Genetic testing for the epilepsy specialist- focal or generalised?

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Genetic testing for the epilepsy specialist-
focal or generalised?

• East Midlands Epilepsy Interest Group
• 11 February 2014
• Abhijit Dixit

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GENOME
3.2 Gb
Protein-coding exons of all genes Just 1 of
the genome
EXOME
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Examining genes, chromosomes, exomes and genomes
ArrayCGH 1000X resolution
Karyotype
Next-gen sequencing
Sanger sequencing
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Outline

• 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)

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Why make a diagnosis?

• The George Mallory argument
• Alter treatment
• Clarify prognosis
• Recurrence risk prenatal diagnosis PGD
• Contribute to basic understanding of human
  biology

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4 yr old boy
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EAST syndrome Homozygous for c.194GgtC
(p.Arg65Pro) mutation in KCNJ10 gene
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No diagnosis obvious(most cases)
Hildebrand MS, et al. J Med Genet 2013
Same model applicable to intellectual disability
and autism
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Inherited Epilepsy
Autosomal Dominant
Autosomal Recessive
X-linked (recessive or dominant)
ADNFLE
MECP2 CASK NEMO
Glut1DS
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Inherited Epilepsy
Autosomal Dominant
Autosomal Recessive
X-linked (recessive or dominant)
Mitochondrial
ADNFLE
Glut1DS POLG
MECP2 CASK NEMO
MERRF
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Inherited Epilepsy
?
Autosomal Dominant
Autosomal Recessive
X-linked (recessive or dominant)
Mitochondrial
ADNFLE
Glut1DS POLG
MECP2 CASK NEMO
MERRF
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Inherited Epilepsy
De novo
Autosomal Dominant
Autosomal Recessive
X-linked (recessive or dominant)
Mitochondrial
ADNFLE
Glut1DS POLG
MECP2 CASK NEMO
MERRF
Mosaic
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Sequencing Standard Next gen Exome
Genome
Karyotype ArrayCGH MLPA
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ArrayCGH vs Next Gen Sequencing
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• Ohtahara syndrome
• GNAO1, STXBP1, ARX, CASK, KCNQ2

Benign familial neonatal seizures KCNQ2 KCNQ3

Early myoclonic encephalopathy
ERBB4
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Migrating partial seizures of infancy KCNT1
West syndrome multiple
Benign familial infantile seizures PRRT2
Dravet syndrome SCN1A 
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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
Febrile seizures plus SCN1A
Childhood absence epilepsy Complex
Autosomal dominant nocturnal frontal lobe
epilepsy CHRNA4 CHRNB2 CHRNA2
Early onset benign childhood occipital epilepsy
(Panayiotopoulos type) Complex
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Autosomal dominant partial epilepsy with auditory
features (ADPEAF) LGI1
Juvenile absence epilepsy Juvenile myoclonic
epilepsy Complex
Progressive myoclonic epilepsies Unverricht-Lundbo
rg disease CSTB, PRIKLE1, SCARB2 Lafora
disease EPM2A EPM2B Others- NCL
Familial partial epilepsy with variable foci
DEPDC5
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Heterogeneity in etiology of epilepsy

• IGE show complex inheritance
• IGELD 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

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Whole Genome Sequencing
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Sequencing is easy
Belly button-ome
Human genome for 5000 in 15 minutes on desktop
size machine
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Courtesy The Channelopathist _at_ EuroEPINOMICS
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Courtesy The Channelopathist _at_ EuroEPINOMICS
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Courtesy The Channelopathist _at_ EuroEPINOMICS
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Courtesy The Channelopathist _at_ EuroEPINOMICS
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Nature. 2013 Sep 12501(7466)217-21
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Neuron 80, October 2, 2013
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Epilepsy Gene Panels
No of genes No of patients Pick-up Reference
1 65 500 10 Carvill et al Nat Genetics 2013
2 265 33 48 Lemke et al Epilepsia 2012
No of genes Cost Pick-up Laboratory
1 45 1200 15 Great Ormond St, London
2 31 1000 ? Cardiff
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ArrayCGH

• Nottingham Cytogenetics Lab 1000 tests in last 5
  years
• 335 CNVs identified

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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

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15q11.2 deletion
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15q13.3 deletion
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16p13.11 deletion
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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!

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Deciphering Developmental Disorders
ddd_help_at_sanger.ac.uk
Health Innovation Challenge Fund and Sanger
Institute
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DDD Study- 1100 results
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Finding genes for genetic disease
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The power of technology..
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Bycatch
Variants of uncertain significance, variants in
more than one gene and incidental but very
significant changes in other (eg cancer) genes
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The analytical bottleneck

• Exome
• 12000 variants
• Genome
• 5000000 variants

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Referral to clinical genetics

• Syndromic presentations
• Complex result on NGS panel or arrayCGH
• Recruitment to DDD study
• Testing unaffected parents or siblings

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