Genetic testing for the epilepsy specialist- focal or generalised?

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

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

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

4. 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)

5. Why make a diagnosis? • The George Mallory argument • Alter treatment • Clarify prognosis • Recurrence risk; prenatal diagnosis; PGD • Contribute to basic understanding of human biology

6. 4 yr old boy

7. EAST syndrome Homozygous for c.194G>C (p.Arg65Pro) mutation in KCNJ10 gene

8. No diagnosis obvious……(most cases) Hildebrand MS, et al. J Med Genet 2013 Same model applicable to intellectual disability and autism

9. Inherited Epilepsy Autosomal Dominant Autosomal Recessive X-linked (recessive or dominant) ADNFLE MECP2 CASK NEMO Glut1DS

10. Inherited Epilepsy Autosomal Dominant Autosomal Recessive X-linked (recessive or dominant) Mitochondrial MERRF ADNFLE Glut1DS POLG MECP2 CASK NEMO

11. Inherited Epilepsy ? Autosomal Dominant Autosomal Recessive X-linked (recessive or dominant) Mitochondrial MERRF ADNFLE Glut1DS POLG MECP2 CASK NEMO

12. Inherited Epilepsy De novo Autosomal Dominant Autosomal Recessive X-linked (recessive or dominant) Mitochondrial MERRF ADNFLE Glut1DS POLG MECP2 CASK NEMO Mosaic

14. Sequencing Standard Next gen Exome Genome Karyotype ArrayCGH MLPA

15. ArrayCGHvsNext Gen Sequencing

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

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

18. 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

19. 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

20. 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

21. Whole Genome Sequencing

23. Sequencing is easy………… Belly button-ome Human genome for $5000 in 15 minutes on desktop size machine

24. Courtesy: The Channelopathist @ EuroEPINOMICS

25. Courtesy: The Channelopathist @ EuroEPINOMICS

26. Courtesy: The Channelopathist @ EuroEPINOMICS

27. Courtesy: The Channelopathist @ EuroEPINOMICS

28. Nature. 2013 Sep 12;501(7466):217-21

29. Neuron 80, October 2, 2013

30. Epilepsy Gene Panels

31. ArrayCGH Nottingham Cytogenetics Lab ~1000 tests in last 5 years 335 CNVs identified

32. 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

34. 15q11.2 deletion

35. 15q13.3 deletion

36. 16p13.11 deletion

37. 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!

38. Deciphering Developmental Disorders ddd_help@sanger.ac.uk Health Innovation Challenge Fund and Sanger Institute

39. DDD Study- ~1100 results

41. Finding genes for genetic disease

42. The ‘power’ of technology…..

43. Bycatch Variants of uncertain significance, variants in more than one gene and incidental but very significant changes in other (eg cancer) genes

44. The analytical bottleneck Exome 12000 variants Genome 5000000 variants

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