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Received on: November 14, 2014; final version accepted on: March 30, 2015.
From the Faculty of Medicine (E.B., A.H., T.G., U.T., G.T., K.S.) and Department of Engineering and Natural Sciences (D.F.G.), University of Iceland,
Reykjavik, Iceland; deCODE Genetics, Reykjavik, Iceland (E.B., D.F.G., A.H., G.T., U.T., K.S.); Department of Medicine (T.G., K.E., G.T.), and
Department of Surgery (T.G.), Landspitali University Hospital, Reykjavik, Iceland; Division of Cardiology, Department of Medicine, Emory University
School of Medicine, Atlanta, GA (R.S.P., N.G., A.A.Q.); and Institute of Cardiovascular Sciences, University College London, London, United Kingdom
(R.S.P.).
*These authors contributed equally to this article.
The online-only Data Supplement is available with this article at http://atvb.ahajournals.org/lookup/suppl/doi:10.1161/ATVBAHA.114.304985/-/DC1.
Correspondence to Kari Stefansson, MD, PhD, deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland. E-mail kstefans@decode.is
2015 American Heart Association, Inc.
Arterioscler Thromb Vasc Biol is available at http://atvb.ahajournals.org
DOI: 10.1161/ATVBAHA.114.304985
Results
Characteristics of the Patients
A total of 8622 Icelandic patients with significant angiographic CAD (50% diameter stenosis) were included in the
main analysis. Replication was sought in 1853 patients from
the Emory Biobank. All participants were of European ancestry. Characteristics of the study patients are shown in Table1.
Diabetes mellitus, hypertension, and hyperlipidemia were more
common in patients from the Emory Biobank, whereas Icelandic
patients tended to be younger and were more likely to be current smokers. On average, patients from the Emory Biobank had
more extensive coronary disease and were more likely to have
history of myocardial infarction and coronary revascularization.
with the number of coronary arteries with at least 50% diameter stenosis in a combined analysis of the samples, adjusting
for traditional cardiovascular risk factors: age, sex, hyperlipidemia, diabetes mellitus, hypertension, current smoking, and
former smoking (Table I in the online-only Data Supplement).
Figure1 illustrates the linear relationship between the magnitude of the effects of individual SNPs on CAD extent and their
respective odds ratio for the risk of CAD, previously reported
in meta-analyses of genome-wide association studies (Table I
in the online-only Data Supplement).
The combined GRS was strongly associated with CAD
extent when adjusting for traditional cardiovascular risk factors (difference per SD increase in GRS, 0.076; P=7.31017).
Estimates in models adjusting for traditional cardiovascular
risk factors did not differ substantially from those in models
adjusted for age and sex only (Table II in the online-only Data
Supplement), and the association remained significant after
further consecutive adjustment for family history of premature
CAD (difference per SD increase in GRS, 0.072; P=3.01015;
Table III in the online-only Data Supplement). To further illustrate this relationship, we divided patients into quintiles based
on the GRS and compared the proportion of patients with
multivessel disease (2 coronary arteries with at least 50%
diameter stenosis) between the top and the bottom quintiles
(Figure2). Roughly 65% of patients in the top quintile had
multivessel disease compared with 56% of patients in the bottom quintile (Table IV in the online-only Data Supplement).
Thus, patients who were in the top quintile of the GRS were
1.67 more likely to have multivessel disease compared with
patients in the bottom quintile (adjusted odds ratio, 1.67; 95%
confidence interval, 1.451.94; Table2).
Iceland (n=8622)
P Value*
<0.001
64.4 (10.7)
65.6 (10.6)
Male sex, %
75.1
73.8
0.24
Diabetes mellitus, %
11.4
31.5
<0.001
Hypertension, %
54.3
70.7
<0.001
Hyperlipidemia, %
50.3
74.6
<0.001
Current smoker, %
27.4
14.7
<0.001
Former smoker, %
47.6
47.9
0.83
Previous MI, %
29.7
49.2
<0.001
Previous PCI, %
4.2
57.5
<0.001
Previous CABG, %
7.6
31.3
<0.001
Family history, %
43.1
44.7
0.21
1.94 (0.88)
2.10 (0.91)
<0.001
1-vessel disease
39.1
32.0
<0.001
2-vessel disease
30.3
31.6
0.30
3-vessel disease
28.1
31.3
0.007
4-vessel disease
2.5
5.1
<0.001
Data are presented as percentages or means (SD). CABG indicates coronary artery bypass grafting; MI, myocardial infarction;
and PCI, percutaneous coronary intervention.
*P values for continuous variables were calculated using Student t test. P values for categorical variables were calculated
using the 2 test.
Total number of coronary arteries with at least 50% stenosis on coronary angiography (left anterior descending, circumflex,
the right main coronary artery, and the left main coronary artery).
Model Performance
Because variants at chromosome 9p21 and LPA have previously been reported to associate with the extent of angiographic CAD,1315 we investigated whether the effect of the
GRS was dominated by these variants. After excluding variants at chromosome 9p21 (rs1333049) and LPA (rs10455872
and rs3798220) from the GRS, the association remained significant (P=8.1108; Table2). Similar results were obtained
in models additionally adjusted for family history of premature CAD and in models adjusted for age and sex only (Table
II and Table III in the online-only Data Supplement).
Figure 2. Adjusted odds ratios for multivessel disease by quintiles of the genetic risk score (GRS) in the Icelandic (black) and
Emory Biobank (gray) samples. Odds ratios are referenced to
the bottom GRS quintile and presented with 95% confidence
intervals.
As shown in Table3, the GRS significantly improved prediction of multivessel disease over cardiovascular risk factors
in models including age and sex only (model 1), traditional
cardiovascular risk factors (model 2), and family history
of premature CAD (model 3), as evaluated by likelihood
ratio tests (P<0.0001). To estimate the improvement in discrimination, we compared the C-statistics (area under the
receiver-operating-characteristic curve) for models with and
without the GRS. The C-statistics for the models without the
GRS ranged from 62.9% to 64.8% (Table3). Addition of
the GRS to the models resulted in modest increases in the
C-statistic, ranging from 0.6% to 0.8% (Table3). Similarly,
the integrated discrimination improvement ranged from
0.46% to 0.53%, indicating a marginal improvement in discrimination for multivessel disease with the addition of the
GRS (Table3).
Replication
In the Emory Biobank sample, the GRS based on 32 SNPs
was significantly associated with CAD extent (difference
per SD increase in GRS, 0.115; P=2.6108; Table2). In the
Emory Biobank sample, 77% of patients in the top quintile
of the GRS had multivessel disease compared with 62% of
patients in the bottom quintile (Table V in the online-only
Data Supplement), corresponding to an adjusted odds ratio
of 2.08 (95% confidence interval, 1.502.90; Table2). As
shown in Table3, The GRS significantly improved prediction of multivessel disease over cardiovascular risk factors
and modestly improved discrimination, as estimated by the
increase in the C-statistics for the models with the addition
of the GRS (ranging from 1.7% to 1.9%) and the integrated
discrimination improvement (1.5% for all models). The GRS
associated with age at angiography when adjusting for sex,
hyperlipidemia, diabetes mellitus, hypertension, current
smoking, and former smoking (difference per SD increase
in GRS, 0.60 years; P=0.011), but the association was not
significant when variants at 9p21 and LPA were excluded
from the GRS (difference per SD increase in GRS, 0.44
years; P=0.062).
No. of SNPs
SE
P Value
Full GRS
50
0.076 (0.0580.094)
0.0091
7.31017
1.67 (1.451.94)
47
0.049 (0.0310.066)
0.0091
8.110
1.32 (1.141.52)
Restricted GRS
32
0.072 (0.0540.089)
0.0091
3.21015
1.55 (1.341.78)
GRS
32
0.115 (0.0750.155)
0.021
2.6108
2.08 (1.502.90)
29
0.070 (0.0290.110)
0.021
7.310
1.50 (1.092.08)
Iceland (n=8622)
8
Associations were tested using linear and logistic regression models adjusted for traditional cardiovascular risk factors (age, sex, hyperlipidemia, diabetes mellitus,
hypertension, current smoking, and former smoking). CI indicates confidence interval; GRS indicates genetic risk score; OR, odds ratio; and SNP, single-nucleotide
polymorphisms.
*Multivessel disease was defined as having at least 2 coronary arteries with 50% stenosis on coronary angiography.
Discussion
In this study, we demonstrate that a genetic score based on known
common CAD risk variants is strongly associated with the extent
of coronary atherosclerosis in patients with established angiographic CAD. This association is independent of traditional cardiovascular risk factors and family history of CAD. We found
that the GRS significantly improved prediction of multivessel
disease over established cardiovascular risk factors although
the improvement in discrimination was modest. Compared
with patients in the bottom quintile of the GRS, patients in the
top quintile were roughly 1.67 (Iceland) and 2.08 (Emory
Biobank) more likely to have multivessel disease. Furthermore,
we found that the GRS associated with younger age at angiography, consistent with an earlier disease onset for individuals with
a high burden of common genetic risk variants for CAD.
Previously, a genetic variant at chromosome 9p21 and 2
variants at LPA were shown to influence the extent of coronary
Table 3. Model Prediction for Multivessel Disease With and Without the GRS
C-Statistic
Model Covariates
Without GRS, %
With GRS, %
Increase, %
IDI, %
LR 2
P Value*
Iceland (n=8622)
Model 1: age and sex only
62.9
63.7
0.8
0.53
48.7
<0.0001
64.0
64.8
0.8
0.52
48.1
<0.0001
64.8
65.4
0.6
0.46
42.7
<0.0001
60.9
62.8
1.9
1.5
28.1
<0.0001
62.1
63.8
1.7
1.5
28.4
<0.0001
62.2
63.9
1.7
1.5
28.4
<0.0001
C-statistics and the IDI are reported as percentages. CAD indicates coronary artery disease; GRS, genetic risk score; IDI, integrated discrimination
improvement; LR, likelihood ratio; and SNP, single-nucleotide polymorphisms.
*All P values reported are from likelihood ratio 2 tests for nested models.
GRS based on 50 SNPs.
Traditional cardiovascular risk factors were defined as age, sex, hyperlipidemia, diabetes mellitus, hypertension, current smoking, and former
smoking.
GRS based on 32 SNPs.
Acknowledgments
We thank all the individuals who participated in this study and whose
contribution made this work possible. We also thank our valued colleagues who contributed to the data collection and phenotypic characterization of clinical samples, as well as genotyping and analysis of
genome-wide association data.
Sources of Funding
The work was supported by Landspitali University Hospital Research
Fund, Jnna Gsladttir fund, Bent Scheving Thorsteinsson research
Disclosures
E. Bjornsson, A. Helgadottir, D.F. Gudbjartsson, G. Thorleifsson,
U. Thorsteinsdottir, and K. Stefansson are employees of deCODE
Genetics/Amgen Inc. The other authors report no conflicts.
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Significance
Previous studies have shown that common genetic risk variants for coronary artery disease at chromosome 9p21 and in the lipoprotein(a)
gene associate with angiographic extent of the disease, suggesting a role for these loci in the development of coronary atherosclerosis.
In this study, we show that the cumulative burden of currently known genetic risk variants for coronary artery disease associates significantly with the extent of coronary atherosclerosis in 2 independent populations of patients with established angiographic coronary artery
disease. Compared with patients in the bottom quintile of the genetic score, patients in the top quintile were significantly more likely to
have multivessel disease.
Common Sequence Variants Associated With Coronary Artery Disease Correlate With the
Extent of Coronary Atherosclerosis
Eythor Bjornsson, Daniel F. Gudbjartsson, Anna Helgadottir, Thorarinn Gudnason, Tomas
Gudbjartsson, Kristjan Eyjolfsson, Riyaz S. Patel, Nima Ghasemzadeh, Gudmar Thorleifsson,
Arshed A. Quyyumi, Unnur Thorsteinsdottir, Gudmundur Thorgeirsson and Kari Stefansson
Arterioscler Thromb Vasc Biol. 2015;35:1526-1531; originally published online April 16, 2015;
doi: 10.1161/ATVBAHA.114.304985
Arteriosclerosis, Thrombosis, and Vascular Biology is published by the American Heart Association, 7272
Greenville Avenue, Dallas, TX 75231
Copyright 2015 American Heart Association, Inc. All rights reserved.
Print ISSN: 1079-5642. Online ISSN: 1524-4636
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SUPPLEMENTAL MATERIAL
Common sequence variants associated with coronary artery disease correlate with
the extent of coronary atherosclerosis
Eythor Bjornsson et al.
Supplementary Table I. Associations of the individual SNPs included in the GRS with CAD extent
Coded
Nearest Gene(s)
allele
SNP info*
SNP
Chr
rs599839
1p13
SORT1
0.80
rs4845625
1q21
IL6R
0.37
rs11206510
1p32
PCSK9
0.83
0.82
0.995
rs17114036
1p32
PPAP2B
0.93
0.91
rs17465637
1q41
MIA3
0.69
0.75
rs1561198
2p11
VAMP5-VAMP8GGCX
0.46
rs6544713
2q21
ABCG5-ABCG8
rs2252641
2q22 ZEB2-AC074093.1
rs515135a
2p24
rs6725887
0.79
1.111
0.014
0.444
1.052
-0.016
0.278
0.996
1.062
0.043
0.998
0.959
1.112
0.998
0.988
0.997
0.975
0.112
0.002
0.033
0.037
0.024
-0.050
0.182
0.024
0.156
-0.008
0.782
-0.031
0.554
-0.013
0.602
1.141
0.007
0.637
0.012
0.732
0.008
0.568
0.999
1.062
0.016
0.268
0.29
0.999
1.062
0.030
0.050
0.44
0.998
1.042
-0.001
0.966
APOB
0.87
0.82
0.999
0.944
1.072
0.013
0.526
0.014
0.718
0.013
0.466
2q33
WDR12
0.13
0.13
0.995
0.982
1.122
0.051
0.015
-0.016
0.715
0.038
0.042
rs9818870
3q22
MRAS
0.16
0.17
1.000
0.982
1.072
0.021
0.261
-0.030
0.454
0.012
0.489
rs1878406b
4q31
EDNRA
0.15
0.16
0.999
0.967
1.082
0.041
0.034
0.019
0.634
0.037
0.034
rs7692387
4q32
GUCY1A3
0.81
0.998
1.072
-0.023
0.200
rs273909
5q31
SLC22A4SLC22A5
0.15
0.999
1.092
0.028
0.158
rs17609940
6p21
ANKS1A
0.75
1.071
0.025
0.124
0.028
0.45
0.025
0.087
rs10947789
6p21
KCNK5
0.78
1.062
0.019
0.252
rs12190287
6q23
TCF21
0.66
0.63
0.995
0.982
1.072
0.020
0.185
0.059
0.050
0.027
0.040
rs12526453
6p24
PHACTR1
0.70
0.68
0.999
0.985
1.101
0.030
0.049
0.020
0.545
0.028
0.041
rs2048327
6q25
SLC22A3-LPAL2LPA
0.41
1.062
0.032
0.025
rs3798220
6q25
SLC22A3-LPAL2LPA
0.02
0.02
1.000
1.000
1.282
0.079
0.087
0.159
0.110
0.093
0.026
rs10455872
6q25
SLC22A3-LPAL2LPA
0.07
0.09
0.984
1.000
1.443
0.160
2.1x10-9
0.187
2.7x10-4
0.165
2.5x10-12
rs4252120
6q26
PLG
0.73
0.998
1.072
0.011
0.472
rs2023938
7p21
HDAC9
0.10
1.000
1.082
0.004
0.859
rs10953541
7q22
BCAP29
0.76
0.999
1.084
0.028
0.090
rs11556924
7q32
ZC3HC1
0.66
1.092
-0.005
0.750
0.022
0.461
0.001
0.967
rs264
8p21
LPL
0.85
1.072
0.014
0.490
rs2954029c
8q24
TRIB1
0.51
0.53
0.998
0.956
1.052
0.005
0.725
0.003
0.933
0.005
0.723
rs1333049d
9p21
CDKN2BAS1
0.48
0.52
0.996
0.972
1.232
0.046
0.001
0.076
0.012
0.051
5.8x10-5
0.998
0.80
0.999
0.996
0.999
0.999
0.62
0.996
0.982
0.995
rs579459e
9q34
ABO
0.15
0.22
0.995
0.984
1.072
-0.012
0.540
-0.028
0.426
-0.016
0.358
rs2505083
10p11
KIAA1462
0.41
0.44
0.995
0.936
1.062
-0.004
0.773
0.023
0.444
0.001
0.945
rs2047009
10q11
CXCL12
0.53
1.052
-0.015
0.292
rs501120f
10q11
CXCL12
0.89
0.88
1.000
0.935
1.072
-0.043
0.053
-0.037
0.416
-0.042
0.036
rs1412444
10q23
LIPA
0.37
0.35
0.997
0.984
1.094
0.014
0.316
0.036
0.242
0.018
0.160
CYP17A1CNNM2-NT5C2
0.93
0.92
0.998
0.998
1.102
-0.008
0.757
0.092
0.087
0.012
0.621
1.072
0.018
0.252
rs12413409g 10q24
0.999
rs974819
11q22
PDGFD
0.29
0.997
rs964184
11q23
ZNF259-APOA5APOA1
0.13
0.15
0.999
0.985
1.131
0.008
0.715
0.034
0.405
0.013
0.483
rs3184504
12q24
SH2B3
0.39
0.49
0.998
0.972
1.072
0.009
0.547
0.045
0.120
0.016
0.220
rs9319428
13q12
FLT1
0.34
1.062
0.020
0.186
0.44
1.072
-0.003
0.836
-0.005
0.875
-0.003
0.799
rs9515203
13q34 COL4A1-COL4A2
0.73
1.082
0.044
0.005
rs2895811
14q32
HHIPL1
0.47
0.44
0.994
0.968
1.062
0.032
0.023
0.031
0.294
0.032
0.012
rs3825807
15q25
ADAMTS7
0.58
0.58
0.998
0.962
1.081
0.028
0.052
0.048
0.116
0.031
0.015
rs17514846 15q26
FURIN-FES
0.47
1.062
-0.003
0.824
rs12936587 17p11
RAI1-PEMTRASD1
0.60
0.56
0.998
0.995
1.062
0.016
0.260
-0.046
0.116
0.004
0.751
0.998
0.45
0.990
0.983
0.992
0.996
rs216172
17p13
SMG6
0.39
0.37
0.998
0.968
1.071
0.001
0.957
0.016
0.594
0.004
0.785
rs46522
17q21
UBE2Z
0.54
0.53
0.999
0.995
1.061
0.000
0.994
-0.017
0.550
-0.003
0.801
rs1122608
19p13
LDLR
0.79
0.75
0.996
0.970
1.102
0.042
0.015
0.041
0.238
0.042
6.9x10-3
rs2075650
19q13
ApoE-ApoC1
0.18
0.15
0.995
0.963
1.112
0.036
0.054
0.125
0.002
0.051
2.5x10-3
rs445925
19q13
ApoE-ApoC1
0.92
1.132
0.002
0.929
0.992
Gene desert
T
0.14
0.14
0.993 0.951
1.132
0.013
0.534
0.010
0.82
0.012
0.509
(KCNE2)
*Imputation information score for the imputed SNPs (Iceland) and SNP call rates for the directly genotyped SNPs (Emory).
For each of the SNPs, the odds ratio for the risk of CAD was obtained from a previously published meta-analysis of genome-wide association studies (as
referenced in the table). In the GRSs, each SNP was weighted using the natural logarithm of the respective odds ratio.
Association analyses were performed using multiple linear regression adjusting for age, sex, hyperlipidemia, diabetes, hypertension, current and former
smoking. The outcome variable was the number of diseased coronary vessels with at least 50% stenosis on coronary angiography (range, 1-4). Results
from the Icelandic and Emory samples were combined using fixed-effects inverse variance-weighted meta-analysis.
a
rs562338 is a proxy for rs515135 (r2=0.98) in the Emory Biobank sample
b
rs6842241 is a proxy for rs1878406 (r2=0.91) in the Emory Biobank sample
c
rs2954021 is a proxy for rs2954029 (r2=0.79) in the Emory Biobank sample
d
rs10757278 is a proxy for rs1333049 (r2=0.95) in the Emory Biobank sample
e
rs651007 is a proxy for rs579459 (r2=0.99) in the Emory Biobank sample
f
rs1746048 is a proxy for rs501120 (r2=0.96) in the Emory Biobank sample
g
rs12411886 is a proxy for rs12413409 (r2=1.00) in the Emory Biobank sample
h
rs3809346 is a proxy for rs4773144 (r2=0.99) in the Emory Biobank sample
rs9982601
21q22
Supplementary Table II. Association of the GRS with the number of diseased coronary arteries on
coronary angiography, adjusted for age and sex only
No. of
SNPs
Difference per SD
increase (95% CI)
Standard
error
P value
Full GRS
50
0.077 (0.059-0.095)
0.0091
3.2x10-17
1.67 (1.45-1.93)
47
0.050 (0.032-0.068)
0.0091
3.7x10-8
1.33 (1.16-1.54)
Restricted GRS
32
0.073 (0.055-0.090)
0.0091
2.2x10-15
1.54 (1.34-1.77)
Iceland (n=8,622)
32
0.113 (0.072-0.153)
0.021
5.0x10-8
2.08 (1.51-2.88)
29
0.067 (0.027-0.108)
0.021
0.0011
1.50 (1.09-2.05)
GRS indicates genetic risk score; SD, standard deviation; OR, odds ratio; CI, confidence interval.
Associations were tested using linear and logistic regression models adjusted for age and sex.
*Multivessel disease was defined as having at least two coronary arteries with 50% stenosis on
coronary angiography.
Supplementary Table III. Association of the GRS with the number of diseased coronary arteries on
coronary angiography, adjusted for age, sex, four cardiovascular risk factors and family history
No. of
SNPs
Difference per SD
increase (95% CI)
Standard
error
P value
Full GRS
50
0.072 (0.054-0.089)
0.0090
3.0x10-15
1.63 (1.41-1.89)
47
0.046 (0.028-0.064)
0.0090
3.5x10-7
1.30 (1.12-1.50)
Restricted GRS
32
0.067 (0.050-0.085)
0.0090
1.1x10-13
1.51 (1.31-1.75)
0.115 (0.075-0.155)
0.021
2.7x10-8
2.08 (1.50-2.90)
Iceland (n=8,622)
32
P value*
Q1
Q2
Q3
Q4
Q5
1725
1724
1725
1724
1724
Age
66.0
64.8
63.6
64.1
63.6
2.5x10-13
Male sex
74.8%
78.2%
77.0%
74.4%
71.0%
8.4x10-5
Diabetes
12.1%
12.3%
9.7%
12.4%
10.6%
0.082
Hypertension
57.4%
53.4%
53.2%
53.8%
53.7%
0.098
Hyperlipidemia
48.8%
47.5%
50.8%
51.6%
52.8%
2.6x10-3
Current smoker
26.3%
28.2%
30.0%
25.9%
26.6%
0.86
Former smoker
50.1%
46.4%
46.0%
49.0%
46.6%
0.051
Prior MI
29.9%
28.5%
29.5%
30.0%
30.7%
0.32
Prior PCI
4.2%
3.6%
3.0%
4.8%
5.2%
0.11
Prior CABG
5.8%
5.7%
7.2%
8.9%
10.6%
4.1x10-11
Family history
36.1%
40.0%
45.0%
45.9%
48.5%
2.3x10-17
Multivessel disease
56.4%
61.8%
60.5%
60.8%
65.1%
1.2x10-6
*Unadjusted P-values calculated using linear and logistic regression considering the GRS as
a continuous variable.
Characteristic
Q1
Q2
Q3
Q4
Q5
372
370
370
371
370
Age
66.8
65.1
66.2
65.2
64.7
0.017
Male sex
74.2%
73.0%
72.4%
71.7%
77.6%
0.49
Diabetes
35.8%
29.7%
35.1%
29.1%
27.6%
0.029
Hypertension
66.9%
73.2%
73.2%
70.6%
69.5%
0.53
Hyperlipidemia
71.8%
73.0%
76.2%
73.3%
78.6%
0.062
Current smoker
14.0%
16.5%
14.9%
14.6%
13.8%
0.94
Former smoker
47.0%
44.3%
45.9%
49.1%
53.2%
0.046
Prior MI
47.3%
44.9%
53.2%
47.7%
53.0%
0.058
Prior PCI
55.6%
51.6%
61.9%
57.1%
61.1%
0.031
Prior CABG
28.0%
24.9%
36.8%
28.6%
38.4%
0.0019
Family history
43.3%
41.4%
46.5%
47.2%
45.1%
0.16
Multivessel disease
61.8%
61.4%
70.8%
69.3%
76.8%
7.2x10-7
*Unadjusted P-values calculated using linear and logistic regression considering the GRS as a
continuous variable.
Supplementary Table VI. Association of the GRS with the number of diseased coronary arteries
among all individuals undergoing coronary angiography, including those with non-significant CAD
(<50% stenosis).
No. of
SNPs
Difference per SD
increase (95% CI)
Standard
error
P value
Full GRS
50
0.145 (0.126-0.165)
0.0094
7.0x10-48
2.01 (1.77-2.28)
47
0.105 (0.085-0.124)
0.0100
1.1x10-25
1.60 (1.41-1.82)
Restricted GRS
32
0.139 (0.119-0.158)
0.0099
8.2x10-44
1.87 (1.65-2.12)
0.198 (0.155-0.240)
0.022
1.8x10-19
2.60 (2.01-3.39)
Iceland (n=11,196)
32
Supplementary Figure. Adjusted odds ratios for multivessel disease by quintiles of the
genetic risk score (GRS) in the Icelandic (black) and Emory Biobank (grey) samples,
including those with non-significant CAD (<50% stenosis). Odds ratios are referenced to the
bottom GRS quintile and presented with 95% confidence intervals.
References
1.
2.
3.
The IBC 50K CAD Consortium. Large-scale gene-centric analysis identifies novel
variants for coronary artery disease. PLoS Genet. 2011;7:e1002260.
4.
were used as weights (odds ratios ranged from 1.04 to 1.44). For SNPs reported in
more than one study, the effect size reported by the study comprising the largest
number of study participants was chosen.
Genotyping of all samples was carried out at deCODE Genetics in Reykjavik,
Iceland. In the Icelandic sample, whole-genome sequencing of 2,230 Icelanders was
used to inform the imputation of the 50 SNPs into 95,085 Icelanders genotyped with
Illumina SNP chips, using long-range phasing-based imputation.5,10 Additionally,
familial imputation methods were used to impute the variants into un-genotyped
relatives of chip-genotyped Icelanders, yielding a total sample size of 8,622 Icelandic
study patients with genotype information. The imputation information score for the
SNPs ranged from 0.984 to 1.000.
In the replication sample (Emory Biobank), analyses were based on an available
subset comprising 32 SNPs previously genotyped as part of ongoing research
collaborations (Table I in the online-only Data Supplement). In this subset, proxy SNPs
were used for SNPs at 2p24, 4q31, 8q24, 9p21, 9q34, 10q11, 10q24 and 13q34 (r2
between 0.79 and 1.00). Information on the remainder of SNP genotyped in the
Icelandic sample was not available for the Emory Biobank sample. Samples from the
Emory Biobank were genotyped using the Centaurus (Nanogen) platform at deCODE
genetics in Reykjavik, Iceland. SNP call rate ranged from 0.935-1.000.
Genetic Risk Scores
For each patient, we calculated a weighted genetic risk score (GRS) by adding the
product of the number of risk alleles for each of the SNPs and the natural logarithm of
the effect size (odds ratio for CAD) reported in the reference studies. As 1 SNP at
chromosome 9p21 and 2 SNPs LPA gene have previously been reported to associate
with extent of angiographic CAD3,11,12, we additionally examined a GRS restricted to
SNPs with no reported association with CAD extent. In the Icelandic sample, the
weighted GRS was calculated based on 50 SNPs whereas, in the Emory Biobank
sample, the GRS was calculated based on the available subset of 32 SNPs (Table I in
the online-only Data Supplement). For comparison, we generated a GRS restricted to
these 32 SNPs for the Icelandic sample. In all analyses, GRSs were standardized to a
mean of 0 and a standard deviation of 1.
Statistical Methods
We used linear regression to test the association of individual SNPs with CAD extent.
The outcome variable was the number of diseased coronary arteries with at least 50%
stenosis on coronary angiography. Estimates were adjusted for traditional
cardiovascular risk factors (age, sex, hyperlipidemia, diabetes, hypertension, current
and former smoking). Results for SNPs genotyped in both the Icelandic and Emory
Biobank samples were combined using fixed-effects inverse variance-weighted metaanalysis. In single-SNP analyses, we considered a P value of less than 0.001 to be
significant to account for the testing of 50 SNPs.
Association analyses of the GRS with extent of CAD were performed using
multivariate linear regression, adjusting for traditional cardiovascular risk factors. In a
further analysis, family history of CAD was included as a covariate. To further illustrate
the association with CAD extent, we divided the study patients into quintiles according
to the GRS and compared the association of the top versus the bottom quintiles with
multivessel disease (2 diseased coronary arteries) in multivariate logistic regression
models adjusted for traditional cardiovascular risk factors. In addition, as early age at
angiography may be an indicator of accelerated development of coronary
atherosclerosis, we tested whether the GRS associated with age at angiography. We
tested whether the GRS provided incremental value to prediction of the presence of
multivessel disease over known cardiovascular risk factors using the likelihood-ratio 2
test for nested models. We evaluated improvement in discrimination by comparing the
areas under the receiver-operating characteristic curve (C-statistic) with and without
the GRS. An increase in the C-statistic reflects improved discrimination between
patients with and without multivessel disease. In addition, we calculated the integrated
discrimination improvement13.
The main analyses were restricted to patients with significant angiographic CAD.
In a separate analysis, we also included data from individuals with non-significant CAD
(<50% stenosis) and genotype information available.
All statistical analyses were performed using R, version 3.1.0 (www.rproject.org). Unless otherwise noted, a two-sided P-value less than 0.05 was
considered statistically significant.
References
1.
2.
Biancari F, Gudbjartsson T, Heikkinen J, et al. Comparison of 30-Day and 5Year Outcomes of Percutaneous Coronary Intervention Versus Coronary Artery
Bypass Grafting in Patients Aged 50 Years (the Coronary aRtery diseAse in
younG adultS Study). Am J Cardiol. 2014;114:198205
3.
4.
Ringqvist I, Fisher LD, Mock M, Davis KB, Wedel H, Chaitman BR, Passamani
E, Russell RO, Alderman EL, Kouchoukas NT, Kaiser GC, Ryan TJ, Killip T, Fray
D. Prognostic value of angiographic indices of coronary artery disease from the
Coronary Artery Surgery Study (CASS). J Clin Invest. 1983;71:185466.
5.
6.
7.
8.
9.
10.
11.
12.
13.
Pencina MJ, DAgostino RB, Vasan RS. Evaluating the added predictive ability
of a new marker: from area under the ROC curve to reclassification and beyond.
Stat Med. 2008;27:15772.