Polygenic Score (PGS) ID: PGS004229

Predicted Trait
Reported Trait Alzheimer's disease
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Released in PGS Catalog: Dec. 15, 2023
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Score Details

Score Construction
PGS Name ad_noapoe_0.1_pgs
Development Method
Name PRSice-2
Parameters Excluded variants in the APOE region (chr 19, GRCh37 coordinates 44,912,079 to 45,912,079). clump-kb = 250, p= 1, r2 = 0.001, threshold = 0.1
Variants
Original Genome Build GRCh37
Number of Variants 8,858
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000527
Citation (link to publication) Green RE et al. Alzheimers Res Ther (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
63,926 individuals (100%)
PGS Evaluation
Not Reported: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007511
Europe PMC: 30820047
 63,926 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
PPM020223 PSS011307|
Ancestry Not Reported|
1,638 individuals
 PGP000527 |
Green RE et al. Alzheimers Res Ther (2023)
 Reported Trait: Alzheimer's disease biomarker (linolenate (18:3n3 or 3n6)) β: -0.05431 [-0.103025695, -0.005590157] — — — —
PPM020222 PSS011307|
Ancestry Not Reported|
1,638 individuals
 PGP000527 |
Green RE et al. Alzheimers Res Ther (2023)
 Reported Trait: Alzheimer's disease biomarker (docosapentaenoate (DPA; 22:5n3)) β: -0.07733 [-0.125825807, -0.028839878] — — — —

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
PSS011307 — — 1,638 individuals,
49.6 % Male samples
 — Not reported — NSHD Outcomes tested were metabolite levels generated by Metabolon Inc, and metabolite modules generated using this data. All outcome (metabolite) data were collected at the 60-64 wave of the NSHD.