Polygenic Score (PGS) ID: PGS000116

Predicted Trait
Reported Trait Coronary Artery Disease
Mapped Trait(s) coronary artery disease (EFO_0000378)
Released in PGS: March 27, 2020

Score Details

Score Construction
PGS Name CAD_EJ2020
Variants
Original Genome Build GRCh37
Number of Variants 40,079
Development Method
Name Lassosum
Parameters INFO score>0.999; N=1,037,385 variants; s=0.5; lambda=0.00428
PGS Source
PGS Catalog Publication (PGP) ID PGP000054
Citation (link to publication) Elliott J et al. JAMA (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003116
EuropePMC: 26343387
11,323 individuals East Asian
GWAS Catalog: GCST003116
EuropePMC: 26343387
25,557 individuals South Asian
GWAS Catalog: GCST003116
EuropePMC: 26343387
2,268 individuals Greater Middle Eastern (Middle Eastern, North African or Persian)
GWAS Catalog: GCST003116
EuropePMC: 26343387
4,095 individuals Hispanic or Latin American
GWAS Catalog: GCST003116
EuropePMC: 26343387
141,217 individuals European
GWAS Catalog: GCST003116
EuropePMC: 26343387
3,139 individuals African American or Afro-Caribbean
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
[
  • 15,947 cases
  • , 64,156 controls
]
,
68.24 % Male samples
Mean = 60.0 years Other
(95% European, 0.2% Chinese, 1,4% Indian,0.4%Other Asian, 0.5% Pakistani, 1.1 % Other ancestries )
UKB Tuning (Case-Control) Set

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)
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
PPM000333 PSS000199 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.78[0.76, 0.79] QRISK3
PPM000332 PSS000195 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.73[0.72, 0.74] QRISK3
PPM000331 PSS000187 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.83[0.81, 0.84] QRISK3
PPM000330 PSS000191 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.75[0.74, 0.76] QRISK3
PPM000295 PSS000196 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.72[0.71, 0.73] pooled cohort equations
PPM000329 PSS000203 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.74[0.73, 0.75] QRISK3
PPM000298 PSS000200 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.76[0.75, 0.78] pooled cohort equations
PPM000294 PSS000196 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.7[0.69, 0.71] age,sex
PPM000292 PSS000188 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.8[0.79, 0.82] pooled cohort equations
PPM000271 PSS000202 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.78[0.77, 0.79] pooled cohort equations
PPM000293 PSS000196 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.62[0.61, 0.63]
PPM000297 PSS000200 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.72[0.7, 0.73] age,sex
PPM000291 PSS000188 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.77[0.75, 0.79] age,sex
PPM000289 PSS000192 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.74[0.73, 0.75] pooled cohort equations
PPM000288 PSS000192 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.72[0.71, 0.73] age,sex
PPM000286 PSS000204 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.79[0.78, 0.8] pooled cohort equations
PPM000285 PSS000204 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.76[0.76, 0.77] age,sex
PPM000283 PSS000198 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.76[0.74, 0.77] pooled cohort equations
PPM000282 PSS000198 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.71[0.7, 0.73] age,sex
PPM000280 PSS000194 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.71[0.7, 0.72] pooled cohort equations
PPM000279 PSS000194 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.68[0.67, 0.69] age,sex
PPM000277 PSS000186 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.8[0.79, 0.82] pooled cohort equations
PPM000276 PSS000186 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.76[0.75, 0.78] age,sex
PPM000274 PSS000190 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.74[0.73, 0.74] pooled cohort equations
PPM000273 PSS000190 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.71[0.7, 0.72] age,sex
PPM000270 PSS000202 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.76[0.75, 0.76] age,sex
PPM000290 PSS000188 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.65[0.63, 0.66]
PPM000287 PSS000192 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.61[0.6, 0.62]
PPM000284 PSS000204 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.61[0.6, 0.62]
PPM000281 PSS000198 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.61[0.6, 0.63]
PPM000278 PSS000194 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.61[0.6, 0.62]
PPM000275 PSS000186 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.64[0.63, 0.66]
PPM000272 PSS000190 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.6[0.59, 0.61]
PPM000269 PSS000202 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease HR: 1.32[1.3, 1.34] C-index: 0.61[0.6, 0.62]
PPM000296 PSS000200 PGP000054
Elliott J et al. (2020)
Reported Trait: Incident coronary artery disease C-index: 0.61[0.6, 0.63]

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
PSS000186 Mean = 8.01 years
Sd = 1.04 years
[
  • 1,350 cases
  • , 146,635 controls
]
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. Lipid-lowering treatment performed
PSS000187 Mean = 8.01 years
Sd = 1.04 years
[
  • 2,826 cases
]
Other
(2,332 Africans, 145 Bangladeshi, 3,165 Carribeans, 1,136 Chinese, 3,790 Indians, 1,258 Other Asians, 1,182 Pakistani, 332,326 White Europeans and Unkown ancestry)
UKB QRISK3 Prospective Cohort/Testing Set. Lipid-lowering treatment performed
PSS000188 Mean = 8.01 years
Sd = 1.04 years
[
  • 1,149 cases
]
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. No baseline treatment
PSS000190 Mean = 8.01 years
Sd = 1.04 years
[
  • 4,922 cases
  • , 199,753 controls
]
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. Lipid-lowering treatment performed
PSS000191 Mean = 8.01 years
Sd = 1.04 years
[
  • 10,824 cases
]
Other
(2,332 Africans, 145 Bangladeshi, 3,165 Carribeans, 1,136 Chinese, 3,790 Indians, 1,258 Other Asians, 1,182 Pakistani, 332,326 White Europeans and Unkown ancestry)
UKB QRISK3 Prospective Cohort/Testing Set. Lipid-lowering treatment performed
PSS000192 Mean = 8.01 years
Sd = 1.04 years
[
  • 3,643 cases
]
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. No baseline treatment
PSS000194 Mean = 8.01 years
Sd = 1.04 years
[
  • 4,439 cases
  • , 142,870 controls
]
,
100.0 % Male samples
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. Lipid-lowering treatment performed
PSS000195 Mean = 8.01 years
Sd = 1.04 years
[
  • 8,536 cases
]
,
100.0 % Male samples
Other
(2,332 Africans, 145 Bangladeshi, 3,165 Carribeans, 1,136 Chinese, 3,790 Indians, 1,258 Other Asians, 1,182 Pakistani, 332,326 White Europeans and Unkown ancestry)
UKB QRISK3 Prospective Cohort/Testing Set. Lipid-lowering treatment performed
PSS000196 Mean = 8.01 years
Sd = 1.04 years
[
  • 3,381 cases
  • , 119,165 controls
]
,
100.0 % Male samples
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. No baseline treatment
PSS000198 Mean = 8.01 years
Sd = 1.04 years
[
  • 1,779 cases
  • , 203,518 controls
]
,
0.0 % Male samples
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. Lipid-lowering treatment performed
PSS000199 Mean = 8.01 years
Sd = 1.04 years
[
  • 5,114 cases
]
,
0.0 % Male samples
Other
(2,332 Africans, 145 Bangladeshi, 3,165 Carribeans, 1,136 Chinese, 3,790 Indians, 1,258 Other Asians, 1,182 Pakistani, 332,326 White Europeans and Unkown ancestry)
UKB QRISK3 Prospective Cohort/Testing Set. Lipid-lowering treatment performed
PSS000200 Mean = 8.01 years
Sd = 1.04 years
[
  • 1,411 cases
  • , 182,464 controls
]
,
0.0 % Male samples
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. No baseline treatment
PSS000202 Mean = 8.01 years
Sd = 1.04 years
[
  • 6,272 cases
  • , 346,388 controls
]
,
41.8 % Male samples
Mean = 55.9 years Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. Lipid-lowering treatment performed
PSS000203 Mean = 8.01 years
Sd = 1.04 years
[
  • 13,648 cases
]
,
41.0 % Male samples
Other
(2,332 Africans, 145 Bangladeshi, 3,165 Carribeans, 1,136 Chinese, 3,790 Indians, 1,258 Other Asians, 1,182 Pakistani, 332,326 White Europeans and Unkown ancestry)
UKB QRISK3 Prospective Cohort/Testing Set. Lipid-lowering treatment performed
PSS000204 Mean = 8.01 years
Sd = 1.04 years
[
  • 4,792 cases
  • , 301,629 controls
]
Other
(98.3% White European, 1.7% Black/Other)
UKB PCE Prospective Cohort. No baseline treatment