Polygenic Score (PGS) ID: PGS000012

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GRS49K
Development Method
Name LD thinning
Parameters r2 threshold = 0.7
Variants
Original Genome Build hg19
Number of Variants 49,310
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000005
Citation (link to publication) Abraham G et al. Eur Heart J (2016)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • South Asian
194,427 individuals (100%)
Score Development/Training
European: 100%
5,883 individuals (100%)
PGS Evaluation
European: 80%
Multi-ancestry (including European): 20%
  • European
  • Not Reported
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 23202125
[
  • 63,746 cases
  • , 130,681 controls
]
 European, South Asian 33 cohorts
  • ADVANCE
  • ,AMC-PAS
  • ,Angio-Lueb
  • ,CARDIOGENICS
  • ,COROGENE
  • ,DILGOM
  • ,Duke
  • ,EGCUT
  • ,EMIL
  • ,EPIC
  • ,FGENTCARD
  • ,FINCAVAS
  • ,FRISCII
  • ,GENRIC
  • ,GLACIER
  • ,GoDARTS
  • ,HPS
  • ,HSIEA
  • ,ITH
  • ,KORA
  • ,LOLIPOP
  • ,LURIC
  • ,METSIM
  • ,MORGAM
  • ,OHGS
  • ,PIVUS
  • ,PMB
  • ,POPGEN
  • ,PROCARDIS
  • ,PROMIS
  • ,SCARFSHEEP
  • ,STR
  • ,ULSAM
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
GWAS Catalog: GCST000340
[
  • 531 cases
  • , 488 controls
]
 European MIGen For MIGen, MI defined cases of early onset MI (men <50 years old, women <60 years old). MI was diagnosed from as one of: • Autopsy evidence of fatal MI • Combination of chest pain with electrocardiographic evidence of MI • Elevation of one or more cardiac biomarkers (creatine kinase or cardiac troponin) — — — Harps subset
GWAS Catalog: GCST000045
[
  • 1,926 cases
  • , 2,938 controls
]
 European WTCCC CAD in the WTCCC was defined as a validated history of either myocardial infarction or coronary revascularization (coronary artery bypass surgery or percutaneous coronary angioplasty) before their 66th birthday. Verification of the history of CAD was required either from hospital records or the primary care physician. — — — Wellcome Trust Case/Control Consortium Coronary Artery Disease

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) 		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
PPM000018 PSS000012|
European Ancestry|
12,676 individuals
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
 Reported Trait: Incident coronary artery disease HR: 1.74 [1.61, 1.86]
OR: 1.74 [1.61, 1.89]		 — — sex, sub-cohort, location (east/west), 5 genetic PCs Used only the 42,364 SNPs that were available in FINRISK
PPM000020 PSS000011|
European Ancestry|
3,406 individuals
 PGP000005 |
Abraham G et al. Eur Heart J (2016)
 Reported Trait: Incident coronary artery disease HR: 1.28 [1.18, 1.38]
OR: 1.28 [1.17, 1.41]		 — — sex, sub-cohort, 5 genetic PCs Used only the 46,773 SNPs that were available in FHS
PPM000028 PSS000018|
Multi-ancestry (including European)|
482,629 individuals
 PGP000007 |
Inouye M et al. J Am Coll Cardiol (2018)
|Ext.		 Reported Trait: Incident coronary artery disease HR: 1.524 [1.498, 1.551] — — sex, genetic PCs (1-10), genotyping array Used GRS46K (excludes A/T and C/G SNPs, with performance similar to GRS49K)
PPM005158 PSS003596|
European Ancestry|
8,946 individuals
 PGP000248 |
Liou L et al. Breast Cancer Res (2021)
|Ext.		 Reported Trait: Incident coronary artery disease in individuals with breast cancer HR: 1.31 [1.19, 1.44] — — Age at diagnosis, genotype array, PCs(1-8), body mass index, smoking, sociodemographic variables, medical variables, oncotherapies —
PPM021300 PSS011680|
European Ancestry|
26,203 individuals
 PGP000627 |
Martikainen P et al. J Epidemiol Community Health (2021)
|Ext.		 Reported Trait: Incident coronary heart disease hospitalization or death — — Hazard Ratio (HR, top 25% vs bottom 25%): 2.26 [1.97, 2.59] Age as timescale, sex, region of residence, calendar year, study batch, PCs(1-10) —
PPM021301 PSS011680|
European Ancestry|
26,203 individuals
 PGP000627 |
Martikainen P et al. J Epidemiol Community Health (2021)
|Ext.		 Reported Trait: Incident coronary heart disease hospitalization or death — — Hazard Ratio (HR, top 25% vs bottom 25%): 2.27 [1.98, 2.61] Age as timescale, sex, region of residence, calendar year, study batch, PCs(1-10), education —
PPM021302 PSS011680|
European Ancestry|
26,203 individuals
 PGP000627 |
Martikainen P et al. J Epidemiol Community Health (2021)
|Ext.		 Reported Trait: Incident coronary heart disease hospitalization or death — — Hazard Ratio (HR, top 25% vs bottom 25%): 2.12 [1.48, 2.43] Age as timescale, sex, region of residence, calendar year, study batch, PCs(1-10), smoking, alcohol use, body mass index, high-density lipoprotein and total cholesterol, blood pressure, diabetes —

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
PSS003596 All individuals had breast cancer. Cases were individuals who suffered incident coronary artery disease (CAD) events. Incident CAD events were defined as a composite endpoint of unstable angina, myocardial infarction, or death due to complications following myocardial infarction according to the International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD-10 codes): I21, I22, I23, I25 and I25. —
[
  • 432 cases
  • , 8,514 controls
]
,
0.0 % Male samples
 — European — SEARCH —
PSS000011 The main outcome of interest was incident CHD event before age 75y. We used the definition of CHD as employed by the Framingham study, namely, one of • MI recognized, with diagnostic ECG (FHS event code #1) • MI recognized, without diagnostic ECG, with enzymes and history (#2) • MI recognized, without diagnostic ECG, with autopsy evidence (new event) (#3) • MI unrecognized, silent (#4) • MI unrecognized, not silent (#5) • Angina pectoris (AP), first episode only (#6) • Coronary insufficiency (CI), definite by both history and ECG (#7) • Questionable MI at exam 1 (#8) • Acute MI by autopsy, previously coded as 1 or 2 (#9) • Death, CHD sudden, with 1 hour (#21) • Death, CHD 1–23 hours, non sudden (#22) • Death, CHD 24-47 hours, non sudden (#23) • Death, CHD, 48 hours or more, non sudden (#24) —
[
  • 587 cases
  • , 2,819 controls
]
,
45.0 % Male samples
 — European — FHS FHS Original, FHS Offspring
PSS000012 Coronary heart disease (CHD) was defined as falling into any of the following categories: • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the direct or as a contributing cause of death or I20-I25 (ICD-10) /410-414 (ICD-9) as the underlying cause of death • I21 or I22 (ICD-10) / 410 (ICD-8/9) as the main or secondary diagnosis at hospital discharge. • Coronary bypass surgery or coronary angioplasty at hospital discharge or identified from the Finnish registry of invasive cardiac procedures. —
[
  • 757 cases
  • , 11,919 controls
]
,
46.0 % Male samples
 — European
(Finnish)		 — FINRISK FR92, FR97, FR02
PSS000018 CAD was defined as fatal or nonfatal myocardial infarction (MI) cases, percutaneous transluminal coronary angioplasty (PTCA), or coronary artery bypass grafting (CABG). Prevalent versus incident status was relative to the UKB enrollment assessment. In UKB self-reported data, cases were defined as having had a heart attack diagnosed by a doctor (data field #6150); “non-cancer illnesses that self-reported as heart attack” (data field #20002); or self-reported operation including PTCA, CABG, or triple heart bypass (data field #20004). In HES hospital episodes data and death registry data, MI was defined as hospital admission or cause of death due to ICD-9 410 to 412, or ICD-10 I21 to I24 or I25.2; CABG and PTCA were defined as hospital admission OPCS-4 K40 to K46, K49, K50.1,or K75. —
[
  • 22,242 cases
  • , 460,387 controls
]
,
45.6 % Male samples
 — European, NR ~95% European ancestry samples, <5% non-European ancestry UKB —
PSS011680 At baseline, all individuals were free from coronary heart disease (CHD). Cases included individuals who were hospitalised due to CHD or suffered a fatal CHD event. CHD events were defined for non-fatal cases as the International Classification of Diseases ninth revision (ICD-9) codes 410 and 4110 (years 1992-1995) and ICD-10 codes I200, I21 or I22 (1996-2015) and Nordic Medico-Statistical Committee codes for coronary artery bypass graft or percutaneous coronary intervention in the hospital discharge register, and for fatal cases as ICD-9 codes 410-414 and 798 (not 7980A) and ICD-10 codes I20-25, I46, R96 and R98 in the causes of death register. Mean = 13.8 years
[
  • 2,063 cases
  • , 24,140 controls
]
,
46.74 % Male samples
 Mean = 48.0 years European
(Finnish)		 — FINRISK —