PGS Publication: PGP000108

Publication Information (EuropePMC)
Title Genome-Wide Polygenic Score, Clinical Risk Factors, and Long-Term Trajectories of Coronary Artery Disease.
PubMed ID 32957805(Europe PMC)
doi 10.1161/atvbaha.120.314856
Publication Date Sept. 22, 2020
Journal Arterioscler Thromb Vasc Biol
Author(s) Hindy G, Aragam KG, Ng K, Chaffin M, Lotta LA, Baras A, Regeneron Genetics Center, Drake I, Orho-Melander M, Melander O, Kathiresan S, Khera AV.
Released in PGS Catalog: Nov. 20, 2020

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000013
(GPS_CAD)
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Coronary artery disease coronary artery disease 6,630,150
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz - Check Terms/Licenses

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000933 PGS000013
(GPS_CAD)
 PSS000469|
Multi-ancestry (including European)|
325,003 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease — C-index: 0.768 [0.76, 0.776] — age, sex, PCs (1-10), Pooled Cohort Equations risk estimator —
PPM000932 PGS000013
(GPS_CAD)
 PSS000469|
Multi-ancestry (including European)|
325,003 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease — C-index: 0.756 [0.75, 0.762] — age, sex, PCs (1-10) —
PPM000929 PGS000013
(GPS_CAD)
 PSS000468|
Multi-ancestry (including European)|
5,685 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease — C-index: 0.802 [0.763, 0.8841] — age, sex, PCs (1-10), Pooled Cohort Equations risk estimator —
PPM000928 PGS000013
(GPS_CAD)
 PSS000468|
Multi-ancestry (including European)|
5,685 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease — C-index: 0.759 [0.724, 0.794] — age, sex, PCs (1-10) —
PPM000927 PGS000013
(GPS_CAD)
 PSS000468|
Multi-ancestry (including European)|
5,685 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.45 [1.34, 1.56] — — age, sex, clinical risk factors (systolic blood pressure, diastolic blood pressure, apolipoprotein B, apolipoprotein A1, total cholesterol, LDL cholesterol, HDL cholesterol, body mass index, current smoker, diabetes), family history of CAD —
PPM000930 PGS000013
(GPS_CAD)
 PSS000469|
Multi-ancestry (including European)|
325,003 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.53 [1.49, 1.56] — — age, sex —
PPM000926 PGS000013
(GPS_CAD)
 PSS000467|
Multi-ancestry (including European)|
28,556 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.45 [1.4, 1.49] — — age, sex —
PPM000931 PGS000013
(GPS_CAD)
 PSS000469|
Multi-ancestry (including European)|
325,003 individuals
 PGP000108 |
Hindy G et al. Arterioscler Thromb Vasc Biol (2020)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.46 [1.42, 1.49] — — age, sex, clinical risk factors (systolic blood pressure, diastolic blood pressure, apolipoprotein B, apolipoprotein A1, total cholesterol, LDL cholesterol, HDL cholesterol, body mass index, current smoker, diabetes), family history of CAD —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000467 Individuals were free of CAD at time of enrollment. CAD was defined as (1)fatal or nonfatal myocardial infarction: defined based on either International Classification of Diseases, Ninth Revision (ICD-9) code 410 or Tenth Revision (ICD-10) code I21, (2)coronary artery bypass graft surgery: defined as procedure codes 3065, 3066, 3068, 3080, 3092, 3105, 3127 or 3158 (the Op6 system) or procedure code FN (the KKA97 system), (3)percutaneous coronary intervention, (4)death due to CAD: defined as ICD-9 codes 412 and 414 or ICD-10 codes I22, I23 and I25. Median = 21.3 years
IQR = [16.1, 23.1] years
[
  • 4,122 cases
  • , 24,434 controls
]
,
38.7 % Male samples
 Mean = 57.9 years European, NR European=28286, NR=270 MDC —
PSS000468 Individuals were free of CAD at time of enrollment. CAD was defined as (1)fatal or nonfatal myocardial infarction: defined based on either International Classification of Diseases, Ninth Revision (ICD-9) code 410 or Tenth Revision (ICD-10) code I21, (2)coronary artery bypass graft surgery: defined as procedure codes 3065, 3066, 3068, 3080, 3092, 3105, 3127 or 3158 (the Op6 system) or procedure code FN (the KKA97 system), (3)percutaneous coronary intervention, (4)death due to CAD: defined as ICD-9 codes 412 and 414 or ICD-10 codes I22, I23 and I25. All individuals included had measured cholesterol concentrations. Median = 23.2 years
IQR = [17.6, 24.2] years
[
  • 815 cases
  • , 4,870 controls
]
,
41.16 % Male samples
 — European, NR European=5640, NR=45 MDC-CC Cardiovascular Cohort
PSS000469 Individuals were free of CAD at time of enrollment. CAD was defined based on hospitalisation with or death due to ICD-10 codes for acute or subsequent myocaridal infarction (I21, I22, I23, I24.1, and I25.2); or hospitalisation with ICD-9 codes for myocaridal. infarction (410, 411, and 412); or hospitalisation with OPCS-4 (Office of Population Censuses and Surveys) codes. for coronary artery bypass grafting (K40, K41, and K45) or coronary angioplasty with or without stenting (K49, K50.2, and K75). Median = 8.1 years
IQR = [7.4, 8.8] years
[
  • 7,708 cases
  • , 317,295 controls
]
,
44.2 % Male samples
 Mean = 56.8 years European, African unspecified, South Asian, East Asian, NR European=304270, African unspecified=5760, South Asian=6832, East Asian (Chinese)=1117, NR=7024 UKB —