Polygenic Score (PGS) ID: PGS000116

Predicted Trait
Reported Trait Coronary Artery Disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: March 27, 2020
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Terms and Licenses
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

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
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
Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings —
[
  • 15,947 cases
  • , 64,156 controls
]
,
68.24 % Male samples
 Mean = 60.0 years European, East Asian, South Asian, Asian unspecified, NR 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
PPM000836 PSS000401 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease — C-index: 0.74 [0.73, 0.75] — QRISK3 —
PPM000837 PSS000389 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (over age 55) — C-index: 0.75 [0.74, 0.76] — QRISK3 —
PPM000838 PSS000385 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (under age 55) — C-index: 0.83 [0.81, 0.84] — QRISK3 —
PPM000839 PSS000393 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in males) — C-index: 0.73 [0.72, 0.74] — QRISK3 —
PPM000840 PSS000397 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in females) — C-index: 0.78 [0.76, 0.79] — QRISK3 —
PPM000807 PSS000399 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease — C-index: 0.76 [0.75, 0.76] — age,sex —
PPM000808 PSS000399 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease — C-index: 0.78 [0.77, 0.79] — pooled cohort equations —
PPM000810 PSS000387 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (over age 55) — C-index: 0.71 [0.7, 0.72] — age,sex —
PPM000811 PSS000387 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (over age 55) — C-index: 0.74 [0.73, 0.74] — pooled cohort equations —
PPM000813 PSS000383 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (under age 55) — C-index: 0.76 [0.75, 0.78] — age,sex —
PPM000814 PSS000383 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (under age 55) — C-index: 0.8 [0.79, 0.82] — pooled cohort equations —
PPM000816 PSS000391 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in males) — C-index: 0.68 [0.67, 0.69] — age,sex —
PPM000817 PSS000391 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in males) — C-index: 0.71 [0.7, 0.72] — pooled cohort equations —
PPM000819 PSS000395 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in females) — C-index: 0.71 [0.7, 0.73] — age,sex —
PPM000820 PSS000395 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in females) — C-index: 0.76 [0.74, 0.77] — pooled cohort equations —
PPM000806 PSS000399 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease HR: 1.32 [1.3, 1.34] C-index: 0.61 [0.6, 0.62] — — —
PPM000809 PSS000387 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (over age 55) — C-index: 0.6 [0.59, 0.61] — — —
PPM000812 PSS000383 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (under age 55) — C-index: 0.64 [0.63, 0.66] — — —
PPM000815 PSS000391 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in males) — C-index: 0.61 [0.6, 0.62] — — —
PPM000818 PSS000395 PGP000054
Elliott J et al. JAMA (2020)
 Reported Trait: Incident coronary artery disease (in females) — C-index: 0.61 [0.6, 0.63] — — —

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
PSS000383 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 1,350 cases
  • , 146,635 controls
]
 Range = [40.0, 55.0] years European, African unspecified, NR 98.3% White European, 1.7% Black/Other UKB PCE Prospective Cohort (lipid-lowering treatment performed)
PSS000385 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 1,339 cases
  • , 145,771 controls
]
 Range = [40.0, 55.0] years European, South Asian, African American or Afro-Caribbean, African unspecified, East Asian, Asian unspecified 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)
PSS000387 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 4,922 cases
  • , 199,753 controls
]
 Range = [55.0, 69.0] years European, African unspecified, NR 98.3% White European, 1.7% Black/Other UKB PCE Prospective Cohort (lipid-lowering treatment performed)
PSS000389 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 4,900 cases
  • , 198,720 controls
]
 Range = [55.0, 69.0] years European, South Asian, African American or Afro-Caribbean, African unspecified, East Asian, Asian unspecified 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)
PSS000391 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 4,493 cases
  • , 142,870 controls
]
,
100.0 % Male samples
 Mean = 55.79 years
Sd = 8.35 years		 European, African unspecified, NR 98.3% White European, 1.7% Black/Other UKB PCE Prospective Cohort (lipid-lowering treatment performed)
PSS000393 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 4,471 cases
  • , 142,102 controls
]
,
100.0 % Male samples
 Mean = 55.8 years
Sd = 8.3 years		 European, South Asian, African American or Afro-Caribbean, African unspecified, East Asian, Asian unspecified 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)
PSS000395 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 1,779 cases
  • , 203,518 controls
]
,
0.0 % Male samples
 Mean = 56.0 years
Sd = 8.01 years		 European, African unspecified, NR 98.3% White European, 1.7% Black/Other UKB PCE Prospective Cohort (lipid-lowering treatment performed)
PSS000397 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 1,768 cases
  • , 202,389 controls
]
,
0.0 % Male samples
 Mean = 56.0 years
Sd = 8.0 years		 European, South Asian, African American or Afro-Caribbean, African unspecified, East Asian, Asian unspecified 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)
PSS000399 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 6,272 cases
  • , 346,388 controls
]
,
41.8 % Male samples
 Mean = 55.9 years
Range = [40.0, 69.0] years		 European, African unspecified, NR 98.3% White European, 1.7% Black/Other UKB PCE Prospective Cohort (lipid-lowering treatment performed)
PSS000401 Coronary artery disease was defined as myocardial infarction and its related sequelae (coronary angioplasty, and coronary artery bypass grafts). ICD-10 codes: I21, I22, I23, I24.1, I25.2 ICD-9 codes: 410, 411, 412, 429.79 OPCS-4 codes: K40.1-4, K41.1-4, K45.1-5, K49.1-2, K49.8-9, K50.2, K75.1-4, K54.8-9 UKBiobank field 20002 code: 1075 UKBiobank field 20004 codes: 1070, 1095 UKBiobank field 6150 code: 1 See eTable 1 for risk factor codings Mean = 8.01 years
Sd = 1.04 years
[
  • 6,239 cases
  • , 344,491 controls
]
,
41.0 % Male samples
 Range = [40.0, 69.0] years European, South Asian, African American or Afro-Caribbean, African unspecified, East Asian, Asian unspecified 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)