Genetic Variants and Genetic Testing in CPVT - SADS 2015... · Genetic Variants and Genetic Testing...
Transcript of Genetic Variants and Genetic Testing in CPVT - SADS 2015... · Genetic Variants and Genetic Testing...
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
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
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
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
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?
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
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
- 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
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
“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“
- “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.
- “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
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
RyR2 Targeted Screening
1000 2000 3000 4000 4967 0
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
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
- 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
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
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%
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
- 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
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
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
Yiel
d 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)
• 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
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
- “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!”
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)
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)
Yiel
d of
Rar
e Va
riant
s (M
AF <
1/1
0,00
0)
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
or corrected QT interval values <480 ms
3:1
Kapplinger … Ackerman. 2015 (submitted)
25.0%
18.0%
11.0% 9.7%
0%
5%
10%
15%
20%
25%
30%
1st 300 2nd 300 3rd 300 4th 300
Yiel
d
27.3 28.6 31.2 33.5
05
10152025303540
1st 300 2nd 300 3rd 300 4th 300
Aver
age
Age
1.1x10-5
0.004
8.7x10-7
0.002 0.003
3.2% ExAC Rate
3:1
Kapplinger … Ackerman. 2015 (submitted)
28.1%
18.4%
4.7%
0%
5%
10%
15%
20%
25%
30%
<18 (n= 335)
18-35 (n= 244)
>35 (n= 387)
Yiel
d of
Rar
e Va
riant
s
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
161
24
7 2
7
0
20
40
60
80
100
120
140
160
180
1 2 3 4 ≥ 5
# of
Uni
que
Varia
nts
# of Unrelated Cases
36/201 case-derived variants were overrepresented (p<4.8x10-4) in disease and completely absent from the ExAC
exomes
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
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
Yiel
d of
Rar
e Va
riant
s (M
AF <
1/1
0,00
0)
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)
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
Yiel
d of
Rar
e Va
riant
s
Exon
ReferralsPhenotyped CasesExAC ExomesIdentified ExonsOREAE
35/105 exons carried an overrepresentation 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)
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
Yiel
d of
Rar
e Va
riant
s (M
AF <
1/1
0,00
0)
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)
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
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
WINDLAND Smith Rice Sudden Death
Genomics Laboratory
“To heal the sick and advance the science” Dr. Charles W. Mayo