Genetic testing for the epilepsy specialist- focal or generalised? East Midlands Epilepsy Interest Group 11 February 2014 Abhijit Dixit

GENOME EXOME Protein-coding ‘exons’ of all genes Just 1% of the genome 3.2 Gb

Examining genes, chromosomes, exomes and genomes ArrayCGH 1000X resolution Karyotype Sanger sequencing Next-gen sequencing

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)

Why make a diagnosis? 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 X-linked (recessive or dominant) Autosomal Recessive ADNFLE Glut1DS MECP2 CASK NEMO

Inherited Epilepsy Autosomal Dominant X-linked (recessive or dominant) Autosomal Recessive Mitochondrial ADNFLEGlut1DS POLG MECP2 CASK NEMO MERRF

Inherited Epilepsy Autosomal Dominant X-linked (recessive or dominant) Autosomal Recessive Mitochondrial ADNFLEGlut1DS POLG MECP2 CASK NEMO MERRF ?

Inherited Epilepsy Autosomal Dominant X-linked (recessive or dominant) Autosomal Recessive Mitochondrial ADNFLEGlut1DS POLG MECP2 CASK NEMO MERRF De novo Mosaic

Karyotype ArrayCGH MLPA Sequencing Standard Next gen Exome Genome

ArrayCGH vs Next Gen Sequencing

Benign familial neonatal seizures KCNQ2; KCNQ3 Early myoclonic encephalopathy ERBB4 Ohtahara syndrome GNAO1, STXBP1, ARX, CASK, KCNQ2

West syndrome multiple Migrating partial seizures of infancy KCNT1 Benign familial infantile seizures PRRT2 Dravet syndrome SCN1A

Early onset benign childhood occipital epilepsy (Panayiotopoulos type) Complex Febrile seizures plus SCN1A EE with continuous spike-and-wave during sleep (CSWS) Landau-Kleffner syndrome (LKS) GRIN2A Lennox- Gastaut syndrome Multiple Autosomal dominant nocturnal frontal lobe epilepsy CHRNA4; CHRNB2; CHRNA2 Benign epilepsy with centro-temporal spikes GRIN2A Childhood absence epilepsy Complex

Progressive myoclonic epilepsies Unverricht-Lundborg disease CSTB, PRIKLE1, SCARB2 Lafora disease EPM2A; EPM2B Others- NCL Familial partial epilepsy with variable foci DEPDC5 Autosomal dominant partial epilepsy with auditory features (ADPEAF) LGI1 Juvenile absence epilepsy Juvenile myoclonic epilepsy Complex

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………… Human genome for $5000 in 15 minutes on desktop size machine Belly button-ome

Courtesy: The EuroEPINOMICS

Nature Sep 12;501(7466):217-21

Neuron 80, October 2, 2013

Epilepsy Gene Panels No of genes No of patients Pick-upReference % Carvill et al Nat Genetics % Lemke et al Epilepsia 2012 No of genes CostPick-upLaboratory 145£1200~15% Great Ormond St, London 231~£1000? 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 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 – variants Genome – variants

Referral to clinical genetics ‘Syndromic’ presentations Complex result on NGS panel or arrayCGH Recruitment to DDD study Testing unaffected parents or siblings