PGS Publication: PGP000007

Publication Information (EuropePMC)
Title Genomic Risk Prediction of Coronary Artery Disease in 480,000 Adults: Implications for Primary Prevention.
PubMed ID 30309464(Europe PMC)
doi 10.1016/j.jacc.2018.07.079
Publication Date Oct. 1, 2018
Journal J Am Coll Cardiol
Author(s) Inouye M, Abraham G, Nelson CP, Wood AM, Sweeting MJ, Dudbridge F, Lai FY, Kaptoge S, Brozynska M, Wang T, Ye S, Webb TR, Rutter MK, Tzoulaki I, Patel RS, Loos RJF, Keavney B, Hemingway H, Thompson J, Watkins H, Deloukas P, Di Angelantonio E, Butterworth AS, Danesh J, Samani NJ, UK Biobank CardioMetabolic Consortium CHD Working Group.
Released in PGS: Oct. 14, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000018 metaGRS_CAD PGP000007
Inouye M et al. J Am Coll Cardiol (2018)
Coronary artery disease coronary artery disease 1,745,179 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000018/ScoringFiles/PGS000018.txt.gz

External PGS Evaluated By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000011 GRS50 PGP000004
Tada H et al. Eur Heart J (2015)
Coronary artery disease coronary artery disease 50 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000011/ScoringFiles/PGS000011.txt.gz
PGS000012 GRS49K PGP000005
Abraham G et al. Eur Heart J (2016)
Coronary artery disease coronary artery disease 49,310 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000012/ScoringFiles/PGS000012.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000029 PGS000011 (GRS50) PSS000018 PGP000007
Inouye M et al. (2018)
Ext.
Reported Trait: Incident coronary artery disease HR: 1.263[1.247, 1.28] sex, genetic PCs (1-10), genotyping array
PPM000028 PGS000012 (GRS49K) PSS000018 PGP000007
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)
PPM000027 PGS000018 (metaGRS_CAD) PSS000018 PGP000007
Inouye M et al. (2018)
Reported Trait: Incident coronary artery disease HR: 1.706[1.682, 1.73] AUROC: 0.79
C-index: 0.623[0.615, 0.631]
AUPRC: 0.161 sex, genetic PCs (1-10), genotyping array age-as-time-scale Cox regression

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
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
Other ~95% European ancestry samples, <5% non-European ancestry UKB