Genetic testing for the epilepsy specialist- focal or generalised?
description
Transcript of Genetic testing for the epilepsy specialist- focal or generalised?
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 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