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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019

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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

2 2 2

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Faculty

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Nicola Specchio, MD, PhD

Head of the Epilepsy Unit, Department of Neuroscience Bambino Gesú Children’s Hospital Rome, Italy

Raman Sankar, MD, PhD

Professor of Neurology and Pediatrics and Chief of Pediatric Neurology David Geffen School of Medicine at UCLA Los Angeles, CA, USA

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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

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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

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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

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CLN2 Disease Genetic Testing & Actionability

• f Results

Epilepsy and Genetics Case Study

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Advances In Understanding The Causes of Epilepsy

New research demonstrates increasing genetic basis

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• 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 Neoplasm Infectious Congenital lesions Birth anoxia Other 2014 paradigm2 Epilepsies with complex inheritance Single-gene epilepsies: Familial, de novo Modifiers and susceptibility alleles Trauma Vascular Neoplasm Infectious Congenital lesions Birth anoxia Other Autoimmune Focal epilepsy with MRI-detectable lesions

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The History Of Gene Identifications In Epilepsy Research

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CLN3 TPP1

NGS demonstrates the spectrum of phenotypes associated with genetic epilepsies

CHRNA4 SCN1B SCN1A GABRG2

Microdeletions

KCNQ2 KCNQ3 SLC2A1 GABRA1 LGI1 ARX CACNA1H CDKL5 15q13.3 16p13.11 15q11.2

STX1B

SLC6A1 GABRA1 GABRB3 SIK1 KCNA2 ALG13 GRIN2B PURA KCNB1 KCNC1 DNM1 HCN1 CHD2 SCN2A GRIN2A DEPDC5 KCNT1 PRRT2 TBC1D24 STXBP1 PCDH19 SCN8A

Channelopathy era Next-generation sequencing Dark ages

2011 2009 2007 2005 2013 2015 2017 2018 2003 2001 1999 1997 1995

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

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Potential for disease-specific management: targeted therapy or clinical trial Initial empirical AED treatment no underlying cause yet identified Genetic assessment: epilepsy gene panel Old paradigm Stepwise approach Emerging paradigm Direct, accurate, cost-effective Genetic assessment: chromosomal microarray

AED Failure

Genetic assessment: epilepsy gene panel

UNINFORMATIVE

Patient with unexplained 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

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Genetic testing

Berkovic SF. Epilepsy Curr. 2015;15:192–196.

Genetic testing

Genetic testing

Can impact clinical management e.g. choice of AED

1

May avoid unnecessary testing

2

Shortens the diagnostic journey for families

3

Allows for specific counseling (family planning)

4

Opportunity to participate in a clinical study

5

Can allow for targeted therapy: precision medicine

6

Connect families with each other and advocacy groups

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CLN2 Disease Genetic Testing & Actionability

• f Results

Epilepsy and Genetics Case Study

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Features of CLN2 disease

0–1 years

• Normal early development

1–2 years

• May have slow language development

2–3 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

skills 4–5 years

• Further loss of skills
• Sleep disorder
• Pain and irritability
• Increasingly dependent for activities of

daily living

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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

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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 decline
• Bedridden
• Blindness
• Death
• Ataxia

Age (yr)

• Language delay

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All photos / videos used with family permission from Bambino Gesù Children’s Hospital.

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Clinical presentation:

Classical late infantile CLN2 disease

Do NOT wait for vision loss to diagnose CLN2 3 yr old

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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 decline
• 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

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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 decline
• 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

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All photos / videos used with family permission from Bambino Gesù Children’s Hospital.

4 yr old 3 yr old

Birth 1 2 3 4 5 6 7 8 9 10 11 12

• Seizures
• Psychomotor decline
• Bedridden
• Blindness
• Death
• Ataxia

Age (yr)

• Language delay

The same patient had a very quick progression

• f 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

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NCL, neuronal ceroid lipofuscinoses. Steinfeld R et al. Am J Med Genet. 2002;112:347–354.

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(Clinical score) Sum of MOTOR and LANGUAGE Normal = 3 Abnormal = 2 Poor = 1 No 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

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• 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

Mean 95% CI

2-yrs delay

Rate of decline 2.1 units/yr

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CI: confidence interval Figure 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 the motor and language score Age (years)

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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

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6 yrs 6 yrs 8 mo 7 yrs 6 mo 3 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)

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EEG, 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

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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)

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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 EEG First IPS First PPR

Specchio N, et al. Epilepsia. 2017;58:1380–1388.

Age (years) Cumulative survival (%)

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Suspicion of NCL disorder

• Neuronal ceroid lipofuscinosis (NCL)

gene panel

• TPP1/PPT1 enzyme activity

screening tests†

Suspicion of genetic basis

• f epilepsy
• Symptom- or disease-based gene

panel (e.g. epilepsy gene panel)

CLN2 disease diagnosis 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

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*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 basis

• f 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

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Genetic testing

Berkovic SF. Epilepsy Curr. 2015;15:192–196.

Genetic testing

Genetic testing

Can impact clinical management e.g. choice of AED

1

May avoid unnecessary testing

2

Shortens the diagnostic journey for families

3

Allows for specific counseling (family planning)

4

Opportunity to participate in a clinical study

5

Can allow for targeted therapy: precision medicine

6

Rapid progression after age ± 3 yrs (CLN2-specific)

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EEG: 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

Earlier diagnosis

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

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CLN2 Disease Genetic Testing & Actionability

• f Results

Epilepsy and Genetics Case Study

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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

Utility

Used 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
• f VUS
• Historic (improving)

– Cost – Turn-around time (2–6 weeks)

• Access/availability
• Detection of most variants/interpretation
• f 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: Utility

Increase understanding of genetic heterogeneity Many epilepsy syndromes reveal genetic heterogeneity1

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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: Utility

Assist 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

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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 encephalopathy

A 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 + ID

OS

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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 Needed

Simultaneously detect both common and rare seizure disorders

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56 genes with <10 pts diagnosed

A total of 67 pathogenic genes were identified in 348 patients

10 20 30 40 50 60 70

SCN1A SCN2A STXBP1 CDKL5 KCNQ2 SCN8A CHD2 SYNGAP1 PCDH19 KCNT1 MECP2 FOXG1 GABRB3 MEF2C UBE3A GABRA2 PNPO TCF4 GABRA1 GNAO1 HNRNPU IQSEC2 KCNB1 PNKP PRRT2 SLC2A1 SPTAN1 ATP1A3 CASJ GRIN1 GRIN2A HCN1 KCNA2 KCNJ10 MBD5 PIGA POLG SLC25A22 SLC9A6 TPP1 ALDH7A1 ARHGEF9 ARX ATP1A2 CACNA1A CNTNAP2 CPA6 DCX DEPDC5 DLG3 EEF1A2 EHMT1 FARS2 GPHN KCNA1 KCNQ3 KCTD7 LGI1 MFSD8 PDHA1 SLC13A5 SLC9A6 SMS STX1B TBC1D24 WDR45 ZEB2

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 Needed

Simultaneously 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

10 20 30 40 50 60 70

SCN1A SCN2A STXBP1 CDKL5 KCNQ2 SCN8A CHD2 SYNGAP1 PCDH19 KCNT1 MECP2 FOXG1 GABRB3 MEF2C UBE3A GABRA2 PNPO TCF4 GABRA1 GNAO1 HNRNPU IQSEC2 KCNB1 PNKP PRRT2 SLC2A1 SPTAN1 ATP1A3 CASJ GRIN1 GRIN2A HCN1 KCNA2 KCNJ10 MBD5 PIGA POLG SLC25A22 SLC9A6 TPP1 ALDH7A1 ARHGEF9 ARX ATP1A2 CACNA1A CNTNAP2 CPA6 DCX DEPDC5 DLG3 EEF1A2 EHMT1 FARS2 GPHN KCNA1 KCNQ3 KCTD7 LGI1 MFSD8 PDHA1 SLC13A5 SLC9A6 SMS STX1B TBC1D24 WDR45 ZEB2

11 genes with ≥10 pts diagnosed

Many pts present with few genetic diagnoses Few pts present with many distinct genetic diagnoses

Panels 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 Costs

High diagnostic yield expedites diagnosis and reduces costs

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Clinical features Metabolic testing

• f 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 *

Genetic causes were identified in 28% (31 of 110) patients studied

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 accessible and efficient Panels continue to become more comprehensive Not all panels are created 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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• 1. 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

40

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 Signs

Consider 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

20 40 60 80 100 Language delay or motor disturbance reported P<0.01

(n=11) (n=114) (n=8)

49% 100%

No genetic diagnosis Any 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 sodium channel 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

• f Results

Epilepsy and Genetics Case Study

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AGE (YEARS) CLN2 DISEASE CLINICAL RATING SCALE SCORE (MOTOR AND LANGUAGE) 6 5 4 3 2 1 1 2 3 4 5 6 7 8 9 10 12 11 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†

44 †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

46

• 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 months

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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 signs

Gene panels are an efficient way to expedite earlier diagnosis

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Genetic epilepsies may be hiding behind non-specific signs

Gene panels are an efficient way to expedite earlier diagnosis

48

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

49

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

• ver 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
• f 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*

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*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!

52

For more information about diagnostic testing programs available through BioMarin, ask your local BioMarin representative or send a request to medinfo@bmrn.com

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APAC/BRIN/0133 EU/CLN2/0735 US/CLN2/0255 December 2019

Not for duplication or distribution

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