Polygenic Score (PGS) ID: PGS004590

Predicted Trait
Reported Trait Alzheimer's disease
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Released in PGS Catalog: Jan. 26, 2024
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Score Details

Score Construction
PGS Name PRS363_rand_eff
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2 threshold = 0.3, clump P value threshold = 1, P value threshold = 5.00E-05, excluding APOE
Variants
Original Genome Build GRCh37
Number of Variants 363
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000569
Citation (link to publication) Lake J et al. Mol Psychiatry (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 97.2%
African: 1.2%
East Asian: 1.2%
Hispanic or Latin American: 0.3%
644,224 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • Additional Diverse Ancestries
  • African
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90027158
Europe PMC: 35379992
 487,511 individuals European NR
[
  • 7,329 cases
  • , 131,102 controls
]
 European FinnGen
GWAS Catalog: GCST012215
Europe PMC: 33654092
 8,036 individuals East Asian NCGG
GWAS Catalog: GCST011696
Europe PMC: 33074286
 8,006 individuals African American or Afro-Caribbean NR
Europe PMC: 37198259
[
  • 1,088 cases
  • , 1,152 controls
]
 Hispanic or Latin American NR

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
PPM020719 PSS011381|
Multi-ancestry (including European)|
368 individuals
 PGP000569 |
Lake J et al. Mol Psychiatry (2023)
 Reported Trait: Alzheimer's disease — AUROC: 0.68 R²: 0.0044 Age, sex, 5 PCs —

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
PSS011381 — —
[
  • 281 cases
  • , 87 controls
]
 — European, Native American, African unspecified — TANGL —