Genetic testing for the epilepsy specialist- focal or generalised?

East Midlands Epilepsy Interest Group11 February 2014

Abhijit Dixit

GENOME

EXOME Protein-coding ‘exons’ of all genesJust 1% of the genome

3.2 Gb

Examining genes, chromosomes, exomes and genomes

ArrayCGH1000X resolutionKaryotype

Sanger sequencingNext-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 syndromeHomozygous 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

AutosomalDominant

X-linked(recessive or dominant)

AutosomalRecessive

ADNFLE Glut1DS MECP2CASKNEMO

Inherited Epilepsy

AutosomalDominant

X-linked(recessive or dominant)

AutosomalRecessive

Mitochondrial

ADNFLE Glut1DSPOLG

MECP2CASKNEMO

MERRF

Inherited Epilepsy

AutosomalDominant

X-linked(recessive or dominant)

AutosomalRecessive

Mitochondrial

ADNFLE Glut1DSPOLG

MECP2CASKNEMO

MERRF

?

Inherited Epilepsy

AutosomalDominant

X-linked(recessive or dominant)

AutosomalRecessive

Mitochondrial

ADNFLE Glut1DSPOLG

MECP2CASKNEMO

MERRF

De novo

Mosaic

KaryotypeArrayCGH

MLPA

Sequencing Standard Next gen Exome Genome

ArrayCGH vs Next Gen Sequencing

Benign familial neonatal seizures KCNQ2; KCNQ3

Early myoclonic encephalopathy ERBB4

Ohtahara syndromeGNAO1, STXBP1, ARX, CASK, KCNQ2

West syndromemultiple

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 plusSCN1A

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 epilepsyComplex

Progressive myoclonic epilepsiesUnverricht-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 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 PanelsNo 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

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_help@sanger.ac.uk

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