Polygenic Score (PGS) ID: PGS003725

Predicted Trait
Reported Trait Coronary artery disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: July 5, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GPS_Mult
Development Method
Name LDpred2
Parameters p= [0.0001, 0.00018, 0.00032, 0.001, 0.0018, 0.0032, 0.0056, 0.01, 0.018, 0.032, 0.056, 0.1, 0.18, 0.32, 0.56, 1], h^scale= [0.7, 1, 1.4], Sparse LD = [T, F]
Variants
Original Genome Build hg19
Number of Variants 1,296,172
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000466
Citation (link to publication) Patel AP et al. Nat Med (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • African
  • East Asian
  • European
  • Hispanic or Latin American
  • South Asian
1,443,386 individuals (100%)
Score Development/Training
European: 100%
116,649 individuals (100%)
PGS Evaluation
African: 25%
European: 25%
South Asian: 25%
Hispanic or Latin American: 12.5%
East Asian: 12.5%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 269,521 cases
  • , 1,173,865 controls
]
 African unspecified, East Asian, European, Hispanic or Latin American, South Asian 11 cohorts
  • AGENT2D
  • ,BBJ
  • ,CARDIoGRAMplusC4D
  • ,DIAMANTE
  • ,FinnGen
  • ,G&H
  • ,GBMI
  • ,GIANT
  • ,GLGC
  • ,MEGASTROKE
  • ,MVP
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 30305743
[
  • 4,412 cases
  • , 112,237 controls
]
,
47.5 % Male samples
 European
(British)		 UKB ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 Mean = 57.5 years — — First released tranche of genotypes from UKBB

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) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM018420 PSS010961|
African Ancestry|
7,281 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.25 [1.07, 1.46]
OR: 1.39 [1.17, 1.67]		 — — age, sex and the first ten principal components of genetic ancestry —
PPM018421 PSS010962|
East Asian Ancestry|
1,464 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.72 [1.13, 2.6]
OR: 2.14 [1.34, 3.49]		 — — age, sex and the first ten principal components of genetic ancestry —
PPM018419 PSS010960|
European Ancestry|
308,264 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.75 [1.71, 1.78]
OR: 2.14 [2.1, 2.19]		 — — age, sex and the first ten principal components of genetic ancestry —
PPM018422 PSS010963|
South Asian Ancestry|
8,982 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.62 [1.49, 1.77]
OR: 2.02 [1.83, 2.23]		 — — age, sex and the first ten principal components of genetic ancestry —
PPM018423 PSS010964|
African Ancestry|
33,096 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease OR: 1.25 [1.21, 1.29] — — age, sex and the first ten principal components of genetic ancestry —
PPM018424 PSS010965|
European Ancestry|
124,467 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease OR: 1.72 [1.69, 1.75] — — age, sex and the first ten principal components of genetic ancestry —
PPM018425 PSS010966|
Hispanic or Latin American Ancestry|
16,433 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease OR: 1.61 [1.53, 1.7] — — age, sex and the first ten principal components of genetic ancestry —
PPM018426 PSS010967|
South Asian Ancestry|
16,874 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease OR: 1.83 [1.69, 1.99] — — age, sex and the first ten principal components of genetic ancestry —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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
PSS010960 ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 Mean = 12.0 years
Range = [11.2, 12.7] years
[
  • 10,492 cases
  • , 297,772 controls
]
,
45.6 % Male samples
 Mean = 57.3 years European — UKB Excluding first released tranche of genotypes from UKBB
PSS010961 ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 Mean = 12.0 years
Range = [11.2, 12.7] years
[
  • 124 cases
  • , 7,157 controls
]
,
43.5 % Male samples
 Mean = 52.4 years African unspecified — UKB —
PSS010962 ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 Mean = 12.0 years
Range = [11.2, 12.7] years
[
  • 22 cases
  • , 1,442 controls
]
,
37.2 % Male samples
 Mean = 53.0 years East Asian — UKB —
PSS010963 ICD 10: I21,I210,I211,I212,I213,I214,I219,I22,I220,I221,I228,I229,I23,I230,I231,I232,I233,I234,I235,I236,I238,I24,I240,I241,I248,I249,I252; ICD9: 410, 411, 412, 4119,4129,4109; OPCS: K40,K401,K402,K403,K404,K408,K409,K41,K411,K412,K413,K414,K418,K419,K42,K421,K422,K423,K424,K428,K429,K43,K431,K432,K433,K434,K438,K439,K44,K441,K442,K448,K449,K451,K452,K453,K454,K455,K456,K458,K459,K46,K461,K462,K463,K464,K465,K468,K469,K471,K491,K492,K493,K494,K498,K499,K501,K502,K504,K751,K752,K753,K754,K758,K759 Mean = 12.0 years
Range = [11.2, 12.7] years
[
  • 542 cases
  • , 8,440 controls
]
,
54.1 % Male samples
 Mean = 53.8 years South Asian — UKB —
PSS010964 ICD 10: I21-I25; Z95.1, Z98.61; ICD9: 0.66, 36.X, 99.1, 410, 411.X, 412, 414.X, V45.81, V45.82 —
[
  • 4,831 cases
  • , 28,265 controls
]
 — African American or Afro-Caribbean — MVP Excluding individuals in published GWAS (GCST90132302)
PSS010965 ICD 10: I21-I25; Z95.1, Z98.61; ICD9: 0.66, 36.X, 99.1, 410, 411.X, 412, 414.X, V45.81, V45.82 —
[
  • 29,171 cases
  • , 95,296 controls
]
 — European — MVP Excluding individuals in published GWAS (GCST90132302)
PSS010966 ICD 10: I21-I25; Z95.1, Z98.61; ICD9: 0.66, 36.X, 99.1, 410, 411.X, 412, 414.X, V45.81, V45.82 —
[
  • 2,140 cases
  • , 14,293 controls
]
 — Hispanic or Latin American — MVP Excluding individuals in published GWAS (GCST90132302)
PSS010967 ICD10: I21.X, I22.X, I23.X, I24.1, or I25.2; K40.1-40.4, K41.1-41.4, K45.1-45.5, K49.1-49.2, K49.8-49.9, K50.2, K75.1-75.4, or K75.8-75.9 ICD9: 410.X, 411.0, 412.X, or 429.79 —
[
  • 853 cases
  • , 16,021 controls
]
 — South Asian
(Bangladeshi, Pakistani)		 — G&H Excluding individuals in published GWAS (GCST90140952)