PGS Publication: PGP000083

Publication Information (EuropePMC)
Title Predictive Utility of Polygenic Risk Scores for Coronary Heart Disease in Three Major Racial and Ethnic Groups.
PubMed ID 32386537(Europe PMC)
doi 10.1016/j.ajhg.2020.04.002
Publication Date May 1, 2020
Journal Am J Hum Genet
Author(s) Dikilitas O, Schaid DJ, Kosel ML, Carroll RJ, Chute CG, Denny JA, Fedotov A, Feng Q, Hakonarson H, Jarvik GP, Lee MTM, Pacheco JA, Rowley R, Sleiman PM, Stein CM, Sturm AC, Wei WQ, Wiesner GL, Williams MS, Zhang Y, Manolio TA, Kullo IJ.
Released in PGS: June 3, 2020

Associated Polygenic Score(s)

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)
PGS000200 GRS28 PGP000082
Tikkanen E et al. Arterioscler Thromb Vasc Biol (2013)
Coronary heart disease coronary heart disease 28 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000200/ScoringFiles/PGS000200.txt.gz
PGS000018 metaGRS_CAD PGP000007
Inouye M et al. J Am Coll Cardiol (2018)
Coronary artery disease coronary artery disease 1,745,180 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000018/ScoringFiles/PGS000018.txt.gz
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
PGS000013 GPS_CAD PGP000006
Khera AV et al. Nat Genet (2018)
Coronary artery disease coronary artery disease 6,630,150 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.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
PPM000589 PGS000011 (GRS50) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.2[1.15, 1.25] C-index: 0.698 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000605 PGS000013 (GPS_CAD) PSS000335 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.42[1.25, 1.61] AUROC: 0.776 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000604 PGS000011 (GRS50) PSS000335 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.2[1.06, 1.35] AUROC: 0.769 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000603 PGS000018 (metaGRS_CAD) PSS000331 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.4[1.3, 1.52] AUROC: 0.775 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000602 PGS000013 (GPS_CAD) PSS000331 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.3[1.21, 1.41] AUROC: 0.771 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000601 PGS000011 (GRS50) PSS000331 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.05[0.98, 1.14] AUROC: 0.763 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000600 PGS000018 (metaGRS_CAD) PSS000333 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.73[1.68, 1.78] AUROC: 0.772 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000599 PGS000013 (GPS_CAD) PSS000333 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.66[1.62, 1.71] AUROC: 0.77 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000598 PGS000011 (GRS50) PSS000333 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.28[1.25, 1.32] AUROC: 0.75 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000597 PGS000018 (metaGRS_CAD) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.53[1.23, 1.9] C-index: 0.683 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000596 PGS000013 (GPS_CAD) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.16[0.96, 1.41] C-index: 0.659 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000595 PGS000011 (GRS50) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.13[0.93, 1.36] C-index: 0.654 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000594 PGS000018 (metaGRS_CAD) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.27[1.13, 1.43] C-index: 0.663 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000593 PGS000013 (GPS_CAD) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.19[1.07, 1.33] C-index: 0.656 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000592 PGS000011 (GRS50) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.05[0.94, 1.17] C-index: 0.649 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000591 PGS000018 (metaGRS_CAD) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.53[1.46, 1.6] C-index: 0.719 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression
PPM000619 PGS000013 (GPS_CAD) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.17[1.04, 1.31] C-index: 0.712 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000618 PGS000011 (GRS50) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.05[0.94, 1.18] C-index: 0.704 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000617 PGS000200 (GRS28) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.11[0.99, 1.25] C-index: 0.706 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000616 PGS000018 (metaGRS_CAD) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.49[1.43, 1.56] C-index: 0.75 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000615 PGS000013 (GPS_CAD) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.47[1.41, 1.54] C-index: 0.75 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000614 PGS000011 (GRS50) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.2[1.15, 1.25] C-index: 0.736 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000613 PGS000200 (GRS28) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.17[1.12, 1.22] C-index: 0.735 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000612 PGS000200 (GRS28) PSS000335 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.27[1.12, 1.42] AUROC: 0.771 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000611 PGS000200 (GRS28) PSS000331 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.07[0.99, 1.16] AUROC: 0.763 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000610 PGS000200 (GRS28) PSS000333 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.24[1.21, 1.28] AUROC: 0.748 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000609 PGS000200 (GRS28) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.14[0.94, 1.37] C-index: 0.655 sex, eMERGE site, first five ancestry-specific principal components
PPM000608 PGS000200 (GRS28) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.11[0.99, 1.24] C-index: 0.652 sex, eMERGE site, first five ancestry-specific principal components
PPM000607 PGS000200 (GRS28) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.18[1.13, 1.23] C-index: 0.697 sex, eMERGE site, first five ancestry-specific principal components
PPM000624 PGS000018 (metaGRS_CAD) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.5[1.21, 1.87] C-index: 0.725 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000623 PGS000013 (GPS_CAD) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.14[0.94, 1.39] C-index: 0.708 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000622 PGS000011 (GRS50) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.12[0.93, 1.36] C-index: 0.708 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000621 PGS000200 (GRS28) PSS000336 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.13[0.93, 1.37] C-index: 0.709 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000620 PGS000018 (metaGRS_CAD) PSS000332 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.25[1.12, 1.41] C-index: 0.723 sex, eMERGE site, diabetes, hypertension, hyperlipidemia, statin use, first 5 ancestry-specific principal components Age-as-time-scale Cox regression
PPM000606 PGS000018 (metaGRS_CAD) PSS000335 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.93[1.67, 2.22] AUROC: 0.794 age at first EHR record, duration of EHR, sex, eMERGE site, first five ancestry-specific principal components
PPM000590 PGS000013 (GPS_CAD) PSS000334 PGP000083
Dikilitas O et al. (2020)
Ext.
Reported Trait: Incident coronary heart disease HR: 1.5[1.43, 1.56] C-index: 0.719 sex, eMERGE site, first five ancestry-specific principal components Age-as-time-scale Cox regression

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000331 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 9.2 years
Iqr = [5.5, 13.0] years
[
  • 838 cases
  • , 6,759 controls
]
,
31.0 % Male samples
Mean = 43.6 years
Sd = 12.5 years
African American or Afro-Caribbean 7 cohorts
  • BioVU
  • ,Columbia
  • ,KP
  • ,Mount Sinai
  • ,Nugene
  • ,Partners
  • ,eMERGE
right censored at age 75 years or at the age of last observation (whichever was first)
PSS000332 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. We identified the first CHD event and classified it as ‘‘incident’’ if the event occurred at least 6 months after the participant’s first record in the EHR and if there were no previous ICD-9-CM or ICD-10-CM codes associated with CHD. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 9.2 years
Iqr = [5.5, 13.0] years
[
  • 311 cases
  • , 7,070 controls
]
,
31.0 % Male samples
Mean = 43.6 years
Sd = 12.5 years
African American or Afro-Caribbean 7 cohorts
  • BioVU
  • ,Columbia
  • ,KP
  • ,Mount Sinai
  • ,Nugene
  • ,Partners
  • ,eMERGE
right censored at age 75 years or at the age of last observation (whichever was first)
PSS000333 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 11.7 years
Iqr = [6.0, 18.5] years
[
  • 8,108 cases
  • , 37,537 controls
]
,
44.6 % Male samples
Mean = 49.0 years
Sd = 14.1 years
European 11 cohorts
  • BioVU
  • ,CCHMC
  • ,Columbia
  • ,KP
  • ,Marshfield
  • ,Mayo
  • ,Mount Sinai
  • ,MyCode
  • ,Nugene
  • ,Partners
  • ,eMERGE
right censored at age 75 years or at the age of last observation (whichever was first)
PSS000334 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. We identified the first CHD event and classified it as ‘‘incident’’ if the event occurred at least 6 months after the participant’s first record in the EHR and if there were no previous ICD-9-CM or ICD-10-CM codes associated with CHD. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 11.7 years
Iqr = [6.0, 18.5] years
[
  • 2,221 cases
  • , 39,758 controls
]
,
44.6 % Male samples
Mean = 49.0 years
Sd = 14.1 years
European 11 cohorts
  • BioVU
  • ,CCHMC
  • ,Columbia
  • ,KP
  • ,Marshfield
  • ,Mayo
  • ,Mount Sinai
  • ,MyCode
  • ,Nugene
  • ,Partners
  • ,eMERGE
right censored at age 75 years or at the age of last observation (whichever was first)
PSS000335 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 10.4 years
Iqr = [5.7, 14.7] years
[
  • 419 cases
  • , 2,074 controls
]
,
36.2 % Male samples
Mean = 41.1 years
Sd = 13.2 years
Hispanic or Latin American 8 cohorts
  • BioVU
  • ,Columbia
  • ,KP
  • ,Mayo
  • ,Mount Sinai
  • ,Nugene
  • ,Partners
  • ,eMERGE
right censored at age 75 years or at the age of last observation (whichever was first)
PSS000336 CHD was defined as occurrence of either myocardial infarction (MI) or coronary revascularization events (such as percutaneous coronary intervention or coronary artery bypass grafting) using ICD codes. Individuals with MI were defined as those whose EHR included at least two related diagnostic codes on separate occasions within a 5-day window, and individuals with coronary revascularization were defined as those who had at least one relevant procedural code in the EHR. We identified the first CHD event and classified it as ‘‘incident’’ if the event occurred at least 6 months after the participant’s first record in the EHR and if there were no previous ICD-9-CM or ICD-10-CM codes associated with CHD. ICD codelists and phenotyping algorithm in PMID:27678441 and PMID:25717410 Median = 10.4 years
Iqr = [5.7, 14.7] years
[
  • 120 cases
  • , 2,194 controls
]
,
36.2 % Male samples
Mean = 41.1 years
Sd = 13.2 years
Hispanic or Latin American 8 cohorts
  • BioVU
  • ,Columbia
  • ,KP
  • ,Mayo
  • ,Mount Sinai
  • ,Nugene
  • ,Partners
  • ,eMERGE
right censored at age 75 years or at the age of last observation (whichever was first)