic deletions of 90 kb and larger, with the largest of 9.3 Mb deleting 49 contiguous genes and extending beyond SCN1A.


CONCLUSIONS
Duplication and amplification involving SCN1A are now added to molecular mechanisms of DS patients. Our findings showed that 12.5% of DS patients who are mutation negative have MLPA-detected SCN1A CNVs with an overall frequency of about 2-3%. MLPA is the established second-line testing strategy to reliably detect all CNVs of SCN1A from the megabase range down to one exon. Large CNVs extending outside SCN1A and involving contiguous genes can be precisely characterized by array CGH.
Marini
Carla
C
Child Neurology Unit, Children's Hospital A. Meyer, University of Florence, Florence, Italy.
Scheffer
Ingrid E
IE
Nabbout
Rima
R
Mei
Davide
D
Cox
Kathy
K
Dibbens
Leanne M
LM
McMahon
Jacinta M
JM
Iona
Xenia
X
Carpintero
Rochio Sanchez
RS
Elia
Maurizio
M
Cilio
Maria Roberta
MR
Specchio
Nicola
N
Giordano
Lucio
L
Striano
Pasquale
P
Gennaro
Elena
E
Cross
J Helen
JH
Kivity
Sara
S
Neufeld
Miriam Y
MY
Afawi
Zaid
Z
Andermann
Eva
E
Keene
Daniel
D
Dulac
Olivier
O
Zara
Federico
F
Berkovic
Samuel F
SF
Guerrini
Renzo
R
Mulley
John C
JC
D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D004831:Epilepsies, Myoclonic / Q000175:diagnosis* / Q000235:genetics*; D005260:Female; D005784:Gene Amplification / Q000235:genetics; D017353:Gene Deletion; D020440:Gene Duplication; D006801:Humans; D007223:Infant; D008297:Male; D009154:Mutation / Q000235:genetics*; D062550:NAV1.1 Voltage-Gated Sodium Channel; D009419:Nerve Tissue Proteins / Q000235:genetics*; D021141:Nucleic Acid Amplification Techniques; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D015222:Sodium Channels / Q000235:genetics*; D013577:Syndrome
D062550:NAV1.1 Voltage-Gated Sodium Channel; D009419:Nerve Tissue Proteins; C568242:SCN1A protein, human; D015222:Sodium Channels