Genetic Variants and Genetic Testing in CPVT Michael J. Ackerman, - - PowerPoint PPT Presentation

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Genetic Variants and Genetic Testing in CPVT Michael J. Ackerman, - - PowerPoint PPT Presentation

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Genetic Variants and Genetic Testing in CPVT Michael J. Ackerman, MD, PhD, FACC Windland Smith Rice Cardiovascular Genomics Research Professor Professor of Medicine, Pediatrics, and Pharmacology Director, Long QT Syndrome Clinic and the Mayo

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Genetic Variants and Genetic Testing in CPVT

2015 SADS Foundation International Meeting New York City, NY May 29, 2015

Michael J. Ackerman, MD, PhD, FACC

Windland Smith Rice Cardiovascular Genomics Research Professor Professor of Medicine, Pediatrics, and Pharmacology Director, Long QT Syndrome Clinic and the Mayo Clinic Windland Smith Rice Sudden Death Genomics Laboratory President, Sudden Arrhythmia Death Syndromes (SADS) Foundation

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SLIDE 2

WINDLAND Smith Rice Sudden Death Genomics Laboratory

Learning Objectives to Disclose:

  • To ASSESS clinical genetic testing for CPVT and

EVALUATE its role and yield

  • To EXPOSE the “dark side” (aka, Genetic Purgatory) of

the CPVT genetic test Conflicts of Interest to Disclose:

  • Consultant – Boston Scientific, Gilead Sciences, Medtronic,
  • St. Jude Medical, and Transgenomic/FAMILION
  • Royalties – Transgenomic/FAMILION

www.StopSADS.org 1-800-Stop SAD

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SLIDE 3

WINDLAND Smith Rice Sudden Death Genomics Laboratory

Learning Objectives to Disclose:

  • To ASSESS clinical genetic testing for CPVT and

EVALUATE its role and yield

  • To EXPOSE the “dark side” (aka, Genetic Purgatory) of

the CPVT genetic test Conflicts of Interest to Disclose:

  • Consultant – Boston Scientific, Gilead Sciences, Medtronic,
  • St. Jude Medical, and Transgenomic/FAMILION
  • Royalties – Transgenomic/FAMILION

www.StopSADS.org 1-800-Stop SAD

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SLIDE 4

Cardiac Channelopathies

LQTS

  • RWS
  • JLNS

CPVT FAVCB IVF IER BrS ATS SSS SIDS FAF DI-TdP SQTS SUDS TS

DCM

August 2011

HRS/EHRA Consensus Statement on the State of Genetic Testing for the Channelopathies and Cardiomyopathies

Ackerman, Priori, et al. Heart Rhythm 8:1308-1339, 2011

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SLIDE 5

Decoding a CPVT Genetic Test Result

  • What is the test’s DIAGNOSTIC, PROGNOSTIC,

and THERAPEUTIC impact?

  • What is the test’s YIELD?
  • What is the test’s Achilles’ heel (its “NOISE”)?
  • What is my index of suspicion?
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SLIDE 6

Clinical

Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT)

Exertion Induced Syncope or Sudden Cardiac Death No Structural Heart Defect Phenotypically Mimics Long QT Syndrome Bi-Directional Ventricular Tachycardia

Hallmark Arrhythmia

Priori et al. J Clin Invest 115:2033-2038, 2005

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SLIDE 7

Clinical

Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT)

Exertion Induced Syncope or Sudden Cardiac Death No Structural Heart Defect Phenotypically Mimics Long QT Syndrome Bi-Directional Ventricular Tachycardia

Hallmark Arrhythmia

Priori et al. J Clin Invest 115:2033-2038, 2005

Exercise-induced PVCs in bigeminy initiating at heart rates > 120 beats per minute – suspicious for CPVT!

Horner … Ackerman. Heart Rhythm 2008

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SLIDE 8
  • What is the test’s DIAGNOSTIC, PROGNOSTIC,

and THERAPEUTIC impact?

  • What is the test’s YIELD?
  • What is the test’s Achilles’ heel (its “NOISE”)?
  • What is my index of suspicion?

Decoding a CPVT Genetic Test Result

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SLIDE 9

Ackerman, Priori, et al. Heart Rhythm 8:1308-1339, 2011

HCM LQTS CPVT BrS Diagnostic Prognostic Therapeutic Disease ARVC DCM CCD SQTS AF LVNC RCM

+++ +

  • +++

+++ ++ +

  • +

+

  • +/-

+ +

  • +++

++ + + +/-

  • +/-
  • +
  • +

+ +

Decoding a CPVT Genetic Test Result

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SLIDE 10

“CPVT genetic testing is recommended for any patient in whom a cardiologist has established a clinical index of suspicion for CPVT…[and] is recommended for family members and appropriate relatives” “…genotype influences the management and treatment of a patient with genetically confirmed CPVT“

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SLIDE 11
  • “Positive” Test Result

Decoding a CPVT Genetic Test Result

Ackerman, Priori, et al. Heart Rhythm 8:1308-1339, 2011

Mutation-specific genetic testing is recommended for family members and other appropriate relatives subsequently following the identification of the disease-causative mutation in an index case.

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SLIDE 12
  • “Negative” Test Result
  • What was my index of suspicion?
  • What exons were included/excluded?
  • Was it a clinical or research test result?

Decoding a CPVT Genetic Test Result

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SLIDE 13

Calcium Induced Calcium Release (CICR) 105

RyR2 (CPVT1, Ch 1q42.1-q43)

1 14 47 49 83 88 90 93 97 100 8 15 44 45 46 102 103 101

CASQ2 (CPVT2, Ch 1p13.1)

1 2 3 4 5 6 7 8 9 10 11

Molecular

105 Exons 4967 amino acids 11 Exons 339 amino acids Cell membrane Sarcoplasmic reticulum

RyR2

–

CASQ2

Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT)

Cellular

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SLIDE 14

RyR2 Targeted Screening

1000 2000 3000 4000 4967

Mutations seem to be distributed across three canonical structure-function domains

Yano et. al, Nat Clin Prac Card 3:43-52,2006 George et al. J Mol Cardiol; 42:34-50, 2007

I II III

77-466 2246-2534 3778-4959

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SLIDE 15

The Cardiac Ryanodine Receptor (RyR2)

Regions of Higher Pathogenicity

Exons 3, 8, 10, 12- 15, 17, 19, 21, 26-28 Exons 38, 40-50 Exon 75 Exons 83, 86-91, 93- 97, 99-105

RYR2 “Hot Spot Domains”

Central Domain Channel Region N-terminal Domain 2246-2534 3778-4959 77-466 3564-3575

Targeted Genetic Test Region

Exons 1 – 28 Exons 37 – 50 Exon 75 Exons 83 – 105 1-1141 1638-2578 3776-4967

Targeted Genetic Test 66/105 exons tested, covering 66% of the protein

RyR2 1 4967 Exon 1 Exon 105

Yano et. al, Nat Clin Prac Card 3:43-52,2006 George et al. J Mol Cardiol; 42:34-50, 2007 Medeiros-Domingo et al. JACC 54:2065-74, 2009

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SLIDE 16
  • What is the test’s DIAGNOSTIC, PROGNOSTIC,

and THERAPEUTIC impact?

  • What is the test’s YIELD?
  • What is the test’s Achilles’ heel (its “NOISE”)?
  • What is my index of suspicion?

Decoding a CPVT Genetic Test Result

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SLIDE 17

Calcium Induced Calcium Release (CICR) 105

RyR2 (CPVT1, Ch 1q42.1-q43)

1 14 47 49 83 88 90 93 97 100 8 15 44 45 46 102 103 101

CASQ2 (CPVT2, Ch 1p13.1)

1 2 3 4 5 6 7 8 9 10 11

Molecular

105 Exons 4967 amino acids 11 Exons 339 amino acids Cell membrane Sarcoplasmic reticulum

RyR2

–

CASQ2

Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT)

Cellular

Medeiros-Domingo…Ackerman. JACC 54:2064-2075, 2009 Medeiros-Domingo…Ackerman. JACC 54:2064-2075, 2009

Yield of Genetic Testing

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SLIDE 18

Calcium Induced Calcium Release (CICR) 105

RyR2 (CPVT1, Ch 1q42.1-q43)

1 14 47 49 83 88 90 93 97 100 8 15 44 45 46 102 103 101

CASQ2 (CPVT2, Ch 1p13.1)

1 2 3 4 5 6 7 8 9 10 11

Molecular

105 Exons 4967 amino acids 11 Exons 339 amino acids Cell membrane Sarcoplasmic reticulum

RyR2

–

CASQ2

Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT)

Cellular

Medeiros-Domingo…Ackerman. JACC 54:2064-2075, 2009 Medeiros-Domingo…Ackerman. JACC 54:2064-2075, 2009

Yield of Genetic Testing

CPVT Strong – 60% CPVT Possible – 30% Real World (N = 1200) – 18% Autopsy Negative SUDS – 10%

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SLIDE 19

Total Cases 1200 Avg Age (years) 31 ± 19 % Female 46% Caucasian 78% African 9% Hispanic 7% Asian 3% Other 3%

Test Version Exons on Panel Exons Sample Count 1 38 3, 8-15, 37, 41, 44-50, 83, 87-105 291 2 66 1-28, 37-50, 75, and 83-105 656 3 105 1-105 253

CPVT Genetic Testing in Real World

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SLIDE 20

Kapplinger … Ackerman. 2015 (submitted)

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  • What is the test’s DIAGNOSTIC, PROGNOSTIC,

and THERAPEUTIC impact?

  • What is the test’s YIELD?
  • What is the test’s Achilles’ heel (its “NOISE”)?
  • What is my index of suspicion?

Decoding a CPVT Genetic Test Result

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SLIDE 22

Is the “X” that marks the spot truly THE disease-causing mutation?

Genetic Testing’s Achilles’ Heel

Non-Synonymous Single Nucleotide Polymorphism

  • Common/rare SNP w/o functional/clinical significance
  • Common/rare SNP w/ functional/clinical significance
  • Pathogenic (“disease-causing”) mutation

“With great power comes great responsibility” Spider Man’s Uncle

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SLIDE 23

Background Noise Issue

2003

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SLIDE 24

RESULTS

2% 1.4% 0.6%

Yield of CPVT Genetic Test in Controls

0.0% 0.5% 1.0% 1.5% 2.0%

All Targeted Region Outside Targeted Region

Yield

N1 C4967

Cytosol SR lumen

1 11

RyR2 (n = 221) Control Variants > 8000 “controls”

FKBP12.6 Binding Domain

754 40 250 328 507 1136 3152 3510 377 1013 1810 2094 2156 2435 2284 2812 3973 4281 4573 4653 4344

Kapplinger … Ackerman. 2015 (submitted)

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SLIDE 25
  • 3% background rate of rare variants

identified in 200 ostensibly healthy controls

  • 15/142 (10.5%) of the previously published

CPVT variants were found in controls

(Medeiros-Domingo…Ackerman JACC 2009)

  • Reconfirmed – 11%

(Jabbari…Olesen Circ. Cardiovasc. Genet. 2013)

Background Rate Issue in CPVT

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SLIDE 26

Reported Variants Represented in Controls*

Mutation Reference (PMID) Count (Out of 8075)

R1013Q PMID: 21964171 13 (0.16%) R4307C PMID: 19926015 10 (0.12%) V2113M PMID: 19926015 7 (0.09%) T1107M PMID: 19926015 5 (0.06%) V919M Kellen et al., HRS 2012 3 (0.04%) V377M PMID: 19926015 3 (0.04%) P466A PMID: 19926015 2 (0.02%) V4010M PMID: 19926015 2 (0.02%) A4556T PMID: 19926015 2 (0.02%)

*Variants found only once in controls were omitted

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SLIDE 27
  • “Maybe” Test Result ?
  • What was my index of suspicion?
  • Have I done my homework?

“Possible Deleterious” “Variant of Uncertain Significance (VUS)”

“Genetic Purgatory”

Decoding a CPVT Genetic Test Result

“Genetic Purgatory is a Real Place and its Scary!”

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SLIDE 28

MAF < 1:10000 MAF > 1:10000 Case

68 non-synonymous variants with a MAF > 1/10,000 alleles 1053 non-synonymous variants with a MAF < 1/10,000 alleles Background rate of 3.2%

Kapplinger … Ackerman. 2015 (submitted)

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SLIDE 29

59.0% 31.2% 18.2% 3.2% 0% 10% 20% 30% 40% 50% 60% 70% Strong (n = 78) Possible (n = 77) Referral (n = 1,200) ExAC (n = 60,706) Yield of Rare Variants (MAF < 1/10,000) Molecular Autopsy

18:1 10:1 5.5:1 Strong = exertional syncope plus documentation of bidirectional or polymorphic ventricular tachycardia

10.0%

3.2% ExAC Rate Possible = exertional syncope plus either stress test induced ventricular ectopy

  • r

corrected QT interval values <480 ms 3:1

Kapplinger … Ackerman. 2015 (submitted)

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SLIDE 30

25.0% 18.0% 11.0% 9.7% 0% 5% 10% 15% 20% 25% 30% 1st 300 2nd 300 3rd 300 4th 300 Yield 27.3 28.6 31.2 33.5 5 10 15 20 25 30 35 40 1st 300 2nd 300 3rd 300 4th 300 Average Age

1.1x10-5 0.004 8.7x10-7 0.002 0.003

3.2% ExAC Rate 3:1

Kapplinger … Ackerman. 2015 (submitted)

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SLIDE 31

28.1% 18.4% 4.7% 0% 5% 10% 15% 20% 25% 30% <18 (n = 335) 18-35 (n = 244) >35 (n = 387) Yield of Rare Variants Age at Genetic Testing

9:1 6:1 3.2% ExAC Rate <18 (n = 335) 18-35 (n = 244) >35 (n = 387) 1.5:1

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SLIDE 32

161 24 7 2 7 20 40 60 80 100 120 140 160 180 1 2 3 4 ≥ 5 # of Unique Variants # of Unrelated Cases

36/201 case-derived variants were

  • verrepresented (p<4.8x10-4) in disease

and completely absent from the ExAC exomes

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SLIDE 33

201)

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SLIDE 34

N1 C4967

Cytosol SR lumen

FKBP12.6 Binding Domain

RyR2

N57_G91del R169Q E243K F329L R332W G357S R420Q E1724K H2168Q C2201Y S2246L E2296Q A2387T R2401H R4959Q F4851L (2x) I4848V V4771I N4763S G4749V G4749E R4497C L4188P N4178S R4157Q S4124T A2403T A2416D R2420W A4091T A4091V E4076K M3972I G3946S C3800F

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SLIDE 35

59.0% 31.2% 18.2% 3.2% 0% 10% 20% 30% 40% 50% 60% 70% Strong (n = 78) Possible (n = 77) Referrals (n = 1200) ExAC Yield of Rare Variants (MAF < 1/10,000)

10:1 5.5:1

3.2% 11.2%

16.9% 35.9% 5.3:1 11:1 18:1 3.5:1

Kapplinger … Ackerman. 2015 (submitted)

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SLIDE 36

0.0% 1.0% 2.0% 3.0% 4.0% 5.0% 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103

Yield of Rare Variants Exon

Referrals Phenotyped Cases ExAC Exomes Identified Exons ORE AE

35/105 exons carried an

  • verrepresentation of “new” rare variants

(exons 1-3, 6, 8, 14, 17, 27, 40, 43-45, 47- 50, 54, 80-81, 83, 86, 88-90, 93, 95-101, 103-105) These 35 exons only account for ~1/3 of the protein (1664/4967 amino acids)

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SLIDE 37

33.3% 15.6% 8.8% 0.8% 2.6% 1.3% 2.3% 2.3% 0% 5% 10% 15% 20% 25% 30% 35%

Strong (n = 78) Possible (n = 77) Referrals (n = 1200) ExAC

Yield of Rare Variants (MAF < 1/10,000) Identified Exons Outside Identified Exons 20:1 42:1 11:1

Outside Identified Exons 1:1 Signal-to-noise Regardless of Phenotype

Kapplinger … Ackerman. 2015 (submitted)

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SLIDE 38
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SLIDE 39

Take Home Points

  • 1. The yield of CPVT genetic testing is 60%, BUT
  • 2. The signal-to-noise ratio can be up to 43:1, BUT
  • 3. “X” does NOT always mark the spot!
  • 4. Genetic purgatory is a real place and it’s scary!
  • 5. Time to go retro with targeted RYR2 testing

(35 exons)?

Decoding a CPVT Genetic Test Result

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SLIDE 40
  • Dr. Scholl Foundation, CJ Foundation for SIDS

Hannah Wernke Memorial Foundation Sheikh Zayed Saif Mohammed Al Nahyan Fund National Institutes of Health

WINDLAND Smith Rice Sudden Death Genomics Laboratory

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SLIDE 41

WINDLAND Smith Rice Sudden Death Genomics Laboratory

“To heal the sick and advance the science”

  • Dr. Charles W. Mayo
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SLIDE 42

If you feel you have benefitted from this presentation, please make a donation now. 1-800-STOP SAD (801) 531-0937 www.StopSADS.org