Download PGS
(Variants and weights)

Polygenic Score (PGS) ID: PGS000012

Predicted Trait

Reported Trait: Coronary artery disease
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): coronary artery disease

Score Details

Name: GRS49K

Original Genome Build: hg19
Number of Variants: 49,310

PGS Development Method: LD thinning
PGS Development Details/Relevant Parameters: r2 threshold = 0.7

Citation: Abraham G et al. Eur Heart J (2016) | PGS Catalog Publication ID: PGP000005

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
PubMed: 23202125.0 194,427 individuals
[ 63,746 cases, 130,681 controls]
Other
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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) 1,019 individuals
[ 531 cases, 488 controls]
European MIGen Harps subset
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. 4,864 individuals
[ 1,926 cases, 2,938 controls]
European WTCCC 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000018 PSS000012 Abraham G et al. (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 Abraham G et al. (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 Inouye M et al. (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)

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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) 3,406 individuals
[ 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. 12,676 individuals
[ 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. 482,629 individuals
[ 22,242 cases, 460,387 controls]
45.6 % Male samples
Other ~95% European ancestry samples, <5% non-European ancestry UKB