1. An Update in Genetics of Epilepsy
Dr Michelle Demos
Pediatric Neurologist, Neurogeneticist
BC Children’s Hospital

2. Outline Overview of Genetics Role of Genetics in Epilepsy
Implications for Patients/Families
Advances in Genetics of Epilepsy and Genetic Testing

3. Overview of Genetics What is Genetics?
Study of heredity or how traits are passed from parent to child

4. Overview of Genetics Traits:
Notable feature or characteristic in a person
Each person has a different combination of traits which makes us unique

5. Physical Traits

6. Physical Traits

7. Examples of Traits: Height, body weight, health or disease
Genetic and environmental contribution
Environmental contribution

8. Examples of Traits: Height, body weight, health or disease
Genetic and environmental contribution
Environmental contribution

9. Gene Basic unit of heredity
Made of lengths of DNA (deoxyribonucleic acid)
Genes proteins normal body function

11. Human Genetic Make-up DNA ~ 20, 000 genes
The entire collection of DNA is called your Genome

12. Human Chromosomes OR
Female
Male

13. Sex Chromosomes

14. DNA, genetic code and making of human protein for normal function of human body
The most important component of chromosomes is DNA; make up of substances or bases called GCTA
The order of these bases make up our genetic code, which provides info needed to make proteins,
Important for proper structure and funciton of human body
Proteins made up of amino acids; each 3 base unit of DNA determines amino acid; gene is unit containing
Blueprint for making specific protein; about genes packed in each parental chromosome set (23)

15. Outline Overview of Genetics Role of Genetics in Epilepsy
Implications for Patients/Families
Advances in Genetics of Epilepsy and Genetic Testing

16. Twin Studies
Vadlamudi et al. Neurology Lennox, JAMA 1951.

17. Family Studies
Relatives of individuals with epilepsy more likely to develop epilepsy compared to general population

18. Linkage Analysis
Early
Epilepsy Gene Discovery

19. Types of Genetic Disorders in Epilepsy
Single Gene
Chromosome
Complex
Mitochondrial

20. Genetic Changes that can Predispose to Epilepsy: Single Gene

21. Single Gene Epilepsy Disorders
caused by changes (mutations) in single genes
recognizable inheritance pattern (dominant, recessive, X-linked) or arise by new mutation or de novo
very few cause primary epilepsy syndromes
Childhood Absence Epilepsy
Juvenile Myoclonic Epilepsy
many more will frequently have epilepsy as one of their symptoms

22. Features of the single gene epilepsy disorders
same gene mutation may produce multiple different seizure types or severity
not all individuals inheriting the affected epilepsy gene will develop seizures
more than one gene can cause the same disorder

23. Types of Genetic Disorders in Epilepsy
Single Gene
Chromosome
Complex
Mitochondrial

24. Genetic Change that can Predispose to Epilepsy: Loss of part of a chromosome

25. Chromosome Disorders
result in loss (deletion) or extra (duplication) chromosome content
often new change in child so recurrence risk is low, but if present in parent then recurrence risk is 50%
often associated with other medical problems

26. Types of Genetic Disorders in Epilepsy
Single Gene
Chromosome
Complex
Mitochondrial

27. Complex Disorders many epilepsies with a genetic basis
Childhood Absence Epilepsy
Juvenile Myoclonic Epilepsy
interactions between multiple genes with or without environment
pattern of inheritance less clear

28. Types of Genetic Disorders in Epilepsy
Single Gene
Chromosome
Complex
Mitochondrial

29. Mitochondria
Mitochondria
Chromosome
Nucleus

30. Mitochondrial Disorders
mitochondrial DNA is passed from mother to child
every child of a mother carrying mitochondrial DNA mutation is at risk of being affected
affects multiple organs within the body
symptoms vary amongst individuals

31. Mitochondrial Disorders
Affected
Abnormal Mitochondria
Normal Mitochondria
Insert pedigree here

32. Question: If a parent or child has epilepsy, what is the risk to other family members?
CAUSE

33. Cause is Known
Acquired brain injury including stroke, brain tumor, brain infection or severe head trauma
Risk is not significantly increased

34. Cause is Known
Genetic Disorder (single gene, chromosome, mitochondrial)
Risk will depend on genetic cause
Remention chromosome and mitochondrial

35. Single Gene Disorders
New dominant mutation recurrence risk is low – severe epilepsy disorders
If not new, depends on inheritance pattern
Dominant, recessive, X-linked
Remention chromosome and mitochondrial

36. Dominant Inheritance: 50% risk

37. Recessive Inheritance: 25% risk

38. X-linked Inheritance: 50% risk to have an affected son

39. Cause Unknown
Many of epilepsy syndromes with genetic basis (Childhood Absence Epilepsy)
Complex inheritance
Risk is an estimate based on past studies

40. Estimated Risks
Risk in close relatives is about 2 to 4 times higher than people in general population
Risk is less than 1 in 10 that a child of a person with epilepsy will also develop epilepsy
Risk is higher in relatives of a person with generalized epilepsy, young onset epilepsy and mothers vs fathers with epilepsy

41. Outline Overview of Genetics Role of Genetics in Epilepsy
Implications for Patients/Families
Advances in Genetics of Epilepsy and Genetic Testing

42. Epilepsy Genetics and Genomics – Now
Chromosome Microarray or Array Comparative Genomic Hybridization (CGH)
Next-Generation Sequencing
Complex etiology Genetic generalized epilepsies and
Nonacquired focal epilepsies with multiple genetic and environmental
Factors contributing to risk requires larger sample sizes to have sufficient power to
Detect responsible genes. One approach is to perform large-scale-genome-wide linkage or
Genome-wide association studies with large collections of families or cases and controls
1-Kasperavicuiute and colleagues 2010 >3000 individuals with focal epilepsies and almost
7000 controls; focal epilepsy any etiology; identified associations modest effect—none reached
Genome-wide significance
2012: Han chinease Guo Y: 1087 focal epilepsy with acquired or unknown;
Single SNP reached singificance on 1q32.1 CAMSAP1L1-calmodulin regulated
Spectrin associated cytoskeletal protein

43. Methods: Array CGH Normal Control DNA Patient DNA DNA fragments
Advances in genetics of epilepsy; technology allows identification of
genomic imbalances at higher resolution compared to routine cytogenetic studies.
DNA fragments representing entire genome are place on array. Genomic
comparison is made by hybridization of differentially labeled test and reference DNA.
relative intensity of test and reference sample fluorescence for each
DNA fragment used to detect gains or losses. Location of that is then
mapped back to the genome. Eg Agilent aberration detection method
uses algorith to detect consistently high or low log2 ratios indicating del/dup.
Patient DNA
Normal Control DNA
From

44. Examining chromosomes or genomes for genomic imbalances or Copy Number Variants (CNVs) causing Epilepsy
ArrayCGH
1000X resolution
Karyotype

45. Copy Number Variants Deletion or Copy Loss Duplication or Copy Gain
>1000bp

46. Chromosome Microarray in Epilepsy: What have we found?
A cause or abnormal CNV is identified in up to 15% of patients
Treatment resistant epilepsy or other severe forms of epilepsy
Epilepsy plus other neurological problem or birth defect
A cause is identified less often in patients with benign epilepsy syndromes (Juvenile Myoclonic Epilepsy)
Including BC
15q13, 15q11, 16p13

47. Chromosome Microarray in Epilepsy: What have we found?
Limitations to testing: negative test does not rule out genetic cause
Results of unclear significance
Incidental findings: finding an abnormality in a gene predisposing to unrelated health problem (example breast cancer gene)
Including BC
15q13, 15q11, 16p13

48. Chromosome Microarray in Epilepsy: Who should be Tested?
Cause of Epilepsy is unknown and:
a more severe form of epilepsy or
epilepsy plus global delay, intellectual disability, autism, other neurological problem and/or birth defect
Patient and/or Family who has received appropriate genetic counselling
Including BC
15q13, 15q11, 16p13

49. Epilepsy Genetics and Genomics – Now
Chromosome Microarray or Array Comparative Genomic Hybridization (CGH) and Copy Number Variants
Next-Generation Sequencing
Complex etiology Genetic generalized epilepsies and
Nonacquired focal epilepsies with multiple genetic and environmental
Factors contributing to risk requires larger sample sizes to have sufficient power to
Detect responsible genes. One approach is to perform large-scale-genome-wide linkage or
Genome-wide association studies with large collections of families or cases and controls
1-Kasperavicuiute and colleagues 2010 >3000 individuals with focal epilepsies and almost
7000 controls; focal epilepsy any etiology; identified associations modest effect—none reached
Genome-wide significance
2012: Han chinease Guo Y: 1087 focal epilepsy with acquired or unknown;
Single SNP reached singificance on 1q32.1 CAMSAP1L1-calmodulin regulated
Spectrin associated cytoskeletal protein

50. Examining genes, exomes and genomes for sequence variants causing Epilepsy
Sanger sequencing
Next-generation
sequencing

51. Next-generation sequencing
Massively parallel sequencing
Sequence millions of fragments simultaneously
Whole genome, exome (protein coding), targeted or gene panels
Massive parallel sequencing as many genes as desired
Sequence quality depends on minimum coverage at a base-pair position and
optimization of enrichment procedures of the genes of interest (target sequence)

52. Whole genome, exome or targeted sequencing in Epilepsy
Targeted= 10 to 500 epilepsy genes
Exome = 1 %

53. Whole Exome sequencing
Single gene disorders
variants per individual
Exome contains 85% of disease-causing mutations

54. Next Generation Sequencing: What is the impact?
Rapid increase in Gene Discovery

55. Next Generation Sequencing: Epilepsy Impact
~ 500 genes associated with epilepsy
Significant increase in diagnoses:
Diagnosis 10 – 50% of those tested
Severe epilepsy conditions or Epilepsy plus
New dominant mutations in multiple different genes

56. Next Generation Sequencing: Challenges
Negative test does not rule out genetic cause
Variants of unclear significance
Proving new or novel gene identified is the cause of epilepsy
Availability in Canada
Ethical Issues
Cost

57. Whole Genome Sequencing

58. Next Generation Sequencing: Positive Impact on Patients/Families
Earlier diagnosis including disorders with specific treatment implications
More accurate counselling regarding outcome and recurrence risk
Prevent additional investigations
A clear genetic diagnosis improves access to therapies/community support

59. Next Generation Sequencing: Negative Impact on Patients/Families
Identifying a disease without specific treatment
Discrimination regarding life, disability or long-term care insurance
Incidental findings (finding an abnormality in a gene that increase risk for developing cancer)
Genetic Counselling Before Testing

60. Genetic Testing in Patients/families with Epilepsy
Chromosome Microarray Analysis:
Available in BC
Indicated in patients with epilepsy of unknown cause and:
Severe forms of epilepsy
Epilepsy plus delay, intellectual disability, autism, other neurological/behavioral problems and/or other congenital abnormalities
Pre-test genetic counselling required

61. Genetic Testing in Patients/families with Epilepsy
Next Generation Sequencing:
Limited Availability in BC
Research, MSP funding
Consider in patients with negative chromosome microarray and:
Severe forms of epilepsy
Epilepsy Plus
Early onset epilepsy
Pre-test genetic counselling required
Gene panels or whole exome sequencing

62. Future Directions Standardized approach to genetic testing
Genetic discoveries leading to development of better treatment options

63. Future Directions Pharmacogenomics of Epilepsy:
The study of the interaction of an individual's genetic makeup and response to a drug.
Adverse drug reactions (HLA-B*1502)
Seizure control
Aim to individualize and optimize treatment based on genetic make-up
Hla b1502 tegretol induced Han Chinese

64. Summary Genetic factors play a role in many epilepsy disorders
New technology (Chromosome Microarray and Next-Generation Sequencing) has revolutionized gene discovery and genetic testing in epilepsy
Recent discoveries and further advances in diagnosis and pharmacogenomics will likely lead to improved individualized treatment of epilepsy

65. Questions?

67. Genetic Contribution to Epilepsy
Complex
Number with Epilepsy
Doesn’t address many genetic factors involved in symptomatic epilepsies
Genetic factors likely involved most epilepsies; impact and heredity is variable
This is important consideration when considering genetic testing
Genetic factors likely play a role in most epilepsies but genetic impact is variable
and have no role in recurrence risk ie low heritability but impact on seizure predisposition after brain injury
And response to medication.
Genetic (high)
Acquired (low)
Genetic Contribution to Epilepsy
Helbig I, et al, 2008. 67