Common Variants in Cardiac Ion Channel Genes are Associated with Sudden
Cardiac Death
Running Title: Albert et al; Common Ion Channel Variants and Sudden Death
Christine M. Albert, MD, MPH, Calum A. MacRae, MB, ChB, PhD, Daniel I. Chasman PhD,
Martin VanDenburgh, BA, Julie E Buring ScD, JoAnn E Manson MD, DrPH, Nancy R Cook,
ScD*, Christopher Newton-Cheh, MD*
From the Center for Arrhythmia Prevention (C.M.A), Division of Preventive Medicine (C.M.A,
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D.I.C, M.V, J.E.B, J.E.M), Cardiovascular Division (C.M.A, C.A.M), Channing Laboratory
e, Brigham an
nd Women’s
(J.E.M), and Division of Aging (J.E.B.), Department of Medicine,
and
he Ce
Cent
nter
nt
er ffor
or H
Hu
u
Hospital (C.M.A.), Harvard Medical School, Boston, MA; and the
Center
Human
Genetic
ovascular Research Center,
Center Massachusetts General Hospital, (C.N.-C.),
Research and Cardiovascular
hool, Boston, MA; Broad Institute of Harvard and MIT (C.N.-C.),
(C.N
Harvard Medical School,
Cambridge, MA.
ntly
tly directed the work
* These authors jointly
work.
Correspondence to:
Christine M. Albert, MD, MPH
Center for Arrhythmia Prevention
Division of Preventive Medicine
Cardiovascular Division
Brigham and Women’s Hospital
900 Commonwealth Avenue East
Boston, MA 02115-1204
Tel: (617)278-0807
Fax: (617)277-0198
Email: [email protected]
Journal Subject Heads: [5] Arrhythmias, clinical electrophysiology, drugs, [109] Clinical
genetics, [8] Epidemiology, [89] Genetics of cardiovascular disease, [152] Ion
channels/membrane transport
1
Abstract:
Background: Rare variants in cardiac ion channel genes are associated with sudden cardiac
death (SCD) in rare primary arrhythmic syndromes; however, it is unknown whether common
variation in these same genes may contribute to SCD risk at the population level.
Methods and Results: We examined the association between 147 single nucleotide
polymorphisms (SNPs) (137 tag, 5 non-coding SNPs associated with QT interval duration and 5
nonsynonymous SNPs) in 5 cardiac ion channel genes, KCNQ1, KCNH2, SCN5A, KCNE1 and
KCNE2 and sudden and/or arrhythmic death in a combined nested case-control analysis among
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516 cases and 1522 matched controls of European ancestry enrolled in six prospective cohort
2222 located
loca
lo
cate
ca
tedd in in
te
iintron
n
studies. After accounting for multiple testing, two SNPs (rs2283222
11 in
0
0524
s
KCNQ1 and rs11720524
located in intron 1 in SCN5A) remained significantly as
associated
with
d
coo of the major
sudden/arrhythmic death
(FDR = 0.01 and 0.03 respectively). Each increasing copy
T allele of rs22832222 or the major C allele of rs1172052 was associated with an OR = 1.36 (95%
CI 1.16-1.60, P=0.0002) and 1.30 (95% CI 1.12-1.51, P=0.0005) respectively. Control for
cardiovascular risk factors and/or limiting the analysis to definite SCDs did not significantly alter
these relationships.
Conclusion: In this combined analysis of 6 prospective cohort studies, two common intronic
variants in KCNQ1 and SCN5A were associated with SCD in individuals of European ancestry.
Further study in other populations and investigation into the functional abnormalities associated
with non-coding variation in these genes may lead to important insights into predisposition to
lethal arrhythmias.
Key words: death, sudden; genetics; ion channels; epidemiology
2
Introduction:
There are an estimated 250,000 to 400,000 sudden cardiac deaths (SCD) annually in the
United States1, and over half are the initial manifestation of heart disease2. Although the majority
of these deaths are associated with coronary artery disease3; the factors determining
predisposition to arrhythmia in the presence of ischemia or infarction remain poorly understood.
There is emerging evidence that a proportion of the familial contribution to SCD risk is distinct
from that associated with other manifestations of atherosclerosis4-6. For example, individuals
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with a familial history of SCD are more likely to experience SCD6 and/or ventricular fibrillation
during acute myocardial infarction5. These data suggest that there
her
eree ma
mayy be ggen
genetic
e
en
factors that
confer a predisposition to fatal ventricular arrhythmias
y
even in the se
sett
setting
ttin
tt
ingg of aatherosclerosis or
in
other acquired disease
s states.
se
Cardiac ion channels
c
play a critical role in cardiac electrophysiology7, an
and
n perturbation of
their function can result in SCD by lethal ventricular arrhythmias in a wide range of conditions8.
While many ion channels and other proteins are involved in the genesis and maintenance of
normal cardiac rhythm, genetic analyses of rare arrhythmic disorders have definitively
established a critical role for 5 particular ion channel genes in arrhythmia vulnerabilitys8, 9. These
genes encode the cardiac sodium channel (SCN5A), and ion channels regulating the slow
component (KCNQ1 and KCNE1) and the rapid component (KCNH2 and KCNE2) of the delayed
rectifier potassium current (IKs and IKr respectively). While the primary arrhythmic disorders
associated with mutations in these same genes are rare, there are data to suggest that common
variants may result in subclinical alterations in ion channel function10-17 that may only become
clinically manifest in the setting of other proarrhythmic factors, such as atherosclerosis or drugs.
3
In order to address the hypothesis that common variants in these genes might be
associated with SCD within the general population, we assembled SCD cases from six NIHfunded prospective cohorts and utilized a prospective nested case-control design to test for
associations between common genetic variation in coding and non-coding regions of these five
ion channel genes and SCD among individuals of European ancestry.
Methods
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Study Populations:
The prospective cohorts included in the present investigation
tio
i n in
incl
include
clud
cl
udee th
ud
thee Physicians’
Health Study (PHS I and II), the Nurses’ Health Study (NHS), the Health Professionals
Profes
Followup Study (HPFS), the
h Women’s Health Study (WHS), and the Women’s Antioxi
he
Antioxidant
i
Cardiovascular Study
y (WACS). Together, these cohorts include a total of 40,8788 men and 67,093
women with stored blood samples. The details of the cohorts along with the proportion of
participants who donated blood samples at baseline are outlined in Supplemental Table 1. In
brief, the NHS and HPFS are prospective observational cohort investigations, and the PHS I,
WHS, and WACS studies were initially randomized trials of aspirin and/or vitamin supplements
in which the intervention phases have ended. Prospective follow-up is ongoing in PHS I and
WHS. The PHS II is an ongoing randomized trial of vitamin supplementation. Information about
medical history, lifestyle choices, and incident disease is assessed either annually or biennially
by self-administered questionnaires.
4
Endpoint Confirmation
The study end points include incident cases of sudden and/or arrhythmic cardiac death
that occurred after return of the blood sample and before April 1, 2007. All cohorts employed
similar methods to document endpoints as has been previously described in detail18. Among the
individuals who donated blood samples at baseline, 540 sudden/arrhythmic deaths were
confirmed, and 536 of these had DNA samples that passed our quality control standards. A
cardiac death was considered a definite SCD if the death or cardiac arrest that precipitated death
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occurred within one hour of symptom onset as documented by medical records or next-of-kin
reports (n=389, 72.6%) or had an autopsy consistent with SCD (i.e.
i.e. acute
acut
ac
utee coronary
ut
coro
co
rona
ro
na thrombosis
r
rtery
disease without myocardial necrosis or other pathologi
i findings to
or severe coronary artery
pathologic
explain death; n=23,, 4.3%). Unwitnessed deaths or deaths that occurred during ssleep were
considered probable SCDs if the participant was documented to be symptom freee when last
observed within the preceding 24 hours, and circumstances suggested that the death could have
been sudden (n= 92, 17.2%)19.
Deaths were also classified as arrhythmic or non-arrhythmic based on the definition of
Hinkle and Thaler20. An arrhythmic death was defined as an abrupt spontaneous collapse of the
circulation (pulse disappeared) without evidence of prior circulatory impairment (shock,
congestive heart failure) or neurologic dysfunction (change in mental status, loss of
consciousness, or seizure). Deaths before which the pulse gradually disappeared and/or those
preceded by circulatory or neurologic impairment were considered non-arrhythmic deaths, and
these deaths were excluded from the SCD endpoint even if the death occurred within one hour
of symptom onset. Deaths which fulfilled the criteria for arrhythmic death, but were preceded
5
by greater than one hour of symptoms (n= 32, 6.0%) were also included in the combined
endpoint of sudden and/or arrhythmic cardiac death.
Selection of Controls:
Using risk-set sampling21, we randomly selected up to three controls for each case
matched on study cohort, sex, age (+/- 1 year), ethnicity, smoking status (current, never, past),
time and date of blood sampling, fasting status, and presence or absence of cardiovascular
disease (MI, angina, CABG, or stroke) prior to death. Since very few cases among other
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ethnicities (n= 20) occurred in these predominantly European-derived cohorts and to reduce the
risk of population stratification, analyses were limited to self-described
crib
ib
bed whites
whi
hittes (n=516).
((nn
i
ium
Linkage Disequilibrium
Characterization and SNP Selection:
Given recent data highlighting the importance
r
of non-coding regions in genetic
g
association studies22 and on ion channel function14, we tested for associations between SNPs in
both coding and non-coding regions of the candidate genes, including 5kb upstream and
downstream using a tag SNP strategy. We used genotypes available from the International
HapMap CEU (release 22) sample of northern and western European ancestry (120 independent
chromosomes), and the program Tagger23 was used to select tag SNPs that capture SNPs with
minor allele frequency •5% in the reference pedigrees at a minimum r2 of 0.8. A total of 137 tag
SNPs were selected and successfully genotyped. We also genotyped 5 additional non-coding
variants shown to be associated with QT interval duration in a recent genome-wide association
study16 as well as 5 single nonsynonymous SNPs with reported frequencies over 1 percent in
Caucasians known either to be associated with intermediate markers, such as QT interval, or
documented to have functional significance in cellular models11, 12, 15, 24, 25. These SNPs captured
6
the majority of common variation at the 5 gene loci, with mean r2 to the target SNPs with minor
allele frequency t5% in HapMap CEU of 0.87 (KCNQ1), 0.90 (KCNH2), 0.95 (SCN5A), 0.77
(KCNE1), and 0.86 (KCNE2). The SNPs captured a large proportion of the SNPs at each locus at
r2 > 0.50 (0.85, 0.96, 1.0, 0.92, 1.0, respectively)
Finemapping of associated SNPs
For tag SNPs found to be associated with sudden/arrhythmic death, we attempted to
further refine the signals of association by additionally genotyping partially correlated SNPs.
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Specifically, we examined all SNPs within 50kb of the associated variant (sentinel SNP) in
h r2 > 0.20
0.220 to the sentinel
HapMap CEU (release 24) and identified variants (target SNPs) with
c a parsimonious subset of finemapping SNPs using Tagge
cted
e such that
SNP. We then selected
Tagger
every target SNP was
a captured by pairwise correlation r2 > 0.80 to any one of th
as
the
h finemapping
SNPs.
Genotyping and Quality Control
Genomic DNA was extracted from the buffy coat fraction of centrifuged blood using
Qiagen Autopure kits (Valencia, CA) in NHS, HPFS, and WACS and from whole blood in PHS
I. In WHS and PHS I, DNA was extracted using the MagNA Pure LC instrument with the
MagNA Pure LC DNA isolation kit (Roche Applied Science, Penzberg, Germany). All assays
were conducted without knowledge of case status, and samples were labeled by study code only.
Matched case-control pairs were handled identically and assayed in the same analytical run. All
cohort DNA samples were genotyped together in the same experiment. For all SNPs except
rs1805123 in KCNH2, genotyping was performed on the Sequenom platform (San Diego, CA)
which resolves allele-specific single-base extension products using mass spectrometry (MALDI7
TOF). DNA samples with successful genotyping on fewer than 60% of SNPs selected were
excluded from analysis. Genotypes for SNPs included in the analysis passed our quality control
thresholds (call rate t95%, Hardy-Weinberg equilibrium p>0.01 in controls). Blinded replicate
quality control samples were included and genotyped with 99.82 percent agreement. Genotyping
for rs1805123 was performed using a TaqMan 5-nuclease allelic discrimination assay with
standard protocols and blinded replicate quality control samples were genotyped with 100%
agreement.
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Statistical analysis
re ccalculated
alcu
al
lculla
late
t d for
fo cases and
Means or proportions for baseline cardiac risk factors were
controls. The significance
c
cance
of risk factor associations were tested with the Chi-squ
Chi-square
u statistic for
categorical variabless and with the Student’s t-test for continuous variables. For eeach cohort, we
investigated deviation
o from Hardy-Weinberg equilibrium among controls using a F2 goodnesson
of-fit test. We analyzed the association between each SNP and the risk of sudden and/or
arrhythmic cardiac death using conditional logistic regression analysis. With risk-set analysis,
the odds ratio derived from the logistic regression directly estimates the hazard ratio, and thus,
the rate ratio or relative risk26.
In the primary meta-analysis, the conditional odds ratios for each of the individual tag SNPs
were estimated for each cohort separately under an additive model of inheritance. For the exonic
SNPs, we assessed genetic effects under all three modes of inheritance: additive, dominant, and
recessive, since prior studies reported testing of different genetic models for the nonsynonymous
SNPs. Fixed effect meta-analyses using inverse variance weights were conducted based on the
summary conditional logistic regression results for each cohort27, and PROC MIXED in SAS
8
was used for estimation of the summary effects. Tests for heterogeneity of the genetic effect
across sites were conducted using the Q-statistic28. To adjust for multiple comparisons, the false
discovery rate (FDR)29 was computed for each SNP based upon the number of SNPs tested for
each candidate gene, and an FDR <0.05 was utilized as the threshold for statistical significance
for tag SNPs without a pre-specified hypothesis.
We then further adjusted these conditional logistic regression models for additional factors. Of
the matching variables, age and smoking were not perfectly matched, and therefore these
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variables were also entered into the conditional logistic regression models to avoid any potential
orr aage,
ge,, an
ge
andd th
thee second
for residual confounding. The first multivariable model adjusted ffor
multivariable model further adjusted for standard cardiac risk factors including bbody-mass index;
history of diabetes, hypertension,
h
hyperlipidemia, and smoking. The third additio
additionally
o
adjusted
for family history off myocardial infarction, alcohol intake, physical activity, and
d aspirin use
(randomized aspirin treatment in WHS, PHS I, and reported aspirin use in the other studies). The
randomized vitamin therapies in the trials had no effect on any cardiovascular outcome, and
therefore, we do not adjust for their use in the model.
Statistical analysis was performed using SAS statistical software (SAS Institute Inc,
Cary, NC), Version 9.1.
Results
A total of 516 cases (188 women and 328 men) of sudden and/or arrhythmic cardiac
deaths occurred among subjects with European ancestry in the six cohorts over an average
follow-up of 13.0 years. The clinical characteristics of the 516 cases and 1522 controls are
displayed by study cohort in Table 1. The mean age of the cases was 64.2 years old and 201
9
(39.0%) reported a history of cardiovascular disease (CVD) prior to the SCD. In pooled
analyses, cases were more likely to report a history of diabetes, hypertension, and a higher body
mass index (p<0.005 for all comparisons). Cases did not differ significantly with respect to a
history of hypercholesterolemia, family history of MI and/or aspirin use from the controls. Of the
total study group, 509 cases and 1507 matched controls were successfully genotyped according
to our pre-specified criteria. The genotyping call rates for the 142 SNPs ranged from 96.1% to
100%. There was no difference in the average call rate between cases and controls (97.2 vs
97.1%).
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Association between Ion Channel Tag SNPs and SCD:
lts from the primary fixed-effects meta-analysis for each of the
t 137 ion
The full results
channel tag SNPs and
n the 5 intronic SNPs known to be associated with QT interval
nd
intervv are outlined
in the supplement (Supplementary
S
Supplementary
Table 2). Fifteen of the 142 SNPs were nomin
nominally
n
significant
(P < 0.05) under an additive genetic model of inheritance in three of the genes. These included 4
out of 9 tested in KCNE1, 7 out of 68 in KCNQ1, and 4 out of 47 in SCN5A. None of the intronic
SNPs known to be associated with QT interval or the tag SNPs in KCNE2 and KCNH2 reached
this level of significance. To account for multiple tests within each gene, we computed the false
discovery rate, and two tag SNPs (rs2283222 in KCNQ1 and rs11720524 in SCN5A) remained
strong candidates for sudden/arrhythmic death (FDR = 0.01 and 0.03 respectively). SNP
rs2283222 is located in intron 11 in KCNQ1 (Figure 1) and rs11720524 is located in intron 1 of
SCN5A near the promoter region (Figure 2). Another SNP in KCNE1, rs11701049, was of
borderline significance (FDR =0.051).
In an attempt to further refine the signals of association at KCNQ1 and SCN5A, we
genotyped an additional 10 SNPs with r2 > 0.20 to rs2283222 (KCNQ1) or rs11720524
10
(SCN5A), respectively, and one SNP at each locus failed. None of the 8 passing finemapping
SNPs were more strongly associated with sudden/arrhythmic death than the two sentinel SNPs
(supplementary table 3).
Table 2 displays the individual cohort specific associations for the “at risk” allele for the
two sentinel SNPs that remained associated with sudden/arrhythmic death after accounting for
multiple testing. Allele frequencies did not differ among the control groups (P=0.33 for
rs2283222 and P=0.84 for rs11720524), and the pooled at-risk or major allele frequency was
0.67 for the T allele in rs2283222 and 0.60 for the C allele in rs11720524. The associations of
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both SNPs with sudden/arrhythmic death were largely consistent across the six studies (Table 2),
and the test for heterogeneity of the odds ratios was non-significant
ant (P=
(P= 0.65
0.6
65 fo
forr rs2283222 and
P=0.58 for rs11720524).
5
524).
Further control
r for age and other cardiovascularr and lifestyle risk factors
rol
factors (Table 3) did
not materially affect these associations. In the full multivariable model, the OR ffor
sudden/arrhythmic death was 1.39 per T-allele copy (95% CI; 1.16 to 1.66, P=0.0003) for
rs2283222 and 1.34 (95% CI; 1.13 to 1.58, P=0.0007) per C-allele copy for rs11720524. Results
for both SNPs were also not materially altered in sensitivity analyses excluding possible SCDs
(Table 3). To demonstrate the independent associations for each SNP, we included both SNPs in
the fully adjusted multivariable model, and found that both SNPs remained strongly associated
with sudden/arrhythmic death (OR=1.38/T-allele copy, 95%CI: 0.1.16-1.64, P= 0.0002 for
rs2283222 and OR=1.36/C-allele copy, 95%CI, 1.16 – 1.60, P= 0.0002 for rs11720524).
Association between Non-Synonymous SNPs and SCD:
In addition to the linkage disequilibrium-based approach relating common genetic
variation in the five candidate genes, we directly tested 5 nonsynonymous SNPs. Table 4 lists the
11
results obtained in the primary fixed-effects meta-analysis for these SNPs under dominant,
additive and recessive genetic modes of inheritance. None of these SNPs achieved a nominal
level of significance in any of the genetic models or after multivariable adjustment (data not
shown).
Discussion:
In this combined nested case-control analysis from six prospective cohorts, two common
intronic variants in KCNQ1 and SCN5A were significantly associated with sudden and/or
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arrhythmic death in individuals of European ancestry after adjustment for multiple testing. The
or th
thee T al
alle
lele
le
le aat rs2283222 in
at-risk alleles are common, with population frequencies of 67% ffor
allele
w
KCNQ1 and 60% forr the C allele at rs11720524 in SCN5A. The associations betw
between
each allele
r
rrhythmic
death were independent of the other and were not mediated by
and sudden and/or arrhythmic
k factors. In the full multivariable models including both var
r
established CHD risk
variants,
each of
the at risk alleles was associated with a 39 to 41% higher odds ratio of sudden/arrhythmic death.
None of the five exonic SNPs tested were associated with sudden/arrhythmic death in the
combined sample.
Rare mutations in these two ion channel genes have been associated with rare Mendelian
arrhythmic disorders, most notably the long QT syndrome. KCNQ1 encodes the alpha subunit of
the slow component of the delayed rectifier potassium current and mutations in this gene account
for the majority of long QT syndrome cases7, 9. Mutations in SCN5A, which encodes the cardiac
sodium channel, are a less common cause of long QT syndrome, but are also associated with
multiple other discrete phenotypes with a propensity for ventricular arrhythmias, most notably
the Brugada syndrome8, 9. Recently, mutations and rare variants with functional effects in SCN5A
12
and KCNQ1 were found in 6.5% of SIDS victims30, and rare variants in SCN5A were found in
10% of a sample of SCD cases among women within one of these populations31.
To our knowledge, this is the first study linking common variation in these ion channel
genes to sudden arrhythmic death within the general population. Common variants in introns and
exons of these genes have previously been documented to modify ion channel function in
cellular electrophysiology studies10, 14 and to be associated with conduction intervals13 and
repolarization phenotypes16, 17 on the electrocardiogram. As has been previously documented for
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intermediate traits such as QT interval32 and other complex phenotypes22, common variation in
intronic DNA sequence exhibited stronger associations with sudden/arrhythmic
den/a
/arr
/a
rrhy
rr
hyth
hy
thmi
th
micc ddeath than
mi
known common exonic
nic missense SNPs. Presumably these intronic variants exertt their influence
through gene expression,
sion, and although neither SNP is in strong LD with a knownn coding variant,
further work will be required to exclude coding variants as the source of these association
ass
signals. Future studies on the genetic basis of arrhythmic risk will need to include functional
analyses of non-coding variants as well as those that result in amino acid changes.
Although, we found that sequence variants at the KCNQ1 and SCN5A loci are associated
with sudden/arrhythmic death risk, it is not known whether these specific SNPs are the
functional variants or are in LD with a functional allele. Our fine-mapping did not find a more
strongly associated correlated allele; however, deep resequencing would be required to fully
define the set of all candidate alleles, and much larger sample sizes would be required to
distinguish among all correlated alleles at the locus. The SNPs are also not in LD with other
common intronic variants in these same genes recently found to be associated with QT interval16,
13
17
, and five non-coding variants in KCNQ, KCNH2 and SCN5A that influence QT interval16 were
not associated with sudden/arrhythmic death in these cohorts.
From a pathophysiologic standpoint, these data suggest that common variation in genes
that directly influence cardiac electrophysiology may influence SCD risk at the population level.
Recently, variation at a genetic locus found to influence QT interval, the nitric oxide synthase 1
adaptor protein (NOS1AP) gene, was also found to be associated with SCD in two populationbased studies33. These genetic markers, once validated in other populations, may eventually be
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useful for SCD risk prediction in combination with markers for other pathways contributing to
egard
rdle
rd
less
le
ss ooff su
suc
ch populationSCD risk such as atherosclerosis and/or autonomic instability. Regardless
such
r
rther
study of the functional consequences of these variants oon cardiac
level application, further
m lead to important advances in our understanding of the m
electrophysiology may
mechanisms
d could ultimately lead to novel therapeutic approaches.
underlying SCD and
Strengths of the present analysis include the large well-characterized cohorts, the
combined large number of rigorously confirmed sudden and/or arrhythmic cardiac deaths, and
the prospective design that allowed us to match on follow-up time at risk reducing survival bias.
The study also has several limitations that deserve consideration. First, the low frequency at
which SCD occurs in the general population and the inherent difficulties in documenting the
circumstances surrounding out of hospital deaths in free living populations limits the number of
rigorously phenotyped SCD cases even in large cohort studies. As a result, we needed to pool
cases from independent cohorts to achieve adequate statistical power. Although the associations
between both of the SNPs and sudden/arrhythmic death were relatively consistent across the six
14
studies, this does not substitute for an independent replication study of comparable size and
phenotype, which would be needed to establish certainty regarding the observed associations.
Second, although CHD underlies the majority of SCDs3, other pathologies account for a sizeable
minority, especially among women34. Therefore, associations may differ depending on presence
and type of underlying structural heart disease. The absence of autopsy data in this population
based study precludes our examination of this important question. Also, we did not have power
to evaluate with certainty other plausible interactions by age, sex, and cardiovascular disease
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status as well as gene-gene interactions. Similarly, there were variants of borderline significance
that may have reached statistical significance in a larger sample si
size.
izee. Th
Thir
Third,
ird,
ir
d oour
d,
ur sstudy sample is
y and the relevance of the 2 variants described to populations
y,
populationn of different
of European ancestry,
n Fourth, baseline electrocardiograms were nott collected in these
n.
t
ancestry is unknown.
cohorts,
and therefore, we did
d not have data on potential electrocardiographic intermediat
intermediate
t markers, such
as QRS duration and QT interval. Finally, the selective composition of the cohorts, U.S. health
professionals, may limit the generalizability of the findings to other populations with differing
prevalence of CVD and/or CVD risk factors.
In summary, common variants in the genes encoding the slow component of the cardiac
potassium channel (KCNQ1) and the alpha subunit of the cardiac sodium channel (SCN5A) are
associated with significantly increased risks of sudden and/or arrhythmic cardiac death in this
combined population of European-derived men and women. These findings highlight the
important role these two cardiac ion channel channels may play in propensity toward fatal
ventricular arrhythmias not only in the rare primary arrhythmic disorders, but also in more
common forms of sudden cardiac death. Therefore, further investigation into the functional
15
abnormalities associated with non-coding variation in these genes may lead to important insights
regarding mechanisms underlying ventricular arrhythmias in the general population. Ultimately,
if these findings are replicated in other populations, variants in these genes in combination with
other validated genetic, biologic and environmental SCD risk markers may advance risk
prediction for this lethal and poorly predicted disease.
Acknowledgement: We are indebted to the participants in the Harvard Cohort Studies and their
families for their outstanding commitment and cooperation, and to Julie Pester, Lisa Dunn,
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Barbara Egan, Helena Judge Ellis, Joanne Smith, and Olga Veysman for their expert assistance.
less, and
le
and Patrick
Pat
atri
rick
ri
ck Ellinor for his
We thank Gabriel Crawford for his genotyping of the SCD samples,
assistance with the genotyping for rs1805123.
g This project was supported by grants from the National He
g:
Heart,
e
Lung, and
Sources of Funding:
Blood Institute (HL068070
0
068070
to Dr. Albert) and the Doris Duke Foundation (Clinic
(Clinical
c Innovation
rt and MacRae)
Award to Drs. Albert
MacRae). Additional support for the DNA extraction iin the Women’s
Health Study came from the Donald W. Reynolds Foundation. Dr. Albert is also supported by
an Established Investigator Award from the American Heart Association. Dr. Newton-Cheh was
supported by an award from the NIH (K23HL080025), a Doris Duke Charitable Foundation
Clinical Scientist Development Award, and a Burroughs Wellcome Fund Career Award for
Medical Scientists. The cohort studies were supported by grants: HL-26490, HL-34595, HL34594, HL-35464, HL-043851, HL-46959, HL-080467 from the National Heart, Lung, and
Blood Institute and CA-34944, CA 40360, CA-47988, CA55075, CA-87969, CA 97193 from the
National Cancer Institute.
Conflict of Interest Disclosures: None
16
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19
Table 1. Cohort Specific* and Pooled Prevalence of Cardiac Risk Factors at the Time of the Blood Draw according to Case and
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Control Status.
n
Age† (SD)
years
Body mass
index (SD)
kg/m2
History of
prior CVD†
N (%)
Current
smoking†
N (%)
Diabetes
N (%)
Hypertension
N (%)
High
cholesterol
N (%)
Family
History of MI
N (%)
case
120
68.0 (7.7)
26.5 (3.8)
50 (41.7 %)
10 (8.9%)
18 (15.0%)
64 (53.3%)
62 (51.7%)
18 (15.0%)
HPFS
control
366
67.7 (7.4)
25.7 (3.5)
150 (41.0 %)
36 (10.1%)
24 (6.6%)
131 (35.8%)
163 (44.5 %)
50 (13.7 %)
PHS I
case
133
59.8 (8.9)
25.4 (3.0)
34 (25.6 %)
16 (12.0%)
14(10.5%)
63 (47.7%)
14 (11.4%)
20 (15.0%)
PHS I
control
391
59.6 (8.8)
24.6 (3.0)
94 (24.0 %)
46 (11.8%)
16 (4.1
.1 %)
97
7 (25.0 %)
45 (12.5 %)
38 (9.7 %)
PHS II
case
75
73.0 (9.0)
26.0 (4.1)
34 (45.3 %)
3 (4.0%)
13 (17.3%)
7.3%
3%)
%)
46 (61.3%)
30 (40.5%)
13 (17.3%)
PHS II
control
223
72.9 (8.8)
25.4 (2.9)
100 (44.8 %)
8(3.6 %)
15 (6.7 %)
115
5 (51.6%)
100 (44.8%)
27 (12.1 %)
NHS
case
113
60.8 (6.1)
27.2 (5.4)
48 (42.5 %)
30 (26.6%)
25 (22.1%)
69 (61.1%)
66 (58.4%)
30 (26.6%)
NHS
control
327
60.7 (6.1)
26.5 (5.1)
134 (41.0 %)
67 (20.5%)
31 (9.5 %)
149 (45.6 %)
188 (57.5%)
65 (19.9%)
WACS
case
37
66.4 (7.1)
29.5 (7.1)
28 (75.7 %)
9 (24.3%)
11 (29.7%)
30 (81.1%)
24 (64.9%)
10 (27.0%)
WACS
control
109
66.1 (6.8)
28.9 (6.0)
83 (76.2 %)
27 (24.8%)
19 (17.4 %)
82 (75.2 %)
83 (76.2 %)
39 (35.8 %)
WHS
case
38
58.8 (8.5)
26.7 (4.6)
7 (18.4 %)
10 (26.3%)
4 (10.5%)
20 (52.6%)
12 (31.6%)
3 (7.9%)
WHS
control
106
58.5 (8.3)
26.9 (5.6)
17 (16.0%)
30 (28.3%)
6 (5.7 %)
38 (35.9 %)
41 (38.7 %)
15 (14.2 %)
Total
case
516
64.2 (9.4)
26.5 (4.5)
201 (39.0 %)
78 (15.3%)
85 (16.5 %)
292 (56.7 %)
208 (41.2 %)
94 (18.2 %)
Total
control
1522
64.1 (9.2)
25.9 (4.3)
578 (38.0 %)
214 (14.1%)
111 (7.3 %)
612 (40.3 %)
620 (41.6 %)
234 (15.4 %)
Cohort*
Case/
Control
HPFS
*PHS I, PHSII, HPFS participants are all men. NHS, WHS, and WACS participants are all men
† Matching Factor
20
Table 2. Cohort Specific Associations between rs2283222 in KCNQ1 and rs11720524 in SCN5A and Sudden Cardiac Death. Shown are the
Downloaded from http://circep.ahajournals.org/ by guest on June 16, 2017
individual cohort specific and combined meta-analysis odds ratios (95% CI) for increasing copy of the “at risk” T allele of rs2283222 in KCNQ1 and
C allele of rs11720524 in SCN5A from the conditional logistic regression models under an additive model of inheritance.
Cohort
Case/
control
rs2283222 (KCNQ1)
rs11720524 (SCN5A)
n
Frequency of TAllele
OR per T-Allele
(95% CI)
P-value
1.24
(0.90-1.72)
0.18
1.27
(0.92-1.75)
0.15
1.58
(1.02–2.44)
0.04
1.57
(1.12-2.21)
0.01
1.69
(0.92-3.11)
0.09
0.99
(0.56 -1.73)
0.96
1.36
(1.16-1.60)
0.0002
HPFS
case
116
0.720
HPFS
control
340
0.671
PHS I
case
130
0.735
PHS I
control
378
0.689
PHS II
case
72
0.771
PHS II
control
208
0.676
NHS
case
109
0.734
NHS
control
320
0.636
WACS
case
37
0.770
WACS
control
109
0.665
WHS
case
38
0.697
WHS
control
103
0.704
Metaanalysis
case
502
0.736
Metaanalysis
control
1458
0.670
n
Frequency of CAllele
OR per C-Allele
(95% CI)
P-value
116
0.599
0.62
339
0.586
1.08
(0.80-1.46)
132
0.686
0.03
385
38
5
0.608
1.40
(1.04-1.87)
73
0.623
0.56
212
0.594
1.12
(0.76-1.64)
108
0.690
0.008
317
0.585
1.56
(1.12-2.17)
36
0.653
0.30
106
0.590
1.34
(0.77-2.35)
38
0.724
0.15
106
0.632
1.53
(0.86-2.75)
503
0.658
1.30
(1.12-1.51)
0.0005
1465
21
0.596
Table 3. Multivariable and Sensitivity Analyses: Association of sudden cardiac death with two ion
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channel variants. Shown are the meta-analysis odds ratios (95% CI) with increasing levels of risk factor
adjustment for increasing copy of the T-allele of rs2283222 in KCNQ1 and the C-allele of rs11720524 in
SCN5A.
Genetic Variant
OR(95% CI)
P-value
OR(95% CI)
for All SCD
for Definite SCD*
(Primary Analysis)
(N= 425)
P-value
rs2283222
Age-adjusted
1.36 (1.15-1.59)
0.0002
1.33 (1.11-1.59)
1.59)
0.002
0.
Multivariate Model 1†
1.37 (1.16-1.63)
0.0003
1.34 (1.11-1.63)
1.6
63)
0.003
0.
Multivariate Model 2‡
1.39 (1.16-1.66)
.66)
0.0003
1.36 (1.11-1.67)
0.003
0.
1.31 (1.12-1.52)
.52)
0.0005
1.32 (1.12-1.56)
0.001
0.
1.33 (1.13-1.55)
0.0004
1.35 (1.13-1.62)
0.0009
1.34 (1.13-1.58)
0.0007
1.35 (1.12-1.64)
0.002
rs11720524
Age-adjusted
Multivariable Model 1
†
‡
Multivariate Model 2
* Sensitivity Analysis: Excluding probable sudden cardiac death cases (i.e. Unwitnessed deaths or deaths that occurred during sleep where the
participant was documented to be symptom free when last observed within the preceding 24 hours)
†
Multivariable Model 1: Controlled simultaneously for age, smoking status (current, past, never), BMI (continuous), history of diabetes,
hypertension, and high Cholesterol.
‡
Multivariable Model 2: Controlled for variables listed above in multivariable Model 2 and family history of myocardial infarction, alcohol intake
(<weekly, weekly, daily, 2 or more per day); physical activity (at least once per week) and aspirin (> or = 11 days/month
22
Downloaded from http://circep.ahajournals.org/ by guest on June 16, 2017
Table 4. Association between Ion Channel Amino Acid Polymorphisms and Sudden Cardiac Death: Primary fixed-effects meta-analysis odds ratios
and 95 percent confidence intervals for the minor allele according to additive, dominant and recessive modes of inheritance.
Gene
Amino
SNP ID
Acid
Genomic
Allele
Context
(A/a)
MAF
Additive
Dominant
Recessive
Change
OR
95% CI
P
OR
95% CI
P
OR
95% CI
-
-
P
KCNE1
D85N
rs1805128
34743550
G/a
0.02
1.18
(0.60-2.31)
0.63
1.18
(0.60-2.31)
0.63
KCNE1
S38G
rs1805127
34743691
C/t
0.35
1.02
(0.88-1.19)
0.77
0.77
1.14
1
1..
(0.93-1.41)
0.20
KCNE2
T8A
rs2234916
34664669
A/g
0.01
1.12
(0.31-4.03)
0.87
1.12
1.
(0.31-4.03)
0.87
KCNH2
K897T
rs1805123
150083182
A/c
0.23
0.91
(0.76-1.10)
0.32
0.89
0.
(0.72-1.10)
0.28
1.02
(0.59-1.77)
0.93
SCN5A
H558R
rs1805124
38620424
A/g
0.23
1.08
(0.91-1.27)
0.39
1.14
1.
(0.92-1.40)
0.23
0.94
(0.61-1.46)
0.79
23
0.82
-
(0.59-1.12)
-
0.21
-
Figure legends
Figure 1. Regional association plot across KCNQ1 locus. Statistical significance of
associated SNPs at each locus are shown on the –log10(p) scale as a function of
chromosomal position (NCBI Build 36). The primary associated SNP at the locus
(rs2283222) is shown as a large red diamond. The correlation of the primary SNP to
other SNPs (smaller diamonds) at the locus is shown on a scale from minimal (white) to
Downloaded from http://circep.ahajournals.org/ by guest on June 16, 2017
maximal (bright red). Estimated recombination rates from HapMap and RefSeq
annotations are shown.
o
onal
association plot across SCN5A locus. Statistical signif
f
Figure 2. Regional
significance
of
associated SNPs at each locus are shown on the –log10(p) scale as a function of
o
osition
l
chromosomal position
(NCBI Build 36). The primary associated SNP at the locus
(rs11720524) is shown as a large red diamond. The correlation of the primary SNP to
other SNPs (smaller diamonds) at the locus is shown on a scale from minimal (white) to
maximal (bright red). Estimated recombination rates from HapMap and RefSeq
annotations are shown.
24
017
017
Common Variants in Cardiac Ion Channel Genes Are Associated with Sudden Cardiac Death
Christine M. Albert, Calum A. MacRae, Daniel I. Chasman, Martin VanDenburgh, Julie E. Buring,
JoAnn E. Manson, Nancy R. Cook and Christopher H. Newton-Cheh
Circ Arrhythm Electrophysiol. published online April 17, 2010;
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Circulation: Arrhythmia and Electrophysiology is published by the American Heart Association, 7272 Greenville Avenue,
Dallas, TX 75231
Copyright © 2010 American Heart Association, Inc. All rights reserved.
Print ISSN: 1941-3149. Online ISSN: 1941-3084
The online version of this article, along with updated information and services, is located on the
World Wide Web at:
http://circep.ahajournals.org/content/early/2010/04/17/CIRCEP.110.944934
Data Supplement (unedited) at:
http://circep.ahajournals.org/content/suppl/2010/04/17/CIRCEP.110.944934.DC1
Permissions: Requests for permissions to reproduce figures, tables, or portions of articles originally published in
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SUPPLEMENTAL MATERIAL
Supplemental Table 1. Details of Prospective Cohorts included in the Present Analyses
Study
Study description
Physicians’ Health
Study I (PHS I)
Randomized
clinical trial of
aspirin and betacarotene
Randomized
clinical trial of
antioxidants and
multivitamin
Prospective cohort
study
Prospective cohort
study
Year of
inceptio
n
1982
Participants
22,071 male physicians, aged
40-84 in 1982, free of prior
CVD or cancer.
Number
with blood
samples
15,124
Years of
Blood
Collection
1982-1984
Follow-up
Years
1,218
1996-1998
8.3
1995-2002
8.4
1989-1990
16.4
1993-1994
10.5
1993-1996
10.6
1993-1996
9.0
11,133†
14,641 male physicians, aged
>=50 years, including 7,641
PHS I and 7,000 new
participants.
Nurses’ Health
1976
121,700 female registered
32,826
Study (NHS)
nurses, aged 30-55 in 1976
Health Professionals
1986
51,529 male health
18,018
Follow-up Study
professionals, aged 40-75 in
(HPFS)
1986
28,345
1992
39,876 female health
Women’s Health
Randomized
professionals, aged 40 or older
Study (WHS)
clinical trial of
in 1992, free of prior CVD or
aspirin and vitamin
cancer
E
5,922
1996
8,171 female health
Randomized
Women’s
professional aged 40 or older
clinical trial of
Antioxidant
with CVD or at least three
antioxidants and BCardiovascular
coronary risk factors
vitamins
Study (WACS)
† Of these, 6,518 blood samples are from men who have not previously donated a blood sample in PHS I
Physicians’ Health
Study II (PHS II)
1997
20.8
Supplemental Table2. Association between ion channel tag SNPs and sudden cardiac death in 516
cases and 1522 matched controls. Primary fixed-effects meta-analysis odds ratios, 95% confidence
intervals, and false discovery rate for the minor allele according to additive mode of inheritance.
Gene
SNP
Position
KCNE1
KCNE1
KCNE1
KCNE1
KCNE1
KCNE1
KCNE1
KCNE1
KCNE1
KCNE2
KCNE2
KCNE2
KCNE2
KCNE2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
KCNH2
rs16991703
rs1547357
rs11088283
rs7277816
rs2070359
rs4239794
rs11701049
rs7279771
rs11700452
rs2834466
rs2834468
rs12626687
rs11702471
rs9305548
rs2968864
rs758887
rs4725982
rs11763311
rs3815459
rs2072413
rs3807375
rs3778873
rs748693
rs11771844
rs2373885
rs2373962
rs2373961
34,742,835
34,744,628
34,745,649
34,747,280
34,748,646
34,760,999
34,790,014
34,793,249
34,815,512
34,648,888
34,653,106
34,655,160
34,656,717
34,664,592
150,059,810
150,072,096
150,075,511
150,076,280
150,082,042
150,085,617
150,104,858
150,107,515
150,109,085
150,113,558
150,115,728
150,118,625
150,118,858
Alleles
A/g
C/t
A/g
G/c
G/a
T/g
T/c
T/c
A/g
T/c
C/t
G/a
T/c
C/t
A/g
G/a
C/t
G/a
G/a
G/a
G/a
G/c
A/g
G/a
A/g
G/c
G/a
MAF in
controls
0.057
0.321
0.465
0.234
0.193
0.389
0.174
0.263
0.115
0.151
0.054
0.294
0.120
0.153
0.235
0.240
0.237
0.119
0.226
0.256
0.369
0.177
0.348
0.070
0.264
0.367
0.372
OR 95% CI
0.86 (0.62-1.20)
1.19 (1.03-1.39)
1.10 (0.95-1.28)
0.97 (0.82-1.15)
1.01 (0.84-1.21)
0.86 (0.74-1.00)
1.30 (1.08-1.55)
0.97 (0.82-1.14)
1.32 (1.07-1.63)
1.00 (0.81-1.24)
1.31 (0.98-1.75)
1.01 (0.86-1.18)
0.84 (0.67-1.06)
1.02 (0.83-1.25)
0.90 (0.75-1.07)
0.91 (0.76-1.08)
0.89 (0.74-1.06)
1.09 (0.87-1.36)
0.93 (0.78-1.12)
0.93 (0.78-1.10)
0.89 (0.76-1.04)
0.93 (0.77-1.14)
1.13 (0.97-1.31)
1.05 (0.79-1.39)
0.92 (0.78-1.10)
0.93 (0.80-1.08)
1.14 (0.98-1.32)
P value
FDR
0.38
0.02
0.18
0.71
0.94
0.04
0.005
0.71
0.01
0.98
0.06
0.92
0.14
0.87
0.23
0.28
0.18
0.45
0.46
0.38
0.16
0.50
0.12
0.74
0.38
0.31
0.08
0.69
0.08
0.40
0.85
0.94
0.12
0.05
0.85
0.06
0.98
0.38
0.98
0.43
0.98
0.53
0.53
0.53
0.53
0.53
0.53
0.53
0.54
0.53
0.74
0.53
0.53
0.53
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
rs739677
rs7951832
rs2074238
rs11604259
rs12576239
rs179409
rs4929992
rs3819506
rs2012618
rs736610
rs179428
rs179429
rs179431
rs1997619
rs9299929
rs7924846
rs7126270
rs2283166
rs2283170
rs2283171
rs12282937
rs12277672
rs4930139
rs2106467
rs2412058
rs2106462
rs6578283
rs231343
rs9666537
rs10832514
rs4930005
rs231361
2,430,556
2,437,277
2,441,379
2,449,192
2,458,895
2,483,882
2,484,809
2,484,900
2,487,832
2,495,168
2,507,085
2,507,306
2,508,724
2,518,807
2,519,077
2,520,985
2,522,381
2,536,465
2,539,717
2,551,863
2,555,128
2,576,539
2,587,879
2,592,373
2,597,705
2,606,100
2,630,151
2,635,229
2,642,440
2,645,102
2,647,107
2,648,076
A/g
C/g
C/t
C/t
C/t
G/c
T/c
C/t
T/c
C/t
G/a
G/a
G/a
G/a
T/c
G/a
G/a
C/t
A/g
A/g
A/g
T/c
A/g
C/a
T/c
T/c
A/g
T/g
C/t
G/a
T/c
C/t
0.269
0.185
0.085
0.196
0.142
0.355
0.453
0.218
0.248
0.131
0.215
0.169
0.288
0.112
0.446
0.107
0.363
0.126
0.341
0.274
0.408
0.119
0.179
0.409
0.176
0.090
0.311
0.112
0.298
0.303
0.263
0.235
0.88 (0.75-1.04)
0.87 (0.72-1.06)
1.08 (0.83-1.40)
1.05 (0.87-1.27)
0.81 (0.65-1.02)
0.90 (0.77-1.06)
0.89 (0.77-1.03)
1.03 (0.86-1.22)
0.91 (0.77-1.08)
1.13 (0.92-1.39)
0.84 (0.71-1.01)
0.87 (0.71-1.06)
0.88 (0.75-1.03)
0.81 (0.64-1.04)
0.90 (0.78-1.03)
0.81 (0.63-1.05)
0.86 (0.75-1.00)
0.81 (0.64-1.02)
0.87 (0.74-1.01)
0.94 (0.80-1.11)
0.96 (0.83-1.12)
1.02 (0.81-1.28)
1.02 (0.85-1.23)
1.05 (0.91-1.21)
1.11 (0.92-1.34)
1.07 (0.84-1.37)
1.07 (0.92-1.25)
1.15 (0.92-1.44)
0.97 (0.83-1.14)
1.00 (0.86-1.17)
1.00 (0.85-1.17)
1.05 (0.89-1.24)
0.15
0.18
0.56
0.59
0.07
0.21
0.12
0.77
0.26
0.23
0.06
0.17
0.11
0.10
0.13
0.11
0.05
0.07
0.07
0.49
0.62
0.87
0.84
0.53
0.28
0.58
0.40
0.21
0.74
0.99
0.98
0.56
0.45
0.49
0.77
0.77
0.42
0.50
0.45
0.92
0.56
0.54
0.42
0.48
0.45
0.45
0.45
0.45
0.42
0.42
0.42
0.77
0.78
0.96
0.94
0.77
0.56
0.77
0.71
0.50
0.90
0.99
0.99
0.77
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
rs11023738
rs231352
rs7939976
rs231901
rs2283202
rs231887
rs10832572
rs2283205
rs231915
rs2283213
rs170786
rs231910
rs231906
rs422316
rs2283222
rs108961
rs1079714
rs7114479
rs2237876
rs231899
rs1971929
rs179785
rs463535
rs4255520
rs234886
rs234873
rs2074200
rs3852525
rs151316
rs11024137
rs2237888
rs2237892
2,655,627
2,667,398
2,668,862
2,687,761
2,694,481
2,695,756
2,696,097
2,697,903
2,705,591
2,707,120
2,707,279
2,707,861
2,709,185
2,711,910
2,712,177
2,714,561
2,717,317
2,719,804
2,721,878
2,724,543
2,729,947
2,738,095
2,738,246
2,742,199
2,758,666
2,764,098
2,773,277
2,775,770
2,776,196
2,776,329
2,789,481
2,796,327
T/c
C/t
A/g
G/a
A/g
C/t
T/g
C/t
T/c
C/t
G/a
C/t
T/c
C/t
C/t
G/a
C/t
T/c
C/t
T/c
G/c
G/a
G/a
A/g
C/g
A/g
C/g
G/a
G/a
G/a
C/t
C/t
0.064
0.494
0.175
0.119
0.432
0.086
0.086
0.185
0.404
0.058
0.281
0.465
0.424
0.499
0.670
0.456
0.095
0.410
0.261
0.294
0.139
0.481
0.175
0.163
0.098
0.469
0.219
0.219
0.198
0.069
0.136
0.057
1.00 (0.74-1.33)
0.92 (0.80-1.07)
1.09 (0.91-1.32)
1.17 (0.95-1.45)
1.00 (0.86-1.16)
1.05 (0.81-1.37)
1.35 (1.06-1.71)
0.87 (0.71-1.05)
0.99 (0.86-1.15)
1.10 (0.81-1.50)
1.09 (0.92-1.28)
1.01 (0.87-1.17)
1.04 (0.90-1.21)
0.84 (0.72-0.98)
1.36 (1.16-1.60)
1.02 (0.88-1.18)
1.33 (1.06-1.67)
0.83 (0.71-0.96)
1.07 (0.90-1.26)
0.88 (0.74-1.03)
0.92 (0.74-1.14)
0.82 (0.71-0.95)
1.11 (0.92-1.33)
0.91 (0.74-1.10)
0.83 (0.64-1.07)
0.87 (0.75-1.01)
0.88 (0.73-1.05)
1.02 (0.86-1.22)
1.05 (0.88-1.26)
0.91 (0.67-1.23)
0.97 (0.78-1.21)
0.87 (0.64-1.20)
0.97
0.28
0.34
0.13
0.95
0.69
0.01
0.15
0.92
0.53
0.32
0.91
0.58
0.03
0.0002
0.82
0.01
0.01
0.46
0.11
0.44
0.008
0.28
0.33
0.15
0.07
0.15
0.79
0.58
0.52
0.80
0.40
0.99
0.56
0.62
0.45
0.99
0.85
0.20
0.45
0.98
0.77
0.62
0.98
0.77
0.30
0.01
0.93
0.20
0.20
0.75
0.45
0.75
0.20
0.56
0.62
0.45
0.42
0.45
0.92
0.77
0.77
0.92
0.71
KCNQ1
KCNQ1
KCNQ1
KCNQ1
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
rs234854
rs4930013
rs10798
rs7108037
rs6767797
rs12053903
rs13059004
rs6799868
rs3935472
rs7374138
rs11129796
rs9812912
rs7374605
rs9861242
rs4130467
rs7428882
rs3922844
rs7374004
rs7340612
rs6599218
rs7374040
rs11708996
rs7373862
rs13062931
rs6599219
rs9871385
rs7427874
rs6770569
rs6599222
rs12491987
rs6797133
rs7433206
2,807,546
2,818,735
2,826,741
2,831,739
38,557,575
38,568,397
38,576,241
38,576,560
38,577,859
38,580,736
38,581,718
38,582,233
38,582,307
38,584,338
38,586,708
38,594,352
38,599,257
38,600,713
38,601,692
38,605,278
38,607,051
38,608,927
38,609,347
38,612,164
38,612,714
38,616,138
38,618,283
38,622,784
38,623,066
38,624,048
38,631,037
38,632,712
A/g
A/c
A/g
A/g
A/g
T/c
A/c
T/c
G/a
C/g
C/t
C/t
C/g
G/a
A/g
G/c
G/a
A/t
G/a
T/c
G/c
G/c
A/g
C/t
A/g
A/c
A/g
G/c
T/c
C/t
G/a
T/a
0.239
0.304
0.322
0.478
0.106
0.334
0.478
0.323
0.157
0.269
0.100
0.149
0.459
0.253
0.278
0.293
0.315
0.431
0.044
0.119
0.189
0.149
0.334
0.425
0.336
0.375
0.405
0.489
0.209
0.110
0.415
0.404
1.06 (0.89-1.25)
1.11 (0.95-1.28)
0.92 (0.79-1.07)
1.04 (0.90-1.20)
0.92 (0.73-1.17)
0.94 (0.81-1.10)
0.92 (0.79-1.06)
0.99 (0.85-1.16)
0.94 (0.77-1.16)
1.10 (0.93-1.30)
1.05 (0.83-1.33)
1.07 (0.87-1.31)
1.07 (0.93-1.24)
1.06 (0.90-1.25)
1.07 (0.92-1.26)
0.99 (0.85-1.17)
1.11 (0.95-1.29)
0.98 (0.84-1.13)
1.22 (0.87-1.71)
1.18 (0.95-1.46)
1.01 (0.83-1.22)
0.95 (0.78-1.17)
0.98 (0.84-1.14)
0.95 (0.82-1.10)
0.97 (0.83-1.13)
1.04 (0.90-1.21)
1.03 (0.89-1.20)
1.00 (0.87-1.15)
0.99 (0.83-1.18)
1.00 (0.79-1.28)
1.03 (0.89-1.20)
0.96 (0.83-1.12)
0.51
0.19
0.27
0.60
0.51
0.44
0.24
0.91
0.56
0.25
0.67
0.54
0.33
0.50
0.38
0.94
0.18
0.74
0.25
0.13
0.95
0.64
0.76
0.52
0.66
0.57
0.67
0.99
0.94
0.98
0.67
0.60
0.77
0.49
0.56
0.77
0.84
0.84
0.84
0.99
0.84
0.84
0.84
0.84
0.84
0.84
0.84
0.99
0.84
0.91
0.84
0.84
0.99
0.84
0.91
0.84
0.84
0.84
0.84
0.99
0.99
0.99
0.84
0.84
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
SCN5A
rs11710077
rs12498069
rs9832895
rs6781731
rs3934936
rs9876660
rs7633974
rs6795580
rs6599229
rs11720524
rs13060541
rs7427106
rs13073578
rs7373102
rs9311195
rs6763048
rs7372712
rs7373934
rs9861643
38,632,903
38,635,940
38,636,537
38,638,711
38,639,313
38,639,719
38,640,927
38,642,577
38,647,589
38,650,416
38,651,690
38,653,505
38,654,368
38,655,632
38,656,222
38,656,398
38,661,196
38,670,712
38,672,343
A/t
C/a
C/t
C/t
C/t
G/c
G/c
G/c
G/a
G/c
A/c
C/g
A/g
C/t
C/g
A/g
C/t
A/g
C/t
0.214
0.116
0.486
0.488
0.276
0.165
0.395
0.408
0.438
0.596
0.247
0.143
0.060
0.473
0.192
0.145
0.208
0.243
0.172
1.02 (0.85-1.22)
0.87 (0.69-1.09)
1.05 (0.91-1.23)
0.95 (0.82-1.10)
1.07 (0.91-1.26)
1.08 (0.89-1.32)
1.02 (0.88-1.19)
1.03 (0.89-1.20)
1.13 (0.98-1.30)
1.30 (1.12-1.51)
0.88 (0.73-1.04)
0.76 (0.61-0.95)
0.85 (0.61-1.19)
1.17 (1.01-1.34)
0.82 (0.68-1.00)
0.93 (0.75-1.16)
0.96 (0.80-1.15)
1.07 (0.90-1.26)
0.84 (0.68-1.03)
0.82
0.23
0.49
0.48
0.40
0.43
0.77
0.66
0.10
0.0005
0.14
0.02
0.34
0.03
0.04
0.53
0.64
0.46
0.09
0.94
0.84
0.84
0.84
0.84
0.84
0.91
0.84
0.82
0.03
0.84
0.37
0.84
0.49
0.53
0.84
0.84
0.84
0.82
Supplemental Table 3. Association between finemapping SNPs for rs2283222 and rs11720524 and sudden cardiac death in 516
cases and 1522 matched controls. Primary fixed-effects meta-analysis odds ratios, 95% confidence intervals, for the minor allele according
to additive mode of inheritance. Also shown is the correlation (r2) between the finemapping SNP and the sentinel SNP for each locus.
Gene
SNP
Position
KCNQ1
KCNQ1
KCNQ1
KCNQ1
KCNQ1
SCN5A
SCN5A
SCN5A
rs2283208
rs231917
rs231907
rs17743926
rs450852
rs7373154
rs6599235
rs11717818
2,700,435
2,701,683
2,708,706
2,709,169
2,712,890
38,696,312
38,697,031
38,697,700
Alleles
MAF
OR (95% CI)
P-value
G/a
C/t
A/t
G/a
G/a
T/c
C/t
C/t
0.47
0.32
0.33
0.13
0.31
0.27
0.16
0.48
0.86 (0.74-0.99)
1.11 (0.95-1.30)
1.04 (0.89-1.21)
0.84 (0.67-1.05)
1.14 (0.98-1.34)
1.05 (0.89-1.24)
1.10 (0.90-1.34)
0.87 (0.76-1.01)
0.04
0.21
0.63
0.13
0.09
0.58
0.35
0.06
r2 to
sentinel
SNP
0.45
0.20
0.27
0.42
0.28
0.20
0.20
0.22