APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019
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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019
NOT FOR DUPLICATION OR DISTRIBUTION
APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019
About this Enduring Webinar
• These slides are from a live webinar held on 14 November 2019 with Professor Nicola Specchio and Dr Raman Sankar
• Videos are not live in this presentation, and some patient images have been removed for privacy purposes. Images which were once videos will have this symbol
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Faculty
3
Nicola Specchio, MD, PhDHead of the Epilepsy Unit,
Department of Neuroscience Bambino Gesú Children’s Hospital
Rome, Italy
Raman Sankar, MD, PhDProfessor of Neurology and Pediatrics and Chief of
Pediatric NeurologyDavid Geffen School of Medicine at UCLA
Los Angeles, CA, USA
3
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Faculty disclosures
Nicola Specchio, MD, PhD• Consultant: BioMarin Pharmaceutical Inc• Grant / Research support: BioMarin Pharmaceutical Inc
Raman Sankar, MD, PhD• Consulting fee, travel support and honoraria from BioMarin Pharmaceutical Inc
All photos are used with family permission
4
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Learning objectives
• Understand benefits of early genetic testing in understanding seizure etiology in pediatric epilepsy patients
• Recognize how genetic research is rapidly advancing our understanding of the underlying causes of epilepsy
• Understand the benefits of epilepsy gene panels in pediatric epilepsy patients to potentially uncover disorders, like CLN2 disease, earlier in the course of the disease
• Understand the urgency to provide a definitive diagnosis to patients, which may enable more precise clinical management and improve patient outcomes
5
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Webinar Agenda
Topic Presenter
Welcome & Introductions Nicola Specchio
Epilepsy and Genetics Raman Sankar
CLN2 Disease and the Need for Early Diagnosis Nicola Specchio
Genetic Testing and Actionability of Results Raman Sankar
Case Study Nicola Specchio
Interactive Q&A Session
6
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CLN2 Disease
Genetic Testing &
Actionability of Results
Epilepsy and
GeneticsCase Study
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Advances In Understanding The Causes of EpilepsyNew research demonstrates increasing genetic basis
8
1. Hauser WA, Kurland LT. Epilepsia. 1975;16:1–66; 2. Thomas RH, Berkovic SF. Nat Rev Neurol. 2014;10:283–292.
19751
Idiopathic
Trauma
Vascular
NeoplasmInfectious
Congenital lesionsBirth anoxia
Other
2014 paradigm2
Epilepsies with complex
inheritance
Single-gene epilepsies: Familial,
de novo
Modifiers and susceptibility
alleles
Trauma
Vascular
NeoplasmInfectious
Congenital lesionsBirth anoxia
Other
Autoimmune Focal epilepsy with MRI-detectable lesions
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The History Of Gene Identifications In Epilepsy Research
9
CLN3TPP1
NGS demonstrates the spectrum of phenotypes associated with
genetic epilepsiesCHRNA4 SCN1B
SCN1AGABRG2
Microdeletions
KCNQ2KCNQ3
SLC2A1
GABRA1 LGI1
ARX
CACNA1H
CDKL5
15q13.316p13.1115q11.2
STX1BSLC6A1
GABRA1GABRB3
SIK1KCNA2
ALG13GRIN2B
PURAKCNB1
KCNC1DNM1
HCN1CHD2
SCN2AGRIN2A
DEPDC5KCNT1
PRRT2TBC1D24
STXBP1PCDH19
SCN8A
Channelopathy era Next-generation sequencingDark ages
2011200920072005 2013 2015 2017 201820032001199919971995
TPP1: tripeptidyl peptidase 1.Adapted from: Helbig I et al. Epilepsia. 2016;57:861–868; Sleat DE et al. Science. 1997;277:1802–1805; The International Batten Disease Consortium. Cell. 1995; 82:949–957; Trump N et al. J Med Genet. 2016;53:310–317.
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The Era of Targeted Therapy for Genetic Epilepsy
10
Potential for disease-specific management:targeted therapy or clinical trial
Initial empirical AED treatmentno underlying cause yet identified
Genetic assessment: epilepsy gene panel
Old paradigmStepwise approach
Emerging paradigmDirect, accurate, cost-effective
Genetic assessment: chromosomal microarray
AEDFailure
Genetic assessment: epilepsy gene panel
UNINFORMATIVE
Patient withunexplained epilepsy
EpiPM Consortium. Lancet Neurol. 2015;14:1219–1228; Helbig K. A Clinician’s Guide to Genetic Test Selection: Navigating the Wild West. Epilepsygenetics.com. http://epilepsygenetics.net/2016/10/16/a-clinicians-guide-to-genetic-test-selection-navigating-the-wild-west (accessed January 18, 2018).
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Reasons For Considering Genetic Testing
11
Genetic testing
Berkovic SF. Epilepsy Curr. 2015;15:192–196.
Genetic testingGenetic
testing
Can impact clinical management e.g. choice of AED1
May avoid unnecessary testing2
Shortens the diagnostic journey for families3
Allows for specific counseling (family planning)4
Opportunity to participate in a clinical study5
Can allow for targeted therapy: precision medicine6
Connect families with each other and advocacy groups7NOT FOR DUPLICATION OR DISTRIBUTION
CLN2 Disease
Genetic Testing &
Actionability of Results
Epilepsy and
GeneticsCase Study
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Features of CLN2 disease
0–1 years• Normal early development1–2 years• May have slow language development2–3 years• Seizures, often polymorphic • Poor mobility• Hospital admissions (seizures)• Increasing medical and developmental
concerns• Referral for diagnostic investigations
3–4 years• Seizures often more troublesome• Developmental stasis• Worsening of mobility and fine motor
skills4–5 years• Further loss of skills• Sleep disorder• Pain and irritability• Increasingly dependent for activities of
daily living
13
CLN2: late-infantile neuronal ceroid lipofuscinosis (NCL) or NCL type 2.
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Late stage may be prolonged
>6 years• Gastrostomy dependent• Unsafe swallowing• Loss of communication• Loss of voluntary movement• Chest infections• Ongoing seizures• Myoclonic status• Spasticity and joint contractures• Spinal scoliosis
14
Retain some understanding and
personality
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Clinical presentation: Classical late infantile CLN2 disease
Do NOT wait for vision loss to diagnose CLN2
Birth 1 2 3 4 5 6 7 8 9 10 11 12
•Seizures
•Psychomotor d
ecline
•Bedridden
•Blindness •Death
•Ataxia
Age (yr)
• Language delay
15
All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019
Clinical presentation: Classical late infantile CLN2 disease
Do NOT wait for vision loss to diagnose CLN2
3 yr old
16
All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
Birth 1 2 3 4 5 6 7 8 9 10 11 12
•Seizures
•Psychomotor d
ecline
•Bedridden
•Blindness •Death
•Ataxia
Age (yr)
• Language delay
Video showing CLN2 patient at 3 years old, who was experiencing some epileptic seizures. This video shows motor development that is still normal
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Clinical presentation: Classical late infantile CLN2 disease
Do NOT wait for vision loss to diagnose CLN2
4 yr old
17
All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
3 yr old
Birth 1 2 3 4 5 6 7 8 9 10 11 12
•Seizures
•Psychomotor d
ecline
•Bedridden
•Blindness •Death
•Ataxia
Age (yr)
• Language delay
The same patient after 1 year, who is starting to present with ataxia and other movement disorders
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Clinical presentation: Classical late infantile CLN2 disease
Do NOT wait for vision loss to diagnose CLN2
5 yr, 7 mo old
18
All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
4 yr old3 yr old
Birth 1 2 3 4 5 6 7 8 9 10 11 12
•Seizures
•Psychomotor d
ecline
•Bedridden
•Blindness •Death
•Ataxia
Age (yr)
• Language delay
The same patient had a very quick progression of disease – soon suffering continuous myoclonic jerks, is bedridden and almost blind
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Clinical scoring for disease severity in late infantile NCL (CLN2): Hamburg scale
Functional categories
Motor function
Language
Visual function
Seizures
Each functional category is scored from 0-3
Normal function = SCORE 3
Slightly abnormal = SCORE 2
Severely abnormal = SCORE 1
No function left = SCORE 0
19NCL, neuronal ceroid lipofuscinoses.Steinfeld R et al. Am J Med Genet. 2002;112:347–354.
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(Clinical score)
Sum of MOTORand LANGUAGE
Normal = 3Abnormal = 2Poor = 1No function = 0
(Maximum = 6)
Rapid and predictable neurodegeneration demonstrated by the CLN2 Clinical Rating Scale (N=58)1
CLN2 disease natural history: DEM-CHILD NCL database
20
1. Schulz A. Presented at the 14th International Child Neurology Congress (ICNC); Amsterdam, the Netherlands: May 1 - 5, 2016.
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Classical late infantile CLN2 disease: natural history
2-yr delay
Mean95% CI
2-yrs delay
Rate of decline2.1 units/yr
21CI: confidence intervalFigure adapted from: Nickel M, et al. Presented as poster at the 12th Annual WORLDSymposium; February-March 2016; San Diego, CA, USA. All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
3 yrs old: Average age at 1st seizure
5 yrs old: Average age at diagnosis
Sum
of t
he m
otor
and
lang
uage
scor
e
Age (years)NOT FOR DUPLICATION OR DISTRIBUTION
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Delayed diagnosis
• There is a 1- to 4-year delay in achieving an appropriate diagnosis after symptoms have begun to appear•Given the irreparable damage to the brain, early identification is crucial– To improve management, information for families and family planning– To implement disease-specific management options
22
6 yrs 6 yrs 8 mo 7 yrs 6 mo3 yrs 4 yrs 5 yrs 4 mo
All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
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Clinical diagnosis of CLN2 Disease
• Developmental history• Seizure history• Examination findings• Initial investigations may provide an
indication– Normal basic “screen”– Brain MRI – disproportionate cerebellar atrophy– EEG – abnormal response to slow rate intermittent
photic stimulation (IPS)
23EEG, electroencephalography; MRI, magnetic resonance imaging.Image from Dr. Specchio, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy.
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Clues leading to clinical suspicion: MRI findings
• Brain MRI at the age of 3.8 (3.0–5.1) yrs revealed cerebellar atrophy in 100% (14 of 14) of patients
• Alteration of the periventricular white matter signal in the posterior hemispheric region was observed in 79% (11 of 14) patients
24
Specchio N, et al. Epilepsia. 2017;58:1380–1388.
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Clues leading to clinical suspicion: EEG findings
• Median delay of 1st IPS from 1st EEG was 4 months (range: 0-23 months)• EEG revealed PPR in 13 out of 14 cases;
PPR from the 1st EEG was seen in 43% of patients• PPR was documented at low frequencies in
9 out of 13 cases with flash-per-flash response evident• Median delay from 1st EEG with IPS and
1st PPR observation was 1.2 months(range: 1.2-16.8 months)
25
Early photosensitivity is a hallmark of CLN2 disease, with PPR typically evident at low frequencies.When it occurs in subjects with seizures and speech delay and/or ataxia,
CLN2 disease should be considered
First EEGFirst IPSFirst PPR
Specchio N, et al. Epilepsia. 2017;58:1380–1388.
Age (years)
Cum
ulat
ive
surv
ival
(%)
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Suspicion of NCL disorder• Neuronal ceroid lipofuscinosis (NCL)
gene panel• TPP1/PPT1 enzyme activity
screening tests†
Suspicion of genetic basisof epilepsy• Symptom- or disease-based gene
panel (e.g. epilepsy gene panel)
CLN2 diseasediagnosis confirmed
Diagnostic for CLN2 disease• Deficient TPP1 enzyme
activity in leukocytes‡
• 2 pathogenic mutations in each allele of TPP1 gene§
Suspicion of CLN2 disease• TPP1 enzyme activity test†
• TPP1 molecular test
Presentation of epilepsy• EEG with low frequency IPS (1-2 Hz)*
*Absence of EEG findings should not preclude follow-on testing for epilepsy syndromes, CLN2 disease or other NCLs
Diagnosing patients along the disease continuum; Genetic testing allows for early diagnosis, prior to disease progression
26
*Additional clinical assessments may be warranted, such as brain MRI, OCT/VEP/ERG/FA, EM biopsy; †TPP1 enzyme activity may be measured in sample types such as dried blood spots or saliva. PPT1 enzyme activity (CLN1 disease) is useful to assess with TPP1; ‡TPP1 enzyme activity testing in other sample types can also be diagnostic (see Table 2); §Includes single gene sequencing, gene panels, or whole exome sequencing.Adapted from Fietz et al. Mol Genet Metab. 2016;119:160–167.
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Suspicion of NCL disorder• Neuronal ceroid lipofuscinosis (NCL)
gene panel• TPP1/PPT1 enzyme activity
screening tests†
Suspicion of genetic basisof epilepsy• Symptom- or disease-based gene
panel (e.g. epilepsy gene panel)
Diagnosing patients along the disease continuum; Genetic testing allows for early diagnosis, prior to disease progression
27
*Additional clinical assessments may be warranted, such as brain MRI, OCT/VEP/ERG/FA, EM biopsy; †TPP1 enzyme activity may be measured in sample types such as dried blood spots or saliva. PPT1 enzyme activity (CLN1 disease) is useful to assess with TPP1; ‡TPP1 enzyme activity testing in other sample types can also be diagnostic (see Table 2); §Includes single gene sequencing, gene panels, or whole exome sequencing.Adapted from Fietz et al. Mol Genet Metab. 2016;119:160–167.
Disease progression
Suspicion of CLN2 disease• TPP1 enzyme activity test†
• TPP1 molecular test
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Age of onset of various epileptic encephalopathies and CLN2 Disease
Age of onset years
Different epilepsy syndromes may be considered in young children presenting with new-onset of seizures at late infantile age
ESES/LKS, electrical status epilepticus in sleep/Landau-Kleffner syndrome; FIRES, febrile infection-related epilepsy syndrome; ABPE, atypical benign partial epilepsy; MPSI, migrating partial seizures of infancy.Adapted from Helbig I and Tayoun A. Mol Syndromol., 2016;(4):172-181.
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Early Diagnosis is Critical for Timely Disease-Specific Management
29
Genetic testing
Berkovic SF. Epilepsy Curr. 2015;15:192–196.
Genetic testingGenetic
testing
Can impact clinical management e.g. choice of AED1
May avoid unnecessary testing2
Shortens the diagnostic journey for families3
Allows for specific counseling (family planning)4
Opportunity to participate in a clinical study5
Can allow for targeted therapy: precision medicine6
Rapid progression after age ± 3 yrs (CLN2-specific) 7NOT FOR DUPLICATION OR DISTRIBUTION
APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019EEG: Specchio N, et al. Presented at the ICNC Symposium, May 2016, Amsterdam, Netherlands; MRI: Image from Dr. Specchio, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy.
Summary
Earlierdiagnosis
Involve the parents:
Is there a delay in language
development
Request an enzymatic test or
a disease/symptom-based gene panel
which includes the TPP1/CLN2 gene
Perform an EEG with IPS at low frequency (1Hz):
Look for PPR
Request an MRI:Atrophy of the cerebellum
and cortex & occasional white matter anomalies in periventricular areas may
point to CLN2 disease
30
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CLN2 Disease
Genetic Testing &
Actionability of Results
Epilepsy and
GeneticsCase Study
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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019
Which Genetic Testing Tools Should You Use?Types and benefits of various genetic testing tools
Chromosomal microarray Gene panels Whole exome sequencing
What is it?Detects duplications and deletions1 Test a wide set of epilepsy-associated
genes;1 number of genes tested may vary (<20 to up to 554)5
Comprehensive testing, simultaneously sequences coding regions of all known genes1
UtilityUsed for pts with epilepsy and developmental delay1,2,3
No specific-disease suspicion needed,efficiently tests for many conditions fitting a clinical phenotype6
Sequencing of exons, beyond known epilepsy associated genes
Yield Low diagnostic yield (~5%)1 High diagnostic yield (up to ~50%4) High diagnostic yield (17%–72%6)
Pros
• Broad insurance coverage • Efficient way to reach an early molecular diagnosis1
• Consistent, reliable, effective & automated• May include deletions, duplications1
• May identify new etiologies for epilepsy-related genes6
• Re-analysis is possible, as more genes discovered
Cons
• Not inclusive of exon level analysis3 • Detection of most variants/interpretation of VUS
• Historic (improving)– Cost – Turn-around time (2–6 weeks)
• Access/availability
• Detection of most variants/interpretation of VUS– Larger deletions/duplications not
usually detected1
• Comparatively higher cost• Turnaround time (8–12 weeks)• Limited insurance coverage
VUS, variant of unknown significance.1. Helbig K. A Clinician’s Guide to Genetic Test Selection: Navigating the Wild West. http://epilepsygenetics.net/2016/10/16/a-clinicians-guide-to-genetic-test-selection-navigating-the-wild-west/ (accessed January 18, 2018). 2. Miller DT et al. Am J Hum Genet. 2010;86(5):749–764. 3. Trakadis Y and Shevell M. Dev Med Child Neurol. 2011;53:994–999. 4. Tucker T et al. Eur J Human Genet. 2014;22:792–800; 5. MNG Laboratories. Improved epilepsy panel portfolio. https://mnglabs.com/improved-epilepsy-panel-portfolio (accessed May 8, 2018). 6. Mei D et al. Mol Diagn Therap. 2017;21:357–373.
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Benefits of Gene Panels: UtilityIncrease understanding of genetic heterogeneity
Many epilepsy syndromes reveal genetic heterogeneity1
33
Phenotype Implicated Genes
Autosomal dominant nocturnal frontal lobe epilepsy DEPDC5, KCNT12
Benign familial neonatal epilepsy KCNQ2,1 KCNQ3,1 SCN2A2
Early infantile epileptic encephalopathy KCNT1, SCN2A, STXBP12
Epilepsy of infancy with migrating focal seizures KCNT1, SCN2A, SNC8A2
Early-onset epileptic encephalopathy SCN2A, STXBP12
West syndrome FOXG1, GRIN2A, GRIN2B, KCNT1, MEF2C, SCN2A, SCN8A, ARX, CDKL52
Gene panels can help elucidate the genetic heterogeneity associated with epilepsy phenotypes
1. Scheffer IE et al. Epilepsia. 2017;58:512–521; 2. Mei D et al. Mol Diagn Therap. 2017;21:357–373.
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Benefits of Gene Panels: UtilityAssist in characterizing phenotypic heterogeneity
Many variants are found in cases where the phenotype is either not easily distinguishable from that caused by a number of other genes or is atypical for the previously reported phenotype(s)1– In only 15% of cases, physicians correctly identified the mutated gene, prior to genetic testing1
Pathogenic variants in a specific gene can manifest in a spectrum comprising both severe and mild spectrum comprising both severe and mild epilepsies2
• SCN2A– Initially associated with BFNIS3
– Subsequently associated with EIMFS and other less well delineated forms of epileptic encephalopathy3
• KCNQ2– Initially associated with BFNS3
– Subsequently associated with early-onset epileptic encephalopathy3
34
BFNIS, benign familial neonatal-infantile seizures; BFNS, benign familial neonatal seizures; EIMFS, epilepsy with migrating focal seizures in infancy.1. Trump N et al. J Med Genet. 2016;53:310–317; 2. Scheffer IE et al. Epilepsia. 2017;58:512–521; 3. Mei D et al. Mol Diagn Therap. 2017;21:357–373.
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STXBP1 encephalopathyA neurodevelopmental disorder including epilepsy
53%
21%
1%
10%
2%
7%
6%
Spectrum of STXBP1-associated phenotypes
EOEE
OS
EME
West
Dravet
ID, no epilepsy
NSE + IDOS
35
Stamberger H et al. Neurology. 2016;86(10):954-962.
EOEE
West
Example of Extreme Phenotypic Pleiotropy
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Benefits of Gene Panels: No Disease-Specific Suspicion NeededSimultaneously detect both common and rare seizure disorders
36
56 genes with <10 pts diagnosed
A total of 67 pathogenic genes were identified in 348 patients
0
10
20
30
40
50
60
70
SCN1A
SCN2A
STXB
P1CD
KL5
KCNQ2
SCN8A
CHD2
SYNGA
P1PC
DH19
KCNT1
MEC
P2FO
XG1
GABR
B3MEF2C
UBE
3AGA
BRA2
PNPO
TCF4
GABR
A1GN
AO1
HNRN
PUIQSEC2
KCNB1
PNKP
PRRT
2SLC2
A1SPTA
N1
ATP1
A3CA
SJGR
IN1
GRIN2A
HCN1
KCNA2
KCNJ10
MBD
5PIGA
POLG
SLC2
5A22
SLC9
A6 TPP1
ALDH
7A1
ARHG
EF9
ARX
ATP1
A2CA
CNA1
ACN
TNAP
2CP
A6 DCX
DEPD
C5DL
G3EEF1A2
EHMT1
FARS2
GPHN
KCNA1
KCNQ3
KCTD
7LG
I1MFSD8
PDHA
1SLC1
3A5
SLC9
A6SM
SSTX1
BTB
C1D2
4WDR
45ZEB2
11 genes with ≥10 pts
diagnosed
Many pts present with few genetic diagnoses
Few pts present with many distinct genetic diagnoses
Mei D et al. Mol Diagn Ther. 2017;21:357–373.
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Benefits of Gene Panels: No Disease-Specific Suspicion NeededSimultaneously detect both common and rare seizure disorders
37
56 genes with <10 pts diagnosed
A total of 67 pathogenic genes were identified in 348 patients
0
10
20
30
40
50
60
70
SCN1A
SCN2A
STXB
P1CD
KL5
KCNQ2
SCN8A
CHD2
SYNGA
P1PC
DH19
KCNT1
MEC
P2FO
XG1
GABR
B3MEF2C
UBE
3AGA
BRA2
PNPO
TCF4
GABR
A1GN
AO1
HNRN
PUIQSEC2
KCNB1
PNKP
PRRT
2SLC2
A1SPTA
N1
ATP1
A3CA
SJGR
IN1
GRIN2A
HCN1
KCNA2
KCNJ10
MBD
5PIGA
POLG
SLC2
5A22
SLC9
A6 TPP1
ALDH
7A1
ARHG
EF9
ARX
ATP1
A2CA
CNA1
ACN
TNAP
2CP
A6 DCX
DEPD
C5DL
G3EEF1A2
EHMT1
FARS2
GPHN
KCNA1
KCNQ3
KCTD
7LG
I1MFSD8
PDHA
1SLC1
3A5
SLC9
A6SM
SSTX1
BTB
C1D2
4WDR
45ZEB2
11 genes with ≥10 pts
diagnosed
Many pts present with few genetic diagnoses
Few pts present with many distinct genetic diagnosesPanels detect both common and rare seizure disorders
Mei D et al. Mol Diagn Ther. 2017;21:357–373.
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Benefits of Gene Panels: Reduction in Healthcare CostsHigh diagnostic yield expedites diagnosis and reduces costs
38
Clinical features
Metabolic testingof CSF
Metabolic testing of urine/plasma
Brain MRI
Chromosome microarray Muscle/skin biopsy
Repeated testing (EEG / MRI) can have a higher than cost of molecular
testing
• Late diagnosis costs more
Diagnosis of epileptic encephalopathy patients (N=31)
Epilepsy panel:
• High diagnostic yield**• Efficient way to potentially reach an
early molecular diagnosis*
Gen
etic
cau
ses w
ere
iden
tifie
d in
28%
(31
of 1
10) p
atie
nts s
tudi
ed
Data are from a large retrospective cohort study (N=110) of diagnostic yield in patients with epileptic encephalopathy conducted at a single epilepsy genetics clinic at an academic pediatric health science center. *Percentage of patients who obtained a genetic diagnosis by targeted next-generation sequencing epileptic encephalopathy panels**Targeted next-generation sequencing identified a genetic cause in 12.7% of the 110 patients.CSF, cerebrospinal fluid; EEG, electroencephalography; MRI, magnetic resonance imaging.Mercimek-Mahmutoglu S et al. Epilepsia. 2015;56:707–716.
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Gene Panels In Patients With Epilepsy
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SNV, single nucleotide variants; CNVs, copy number variants. Mei D et al. Mol Diagn Therap. 2017;21:357–373); Helbig K. A Clinician’s Guide to Genetic Test Selection: Navigating the Wild West. Epilepsygenetics.com; Chambers C, et al. J Genet Couns. 2016 Apr;25(2):213-7; Berg AT et al. JAMA Pediatr. 2017;171:863–871; MNG Laboratories. Improved epilepsy panel portfolio. https://mnglabs.com/improved-epilepsy-panel-portfolio (accessed May 8, 2018).
Studies confirm utility of NGS panels
Panel testing is becoming increasingly accessibleand efficient
Panels continue to become more comprehensive
Not all panels arecreated equal3
• High diagnostic yield (up to ~50%1)
• Yield varies by population, many studies produced yields of ~20%2
• Variants of Uncertain Significance still pose interpretation challenges3
• Costs vary by country, but are declining overall
• Turnaround time continues to improve
• Additional genes continually added as new genetic etiologies are identified
• In addition to SNV, short and long indels, exon level deletions / duplications (CNVs), structural rearrangements and triplet repeat expansions can be studied in some modern NGS panels
• Turnaround time varies
• Number of genes <20 –approximately 5544
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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 20191. http://www.omim.org/search/?index=clinicalSynopsis&start=1&limit=10&search=%22seizure%22+ AND%22ataxia%22&sort=score+desc%2C+prefix_sort+desc (accessed Aug 2017).
When to Use a Gene Panel for Epilepsy Diagnosis
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Gene panel• Testing for many conditions
fitting the clinical picture• Efficient way to reach an early
molecular diagnosis
Patient X• Non-specific symptoms– Seizures– Ataxia (motor disturbance)– Language development delay
Diagnosis?
• >500 possible diagnoses1
• Each condition is unlikely • Testing one-by-one = inefficient• Rarely biochemical test available
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Genetic Epilepsies May Be Hiding Behind Non-Specific SignsConsider testing when you see language development delay and/or motor disturbance
• In an evaluation of results from an industry-sponsored, no-cost testing program:– Language delay, motor disturbance: the best predictors of genetic testing outcome• Language delay and/or motor disturbance symptoms were associated with most (92/133) genes on this panel
0
20
40
60
80
100
Language delay or motor disturbance reported
P<0.01
(n=11)(n=114) (n=8)
49%
100% No genetic diagnosisAny genetic diagnosis
Clinical presentation by outcome group
Total number of orders where clinicians indicated presence or lack of presence of clinical feature for each outcome group. Non-responders not included in total. Review of 176 Invitae Epilepsy Panel (125 genes) tests in children ages 2 to 4, who had their first unprovoked seizure after the age of 2. There were 2 outcomes groups: no genetic diagnosis or any genetic diagnosis in a gene included in the Invitae Epilepsy Panel. Adapted from Miller N et al. Behind the Seizure™: A no-cost, 125-gene epilepsy panel for pediatric seizure onset between 2-4 years. Poster session presented at: The ACMG Annual Clinical Genetics Meeting; April 10-14, 2018; Charlotte, NC.
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GLUT1: glucose transporter type 1; SCN1A: sodium voltage-gated channel alpha subunit 1.Adapted from Poduri A, et al. Nat Rev Neurol. 2014;10:293-299.1. Fulgent Genetics. Actionable Epilepsy NGS Panel. https://www.fulgentgenetics.com/actionable-epilepsy (accessed May 8, 2018).
Identifying a seizures’ underlying etiology can enable more precise treatment • Many genes are actionable: Gene panels increasingly help tailor the approach to treatment – more than 20 genes1
have been linked to specific treatment strategies
GLUT1 deficiency
SCN1A
Ketogenic diet should be tried
SLC2A1
Avoidance of certain sodiumchannel agents
Early diagnosis is critical
Dravet syndrome
Even if there is no known therapy for a detected variant, the knowledge can help modify clinical management, including evaluating patient for clinical trial enrollment or determining additional tests to pursue
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CLN2 Disease
Genetic Testing &
Actionability of Results
Epilepsy and
GeneticsCase Study
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AGE (YEARS)
CLN
2 D
ISEA
SE C
LIN
ICA
L R
ATI
NG
SC
ALE
SC
OR
E (M
OTO
R A
ND
LA
NG
UA
GE)
6
5
4
3
2
1
00 1 2 3 4 5 6 7 8 9 10 1211
Loss of voluntary movements/bedridden
Death
Blindness
Dysphagia Tube feeding
Visual decline
Cognitive decline Loss of cognitive functions/dementia
Myoclonus/spasticity/dystonia
Ataxia Loss of ambulation
New-onset seizures Drug-resistant seizures
Language delay
Language decline Loss of language
1. Schulz A, et al. Biochim Biophys Acta. 2013;1832:1801-1806; 2 Mole S, et al. Gene Reviews [online]. 2013; 3. Nickel M et al. Lancet Child Adolesc Health. 2018;2(8):582–590.
Children experience a dramatic loss of function as symptoms compound with age1,2†
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†Age ranges depicted are averages for the classic late-infantile phenotype. Atypical phenotypes of CLN2 disease can vary in age of onset, rate of progression, and disease manifestation.
Two hallmark presenting
symptoms of CLN2
disease are early
language delay and
new-onset seizures3
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Age of onset of various epileptic encephalopathies and CLN2 Disease
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Age of onset years
Different epilepsy syndromes may be considered in young children presenting with new-onset of seizures at late infantile age
ESES/LKS, electrical status epilepticus in sleep/Landau-Kleffner syndrome; FIRES, febrile infection-related epilepsy syndrome; ABPE, atypical benign partial epilepsy; MPSI, migrating partial seizures of infancy.Adapted from Helbig I et al. Epilepsia. 2016;57:861–868.
CLN2 Disease
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Traditional vs genomic diagnosis
• Male, 7 yrs (currently 12 yrs)• Onset: 2 yrs 8m, focal seizure, Status epilepticus• EEG: diffuse abnormalities • VPA, PB, PHT, LEV• 3 brain MRI, multiple hospital admission, ataxia, cognitive regression, repetitive
myoclonus• Genetic tests: Karyotype → CGH array → SCN1A → NGS panel → CLN2 diagnosis• Limited disease-specific management• Time for diagnosis: 5 years
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• Female, 3 yrs (currently 5 yrs)• Onset: 2 yrs 6, focal seizures, repetitive
seizures• EEG: PPR and diffuse abnormalities• VPA, LEV (then withdrawn)• 1 brain MRI; lumbar puncture, only one
hospital admission for repetitive seizures• Genetic test: NGS panel → CLN2 diagnosis• Early evaluation of disease-specific
management• Time for diagnosis: 2 monthsNOT FOR DUPLICATION OR DISTRIBUTION
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Video showing CLN2 patient running, chasing a ball without any motor disturbance
Video showing patient drawing, talking and interacting with parents
These are videos of the female Case Study on previous slide. In very early stages of CLN2 disease, it may be difficult to diagnose without an epilepsy gene panel, as motor disturbance may not be immediately apparent.
All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
Genetic epilepsies may be hiding behind non-specific signsGene panels are an efficient way to expedite earlier diagnosis
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Genetic epilepsies may be hiding behind non-specific signsGene panels are an efficient way to expedite earlier diagnosis
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All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
Video showing patient walking unassisted, with no motor disturbance
Video showing running and playing soccer with a sibling - with no motor disturbance
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January 2019 – EEG
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All photos / videos used with family permission from Bambino Gesù Children’s Hospital.
This same patient’s EEG at a similar time as the videos were taken – showing normal brain function with some spikes over the frontal bilateral regions.
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Conclusion
• Careful evaluation of symptoms of disease onset• Look at seizure semiology, EEG findings and other possible associated symptoms• Early use of epilepsy gene panels including genes for NCLs• Evolution of disease• Refer patients to specialized centers for genetic counseling and better management• Avoid AEDs with potential negative impact on seizures (i.e. sodium channel blockers)
and on motor and cognitive development (i.e. barbiturates)• Evaluation of the disease stage in order to better prescribe the right drug
(i.e. anti-dystonic, anti-cholinergic, muscle relaxant)• Ask to parents to film children time to time, in order to document the progression
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Take-home messages
• Genetic research is rapidly advancing our understanding of the underlying causes of epilepsy
• Gene panels are an efficient way to expedite diagnosis• CLN2 disease is rapidly progressing, fatal neurodegenerative disorder. Early diagnosis
is critical• When there is a suspicion of genetic basis of epilepsy, a symptom or disease based
gene panel can allow for early diagnosis, prior to progression of disease • Identifying the genetic etiology in patients with early-onset epilepsy can impact
clinical management • Genetic epilepsies may be hiding behind non-specific signs• Language development delay and/or motor disturbance were found to be common
predictors of genetic testing outcome*
51*Based on review of 176 Invitae Epilepsy Panel (125 genes) tests in children ages 2 to 4, who had their first unprovoked seizure after the age of 2.
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Thank you
Thank you for participating!
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For more information about diagnostic testing programs available through BioMarin, ask your local BioMarin representative or send a request to [email protected]
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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019
Not for duplication or distribution
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