Genetic testing for the epilepsy
specialist- focal or generalised?
East Midlands Epilepsy Interest Group
11 February 2014
Abhijit Dixit
GENOME
3.2 Gb
EXOME
Protein-coding ‘exons’ of all genes
Just 1% of the genome
Examining genes, chromosomes, exomes and
genomes
Karyotype
Sanger sequencing
ArrayCGH
1000X resolution
Next-gen sequencing
Outline
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Why?
Types (new) of inheritance in epilepsy
New genes
Emerging landscape of epilepsy genetics
Role of next generation sequencing
– Multi-gene panels
– Exome and genome sequencing
• Changing role of the genetics service (and neurology)
Why make a diagnosis?
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The George Mallory argument
Alter treatment
Clarify prognosis
Recurrence risk; prenatal diagnosis; PGD
• Contribute to basic understanding of human
biology
4 yr old boy
EAST syndrome
Homozygous for c.194G>C (p.Arg65Pro) mutation in KCNJ10 gene
No diagnosis obvious……(most cases)
Hildebrand MS, et al. J Med Genet 2013
Same model applicable to intellectual disability and autism
Inherited Epilepsy
Autosomal
Dominant
Autosomal
Recessive
ADNFLE
Glut1DS
X-linked
(recessive or dominant)
MECP2
CASK
NEMO
Inherited Epilepsy
Autosomal
Dominant
Autosomal
Recessive
ADNFLE
Glut1DS
POLG
X-linked
(recessive or dominant)
MECP2
CASK
NEMO
Mitochondrial
MERRF
Inherited Epilepsy
?
Autosomal
Dominant
Autosomal
Recessive
ADNFLE
Glut1DS
POLG
X-linked
(recessive or dominant)
MECP2
CASK
NEMO
Mitochondrial
MERRF
Inherited Epilepsy
De novo
Autosomal
Dominant
Autosomal
Recessive
ADNFLE
Glut1DS
POLG
X-linked
(recessive or dominant)
MECP2
CASK
NEMO
Mosaic
Mitochondrial
MERRF
Sequencing
Standard
Next gen
Exome
Genome
Karyotype
ArrayCGH
MLPA
ArrayCGH vs Next Gen Sequencing
Ohtahara syndrome
GNAO1, STXBP1, ARX, CASK, KCNQ2
Benign familial neonatal seizures
KCNQ2; KCNQ3
Early myoclonic encephalopathy
ERBB4
Migrating partial seizures of infancy
KCNT1
West syndrome
multiple
Dravet syndrome
SCN1A
Benign familial infantile seizures
PRRT2
EE with continuous spike-and-wave
during sleep (CSWS)
Landau-Kleffner syndrome (LKS)
GRIN2A
Lennox- Gastaut syndrome
Multiple
Benign epilepsy with centro-temporal
spikes GRIN2A
Childhood absence epilepsy
Complex
Autosomal dominant nocturnal
frontal lobe epilepsy
CHRNA4; CHRNB2; CHRNA2
Febrile seizures plus
SCN1A
Early onset benign childhood occipital
epilepsy (Panayiotopoulos type)
Complex
Juvenile absence epilepsy
Juvenile myoclonic epilepsy
Complex
Autosomal dominant partial epilepsy
with auditory features (ADPEAF)
LGI1
Progressive myoclonic epilepsies
Unverricht-Lundborg disease
CSTB, PRIKLE1, SCARB2
Lafora disease
EPM2A; EPM2B
Others- NCL
Familial partial epilepsy with variable foci
DEPDC5
Heterogeneity in etiology of epilepsy
• IGE show complex inheritance
– IGE+LD has ~10% yield on arrayCGH
• Few EE have single gene for majority of cases
– Dravet/SCN1A (~80%) and MPSI/KCNT1 (~50%)
– Lesser extent CSWS-LKS/GRIN2A (~20%)
• Most EE (West/LGS) very heterogeneous
– Multiple genes each accounting for ~1%
• Same gene can appear in EE and ‘benign’ lists
Whole Genome Sequencing
Sequencing is easy…………
Belly button-ome
Human genome for $5000 in 15 minutes on desktop size machine
Courtesy: The Channelopathist @ EuroEPINOMICS
Courtesy: The Channelopathist @ EuroEPINOMICS
Courtesy: The Channelopathist @ EuroEPINOMICS
Courtesy: The Channelopathist @ EuroEPINOMICS
Nature. 2013 Sep 12;501(7466):217-21
Neuron 80, October 2, 2013
Epilepsy Gene Panels
No of
genes
Pick-up
Reference
1 65 500
10%
Carvill et al Nat Genetics 2013
2 265 33
48%
Lemke et al Epilepsia 2012
Cost
Pick-up
Laboratory
1 45
£1200
~15%
Great Ormond St, London
2 31
~£1000
?
No of
genes
No of
patients
Cardiff
ArrayCGH
• Nottingham Cytogenetics Lab ~1000 tests in last 5 years
– 335 CNVs identified
ArrayCGH
• Pick-up depends on resolution of arrayCGH
– Pathogenic CNV
• 1q21.1, 15q11.2, 15q13.3, 16p11.2, 16p13.11, 17q12, 22q11.2
• Other ‘large’ deletions/duplications esp if de novo
– Possibly pathogenic
– Variant of unknown significance
– Benign
• 69/335 Nottingham arrayCGH are above common CNVs
15q11.2 deletion
15q13.3 deletion
16p13.11 deletion
Genetic testing in epilepsy
• All patients with GGE plus learning difficulties
– ArrayCGH
– Consider testing on suitable NGS panel
• All patients with ‘epileptic encephalopathy’
– NGS panel
– Single gene targeted test in Dravet, MPSI or
epilepsy-aphasia syndromes….may only be
available as part of panel!
Deciphering Developmental Disorders
ddd_help@sanger.ac.uk
Health Innovation Challenge Fund and Sanger Institute
DDD Study- ~1100 results
Finding genes for genetic disease
The ‘power’ of technology…..
Bycatch
Variants of uncertain significance, variants in more than one gene and
incidental but very significant changes in other (eg cancer) genes
The analytical bottleneck
• Exome
– 12000 variants
• Genome
– 5000000 variants
Referral to clinical genetics
• ‘Syndromic’ presentations
• Complex result on NGS
panel or arrayCGH
• Recruitment to DDD study
• Testing unaffected parents
or siblings