Improving molecular diagnosis in epilepsy by a dedicated high-throughput sequencing platform.
We analyzed by next-generation sequencing (NGS) 67 epilepsy genes in 19 patients with different types of either isolated or syndromic epileptic disorders and in 15 controls to investigate whether a quick and cheap molecular diagnosis could be provided. The average number of nonsynonymous and splice site mutations per subject was similar in the two cohorts indicating that, even with relatively small targeted platforms, finding the disease gene is not an univocal process. Our diagnostic yield was 47% with nine cases in which we identified a very likely causative mutation. In most of them no interpretation would have been possible in absence of detailed phenotype and familial information. Seven out of 19 patients had a phenotype suggesting the involvement of a specific gene. Disease-causing mutations were found in six of these cases. Among the remaining patients, we could find a probably causative mutation only in three. None of the genes affected in the latter cases had been suspected a priori. Our protocol requires 8-10 weeks including the investigation of the parents with a cost per patient comparable to sequencing of 1-2 medium-to-large-sized genes by conventional techniques. The platform we used, although providing much less information than whole-exome or whole-genome sequencing, has the advantage that can also be run on 'benchtop' sequencers combining rapid turnaround times with higher manageability.
Department Molecular Medicine, University of Pavia, Pavia, Italy.
Erika
E
Della Mina
Department Molecular Medicine, University of Pavia, Pavia, Italy.
Roberto
0000000213086646
R
Ciccone
National Neurological Institute C. Mondino, Pavia, Italy.
Francesca
F
Brustia
Department Molecular Medicine, University of Pavia, Pavia, Italy.
Baran
B
Bayindir
National Neurological Institute C. Mondino, Pavia, Italy.
Ivan
0000000297812974
I
Limongelli
Department Molecular Medicine, University of Pavia, Pavia, Italy.
Annalisa
A
Vetro
USSD Medical Genetics Laboratory of Ospedali Riuniti, Bergamo, Italy.
Maria
M
Iascone
USSD Medical Genetics Laboratory of Ospedali Riuniti, Bergamo, Italy.
Laura
L
Pezzoli
1] Department of Industrial and Information Engineering, University of Pavia, Pavia, Italy [2] IRCCS Foundation Salvatore Maugeri, Pavia, Italy.
Riccardo
R
Bellazzi
IRCCS Foundation Policlinico San Matteo, Pavia, Italy.
Gianfranco
G
Perotti
National Neurological Institute C. Mondino, Pavia, Italy.
Valentina
V
De Giorgis
National Neurological Institute C. Mondino, Pavia, Italy.
Simona
S
Lunghi
Child and Adolescent Neuropsychiatry, Medical School, University of Salerno, Salerno, Italy.
Giangennaro
G
Coppola
National Neurological Institute C. Mondino, Pavia, Italy.
Simona
S
Orcesi
IRCCS Foundation Policlinico San Matteo, Pavia, Italy.
Pietro
P
Merli
IRCCS Foundation Policlinico San Matteo, Pavia, Italy.
Salvatore
S
Savasta
National Neurological Institute C. Mondino, Pavia, Italy.
Pierangelo
P
Veggiotti
1] Department Molecular Medicine, University of Pavia, Pavia, Italy [2] National Neurological Institute C. Mondino, Pavia, Italy.
Orsetta
O
Zuffardi
D000293:Adolescent; D000328:Adult; D016022:Case-Control Studies; D002648:Child; D002675:Child, Preschool; D019295:Computational Biology; D004827:Epilepsy / Q000175:diagnosis* / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D056726:Genetic Association Studies; D005820:Genetic Testing; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D009154:Mutation; D057188:Workflow; D055815:Young Adult