Polygenic Score (PGS) ID: PGS004054

Predicted Trait
Reported Trait Stroke
Mapped Trait(s) stroke (EFO_0000712)
Released in PGS Catalog: Dec. 19, 2023
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Score Details

Score Construction
PGS Name megaprs.auto.GCST005838.Stroke
Development Method
Name megaprs.auto
Parameters Model:Model186,Type:bayesr,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:0.975,BayesR_p2:0.01,BayesR_p3:0.01,BayesR_p4:0.005
Variants
Original Genome Build GRCh38
Number of Variants 852,173
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 85.2%
East Asian: 8.7%
African: 3.9%
South Asian: 1.7%
Hispanic or Latin American: 0.3%
Additional Asian Ancestries: 0.1%
524,354 individuals (100%)
Score Development/Training
European: 100%
8,142 individuals (100%)
PGS Evaluation
European: 66.7%
South Asian: 33.3%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST005838
Europe PMC: 29531354
 45,564 individuals East Asian NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 698 individuals Asian unspecified NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 1,557 individuals Hispanic or Latin American NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 9,144 individuals South Asian NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 20,695 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 446,696 individuals European NR
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
— 8,142 individuals European UKB — — — — —

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
PPM019473 PSS011223|
European Ancestry|
48,148 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Stroke excluding subarachnoid hemorrhage β: 0.11337 [0.0838625, 0.14287805]
OR: 1.12005 [1.08747936, 1.15358912]		 AUROC: 0.53265 [0.52410638, 0.54119598] R²: 0.00266 [0.00137051, 0.00420657] 0 beta = log(or)/sd_pgs
PPM019474 PSS011234|
European Ancestry|
376,733 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Stroke excluding subarachnoid hemorrhage OR: 1.16971 [1.15508988, 1.18450788]
β: 0.15675 [0.14417816, 0.16932739]		 AUROC: 0.54467 [0.54105858, 0.54827219] R²: 0.00508 [0.00428569, 0.00597661] 0 beta = log(or)/sd_pgs
PPM019475 PSS011247|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Stroke excluding subarachnoid hemorrhage OR: 1.09218 [0.99244315, 1.20193532]
β: 0.08817 [-0.0075855, 0.18393302]		 AUROC: 0.52469 [0.49822599, 0.55115016] R²: 0.0012 [0.0, 0.00477209] 0 beta = log(or)/sd_pgs
PPM019476 PSS011263|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Stroke excluding subarachnoid hemorrhage OR: 1.1469 [1.11485209, 1.17987041]
β: 0.13706 [0.10872174, 0.16540461]		 AUROC: 0.53902 [0.53097366, 0.54705807] R²: 0.00388 [0.00235764, 0.00565486] 0 beta = log(or)/sd_pgs
PPM019477 PSS011290|
South Asian Ancestry|
9,326 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Stroke excluding subarachnoid hemorrhage OR: 1.23492 [1.07805871, 1.41460106]
β: 0.211 [0.07516194, 0.34684756]		 AUROC: 0.56842 [0.52959783, 0.60723511] R²: 0.00696 [0.000789, 0.01932319] 0 beta = log(or)/sd_pgs
PPM019478 PSS011276|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Stroke excluding subarachnoid hemorrhage OR: 1.21483 [1.16243507, 1.26958012]
β: 0.1946 [0.15051701, 0.23868624]		 AUROC: 0.55421 [0.54154316, 0.56688511] R²: 0.00779 [0.00457599, 0.01180516] 0 beta = log(or)/sd_pgs

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
PSS011276 — —
[
  • 2,035 cases
  • , 88,239 controls
]
 — European — UKB —
PSS011247 — —
[
  • 424 cases
  • , 43,633 controls
]
 — South Asian — G&H —
PSS011223 — —
[
  • 4,515 cases
  • , 43,633 controls
]
 — European — EB —
PSS011290 — —
[
  • 211 cases
  • , 9,115 controls
]
 — South Asian — UKB —
PSS011263 — —
[
  • 5,204 cases
  • , 61,661 controls
]
 — European — HUNT —
PSS011234 I9_STR, ICD10: I61 | I63 | I64 (exclude I636), ICD9:431|4330A|4331A|4339A|4340A|4341A|4349A|436 —
[
  • 26,166 cases
  • , 350,567 controls
]
 — European — FinnGen —