Polygenic Score (PGS) ID: PGS019947

Predicted Trait
Reported Trait Ischemic stroke
Mapped Trait(s) Ischemic stroke (HP_0002140)
Released in PGS Catalog: Oct. 23, 2026
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Score Details

Score Construction
PGS Name IS_PRSCS_HM3_AFR
Development Method
Name PRS-CS
Parameters phi=1E-02, HapMap3 reference panel
Variants
Original Genome Build GRCh38
Number of Variants 983,900
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000839
Citation (link to publication) Armstrong ND et al. Front Bioinform (2026)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
20,924 individuals (100%)
Score Development/Training
African: 100%
6,342 individuals (100%)
PGS Evaluation
African: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90104550
Europe PMC: 36180795
 20,924 individuals African American or Afro-Caribbean 10 cohorts
  • ARIC
  • ,CHS
  • ,COMPASS
  • ,INTERSTROKE
  • ,JHS
  • ,MESA
  • ,Other
  • ,REGARDS
  • ,SIGNET
  • ,SiGN
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
—
[
  • 422 cases
  • , 5,920 controls
]
,
39.1 % Male samples
 African American or Afro-Caribbean REGARDS — Mean = 63.6 years
Sd = 9.2 years		 — — ischemic stroke - ischemic stroke events in REGARDS were identified through biannual surveillance and adjudicated via medical record review. For participants aligned to Medicare claims, additional ischemic stroke events were identified from inpatient claims using ICD-9 codes 433.x1 or 434.x1 or ICD-10 codes I63.xx in the primary diagnosis position. Hospitalizations occurring within one day of each other were merged into a single episode of care. Participants with self-reported stroke at baseline were excluded.

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
PPM038125 PSS013828|
African Ancestry|
29,594 individuals
 PGP000839 |
Armstrong ND et al. Front Bioinform (2026)
 Reported Trait: ischemic stroke OR: 1.04 [0.988, 1.095] AUROC: 0.66597 — age, sex, PC 1-10 —
PPM038131 PSS013830|
African Ancestry|
6,908 individuals
 PGP000839 |
Armstrong ND et al. Front Bioinform (2026)
 Reported Trait: Stroke OR: 1.114 [0.978, 1.268] AUROC: 0.6439 [0.6159, 0.6719] — age, sex, PC 1-10, trial antihypertensive group —

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
PSS013828 — —
[
  • 311 cases
  • , 29,283 controls
]
,
46.1 % Male samples
 Mean = 63.3 years
Sd = 8.1 years		 African American or Afro-Caribbean — AllofUs To harmonize phenotype definitions with REGARDS, analyses in All of Us were restricted to participants aged ≥45 years. IS cases were defined as individuals with an inpatient encounter associated with ICD-9 codes 433.x1 or 434.x1, or ICD-10 codes I63.xx. Stroke codes identified only in non-inpatient encounters, SNOMED stroke codes, and hemorrhagic stroke codes (ICD-9 430.x, 431.x; ICD-10 I60.x, I61.x) were excluded from both case and control sets.
PSS013830 — —
[
  • 366 cases
  • , 6,542 controls
]
,
44.6 % Male samples
 Mean = 66.2 years
Sd = 7.8 years		 African American or Afro-Caribbean — GenHAT Incident stroke in GenHAT was defined as a persistent neurological deficit resulting from arterial occlusion or rupture, lasting >24 hours (unless fatal), or with CT/MRI evidence consistent with acute stroke, excluding stroke due to trauma, infection, tumor, or other non-ischemic causes. Events occurring perioperatively were included. In the primary ALLHAT study, the type of stroke (specifically differentiating between ischemic and hemorrhagic) was not systematically classified or reported as part of the trial's pre-specific secondary outcomes; therefore, stroke was analyzed as an all-stroke phenotype in this cohort.