The Promise of Epilepsy Genetics A Personal & Scientific Perspective December 3, 2012

Transcription

1 The Promise of Epilepsy Genetics A Personal & Scientific Perspective December 3, 2012 Tracy Dixon-Salazar, Ph.D. University of California, San Diego American Epilepsy Society Annual Meeting 1

2 Disclosure Nothing to disclose American Epilepsy Society Annual Meeting

3 Learning Objectives Understand how exome sequencing in the clinic, one family at a time, can be used for: Gene identification Diagnosis To guide treatment American Epilepsy Society Annual Meeting

4 Logarithm of odds (LOD) score Gene identification in consanguineous families 1 LOD 3.0 = Chr 21 Chromosome 4

5 Logarithm of odds (LOD) score Small families with many linkage peaks make exome sequencing useful 1 1 Chromosome 5

6 Genomic variant filtering and prioritization Sequence exome Mapping Variant calling Variant filtering Variant prioritization 6

7 Exome sequencing is useful for finding known and novel genes 158 probands 40 known gene mutations (25%) 22 new genes identified (14%) 86 with 2-10 variants (54%) (likely new genes) Modified from Dixon-Salazar et al.,

8 Exome sequencing can correct diagnosis in some cases 158 probands 40 known genes mutations (25%) 22 new genes identified (14%) 86 with 2-10 variants (54%) (likely new genes) 10 probands with corrected genetic diagnosis (7%) Modified from Dixon-Salazar et al.,

9 Private mutations/genes may be the rule and not the exception 87 new genes confirmed ~1000 exomes 76 genes found in a single family (87%) 11 new genes found in >1 family (13%) 9

10 Finding the cause may guide treatment Phenotype -Full term, normal delivery -Seizure onset at ~1 year old, normal initial work-up, followed by mental and physical deterioration -Later work-up reveals neurodegeneration -Increased sensitivity to infections (flu), which were followed by rapid physical and mental regression -Death by age 2-4 years unless intensive medical intervention is used (tube feeding, tracheostomy, ventilator, resuscitation) 10

11 Finding the cause may guide treatment LOD = 3.4 Chr 1 11

12 Mutations in PAR-degrading enzyme underlie this novel syndrome Oxidative stress Hypoxia 12

13 Comorbid autism and epilepsy due to BCKDK mutations may be treatable Valine, Leucine, Isoleucine BCAT BCKA BCKDH Science 2012 Co-enzyme A derivative 13

14 Case Study- 19 y female Lennox-Gastaut Syndrome - Unknown Cause Normal birth and development First seizure age 2 years (GTCS) By 18 years she had failed a total of 26 antiseizure therapies seizures per month (GTCS, myoclonic, atypical absence) Receiving rectal valium between 3-10 times a month for NCSE. In special education class and is judged to be functioning at ~5 year old level. 14

15 Number of seizures Number of seizures from 1995 to 2011 in LGS patient

16 Jan May Sep Jan May Sep Jan May Sep Jan May Sep Jan May Sep Jan May Sep Number of times Diastat used 10 Diastat use for NCSE 2006 to 2011 in patient with LGS

17 Exome sequencing analysis with the goal of improving treatment Recessive? Dominant? De novo? Coding Splice Indels UTR (20K variants) Exclude common homozygous & heterozygous (4.5K) Exclude poorly conserved (350) Analyzed by: Damage prediction Type of variant Disease relation Gene clustering Treatable 17

18 Gene clustering analysis of filtered exome data 18

19 Gene clustering analysis of filtered exome data 19

20 Exome identified numerous high impact variants in calcium channel subunits Gene Type Conservation Genotype Depth Quality Subunit CACNA1B splice / N-type alpha CACNA1B splice / N-type alpha CACNA1B missense / N-type alpha CACNA1C missense / L-type alpha CACNA1D frameshift / L-type alpha CACNA1D coding / L-type alpha CACNA1D frameshift / L-type alpha CACNA1F missense 4.4 0/ L-type alpha CACNA1H missense / T-type alpha CACNA1S missense / L-type alpha CACNB2 missense / Beta 2 subunit CACNG4 missense / Gamma 4 subunit 20

21 Exome identified numerous high impact variants in calcium channel subunits Approximate variant location 21

22 Rationale for trying L-type calcium channel blocker in this patient Patient need Half of genetic variants in L-type Some predicted gain-of-function Calcium supplementation in patient lead to substantial seizure increase (3 separate tries) No contraindications present in patient 22

23 Risk/Benefit Analysis Risks Verapamil may increase seizures (functional consequences of variants unknown) Drug not without sideeffects Verapamil/AED interactions not known for all AEDs Benefits Potential seizure decrease Potential non-convulsive status decrease Potential improved comorbid conditions if seizures can be controlled FDA-approved drug, safety and tolerability known 23

24 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Number of seizures Patient seizures before and after Verapamil* Verapamil *FDA approved for arrhythmia

25 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Number of time Diastat used Patient Diastat use before and after Verapamil Verapamil

26 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Number of seizures Patient seizures before and after Verapamil* Verapamil *FDA approved for arrhythmia

27 How quality of life has changed with Verapamil 27

28 Impact on Clinical Care and Practice Exome sequencing is useful for: Finding novel disease genes in genetically enriched families Identification of known causes of disease in patients Correcting diagnosis & prognosis Guiding treatment Exome analysis must be approached with a clear goal in mind. Exomes provide the possibility of personalizing medicine for our patients. Are private mutations/genes the rule rather than the exception? Can we find which drugs help which people? Can we repurpose medications to help our patients? 28

29 Acknowledgements Collaborators - Lihadh Al-Gazali - Stacey Gabriel - Carsten Russ - Nitin Udpa - Vineet Bafna - Huang He - Gaby Haddad Gleeson Lab - Joseph Gleeson - Gaia Novarino - Maria Nguyen Funding - NIH - Epilepsy Foundation 29

30 Conclusions American Epilepsy Society Annual Meeting

31 Genetics may explain much of the 75% of epilepsies of unknown cause Complex inheritance; Mendelian epilepsies uncommon De novo mutagenesis emerging as very important Private mutations may be the rule rather than the exception Multiple diagnostic approaches are available: Consider CGH array studies to evaluate for CNVs in patients with: Epilepsy Plus (autism, ID or malformations) Gene panels should be considered when: Multiple genes can cause the phenotype Phenotype is nonspecific but fits a class of disorders Exome sequencing is increasingly available & is useful for: Finding novel disease genes in genetically enriched families Determining the disease causing mutation among many rare individual variants is a challenge May lead to personalized therapy in the future

32 Genetics in the management of people with Epilepsy Closure to causation; avoid unnecessary investigation Directly alter treatment: GLUT1, SCN1A Diagnosis essential for counseling Decisions re when and how much to test must weigh clinical benefits versus cost Multiple methods available to examine how a mutation causes epilepsy Cell culture Animal models ipscs Determining the disease causing mutation among many rare individual variants remains a major challenge