Polygenic Score (PGS) ID: PGS001793

Predicted Trait
Reported Trait Stroke
Mapped Trait(s) stroke (EFO_0000712)
Released in PGS Catalog: Sept. 8, 2022
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Score Details

Score Construction
PGS Name 1kgeur_gbmi_leaveUKBBout_Stroke_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 910,099
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. Cell Genom (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 67%
East Asian: 28.6%
African: 2.7%
Additional Diverse Ancestries: 1.6%
939,362 individuals (100%)
PGS Evaluation
Additional Asian Ancestries: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 1,161 cases
  • , 24,416 controls
]
 African unspecified G&H
—
[
  • 903 cases
  • , 14,161 controls
]
 Native American BioVU
—
[
  • 23,345 cases
  • , 245,585 controls
]
 East Asian BioMe
—
[
  • 32,545 cases
  • , 597,246 controls
]
 European BBJ, CKB

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
PPM009306 PSS007705|
Additional Asian Ancestries|
8,091 individuals
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Reported Trait: Stroke — AUROC: 0.745 Nagelkerke's R2 (covariates regressed out): 0.01187 sex,age,age2,age*sex,age^2*sex, 20PCs —
PPM009297 PSS007716|
European Ancestry|
350,408 individuals
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Reported Trait: Stroke — AUROC: 0.706 Nagelkerke's R2 (covariates regressed out): 0.00278 sex,age,age2,age*sex,age^2*sex, 20PCs —

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
PSS007705 — —
[
  • 50 cases
  • , 8,040 controls
]
 — Asian unspecified Central and South Asian UKB —
PSS007716 — —
[
  • 1,650 cases
  • , 348,757 controls
]
 — European — UKB —