PGS Publication: PGP000466

Publication Information (EuropePMC)
Title A multi-ancestry polygenic risk score improves risk prediction for coronary artery disease.
PubMed ID 37414900(Europe PMC)
doi 10.1038/s41591-023-02429-x
Publication Date July 6, 2023
Journal Nat Med
Author(s) Patel AP, Wang M, Ruan Y, Koyama S, Clarke SL, Yang X, Tcheandjieu C, Agrawal S, Fahed AC, Ellinor PT, Genes & Health Research Team; the Million Veteran Program, Tsao PS, Sun YV, Cho K, Wilson PWF, Assimes TL, van Heel DA, Butterworth AS, Aragam KG, Natarajan P, Khera AV.
Released in PGS Catalog: July 5, 2023

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003725
(GPS_Mult)
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Coronary artery disease coronary artery disease 1,296,172
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003725/ScoringFiles/PGS003725.txt.gz
PGS003726
(GPS_CADANC)
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Coronary artery disease coronary artery disease 1,296,172
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003726/ScoringFiles/PGS003726.txt.gz
PGS003727
(GPS_CADEUR)
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Coronary artery disease coronary artery disease 1,125,113
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003727/ScoringFiles/PGS003727.txt.gz

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) 		Evaluated Score 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 PGS003725
(GPS_Mult)
 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 —
PPM018427 PGS003726
(GPS_CADANC)
 PSS010960|
European Ancestry|
308,264 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.73 [1.69, 1.76] — — age, sex and the first ten principal components of genetic ancestry —
PPM018428 PGS003726
(GPS_CADANC)
 PSS010961|
African Ancestry|
7,281 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.18 [1.01, 1.37] — — age, sex and the first ten principal components of genetic ancestry —
PPM018430 PGS003726
(GPS_CADANC)
 PSS010963|
South Asian Ancestry|
8,982 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.6 [1.47, 1.74] — — age, sex and the first ten principal components of genetic ancestry —
PPM018431 PGS003727
(GPS_CADEUR)
 PSS010960|
European Ancestry|
308,264 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.67 [1.64, 1.7] — — age, sex and the first ten principal components of genetic ancestry —
PPM018432 PGS003727
(GPS_CADEUR)
 PSS010961|
African Ancestry|
7,281 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.15 [0.99, 1.34] — — age, sex and the first ten principal components of genetic ancestry —
PPM018433 PGS003727
(GPS_CADEUR)
 PSS010962|
East Asian Ancestry|
1,464 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.54 [1.03, 2.32] — — age, sex and the first ten principal components of genetic ancestry —
PPM018434 PGS003727
(GPS_CADEUR)
 PSS010963|
South Asian Ancestry|
8,982 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.57 [1.44, 1.7] — — age, sex and the first ten principal components of genetic ancestry —
PPM018429 PGS003726
(GPS_CADANC)
 PSS010962|
East Asian Ancestry|
1,464 individuals
 PGP000466 |
Patel AP et al. Nat Med (2023)
 Reported Trait: Coronary artery disease HR: 1.64 [1.09, 2.48] — — 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)