Polygenic Score (PGS) ID: PGS004062

Predicted Trait
Reported Trait Alzheimer's disease
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Released in PGS Catalog: Dec. 19, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name megaprs.auto.GCST90012877.AD
Development Method
Name megaprs.auto
Parameters Model:Model123,Type:bolt,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:0.05,Bolt_f2:0.35,BayesR_p1:NA,BayesR_p2:NA,BayesR_p3:NA,BayesR_p4:NA
Variants
Original Genome Build GRCh38
Number of Variants 691,136
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: 100%
472,868 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90012877
Europe PMC: 33589840
 472,868 individuals European 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
PPM019931 PSS011213|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: AD OR: 1.46172 [1.35265857, 1.57957283]
β: 0.37961 [0.30207197, 0.45715445]		 AUROC: 0.60579 [0.58137466, 0.63020687] R²: 0.02494 [0.01482857, 0.03780255] 0 beta = log(or)/sd_pgs
PPM019933 PSS011252|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: AD OR: 1.73895 [1.66108385, 1.82046629]
β: 0.55328 [0.50747031, 0.59909267]		 AUROC: 0.66036 [0.64617344, 0.67454912] R²: 0.05664 [0.04705507, 0.0684223] 0 beta = log(or)/sd_pgs
PPM019932 PSS011226|
European Ancestry|
389,004 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: AD OR: 1.48022 [1.45673427, 1.50408347]
β: 0.39219 [0.37619713, 0.40818372]		 AUROC: 0.61101 [0.6061323, 0.6158922] R²: 0.02634 [0.02407498, 0.02873899] 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
PSS011226 G6_AD_WIDE, ICD10: G30|F00, ICD9: 3310 —
[
  • 13,823 cases
  • , 375,181 controls
]
 — European — FinnGen —
PSS011252 — —
[
  • 1,562 cases
  • , 65,303 controls
]
 — European — HUNT —
PSS011213 — —
[
  • 555 cases
  • , 198,719 controls
]
 — European — EB —