Polygenic Score (PGS) ID: PGS000898

Predicted Trait
Reported Trait Alzheimer's disease
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Released in PGS Catalog: Sept. 17, 2021
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Score Details

Score Construction
PGS Name PRS39_AD
Development Method
Name Genome-wide significant variants
Parameters p < 5e-8
Variants
Original Genome Build GRCh37
Number of Variants 40
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000231
Citation (link to publication) de Rojas I et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
409,435 individuals (100%)
Score Development/Training
European: 64.6%
Not Reported: 35.4%
151,811 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST012182
Europe PMC: 34099642
 409,435 individuals European GR@ACE, IGAP, UKB
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
GWAS Catalog: GCST007511
Europe PMC: 30820047
 63,926 individuals European ADGC, CHARGE, EADI, GERAD, PERADES — — — — This dataset was used to weight SNPs within the PRS.
GWAS Catalog: GCST005549
Europe PMC: 28714976
 34,174 individuals European CHARGE, GERAD, PERADES — — — — This dataset was used to weight SNPs within the PRS.
GWAS Catalog: GCST002813
Europe PMC: 25778476
 19,559 individuals Not reported 7 cohorts
  • ADGC
  • ,AGES
  • ,CHS
  • ,EADI
  • ,FHS
  • ,GERAD
  • ,RS
 — — — — This dataset was used to weight SNPs within the PRS.
GWAS Catalog: GCST002817
Europe PMC: 25778476
 34,152 individuals Not reported 7 cohorts
  • ADGC
  • ,AGES
  • ,CHS
  • ,EADI
  • ,FHS
  • ,GERAD
  • ,RS
 — — — — This dataset was used to weight SNPs within the PRS.

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
PPM002634 PSS001167|
European Ancestry|
2,394 individuals
 PGP000231 |
de Rojas I et al. Nat Commun (2021)
 Reported Trait: Alzheimer's disease (clinically confirmed) OR: 1.3 [1.18, 1.44] — — PCs(1-4) —
PPM002635 PSS001167|
European Ancestry|
2,394 individuals
 PGP000231 |
de Rojas I et al. Nat Commun (2021)
 Reported Trait: Alzheimer's disease (pathologically confirmed) OR: 1.38 [1.21, 1.58] — — PCs(1-4) —
PPM002636 PSS001167|
European Ancestry|
2,394 individuals
 PGP000231 |
de Rojas I et al. Nat Commun (2021)
 Reported Trait: Alzheimer's disease (pathologically confirmed, males) OR: 1.33 [1.13, 1.56] — — PCs(1-4) —
PPM002637 PSS001167|
European Ancestry|
2,394 individuals
 PGP000231 |
de Rojas I et al. Nat Commun (2021)
 Reported Trait: Alzheimer's disease (pathologically confirmed, females) OR: 1.32 [1.19, 1.47] — — PCs(1-4) —
PPM002638 PSS001167|
European Ancestry|
2,394 individuals
 PGP000231 |
de Rojas I et al. Nat Commun (2021)
 Reported Trait: Early-onset Alzheimer's disease (< 65 years) OR: 1.58 [1.22, 2.05] — — PCs(1-4) —
PPM002639 PSS001167|
European Ancestry|
2,394 individuals
 PGP000231 |
de Rojas I et al. Nat Commun (2021)
 Reported Trait: Late-onset Alzheimer's disease (> 85 years) OR: 1.29 [1.1, 1.51] — — PCs(1-4) —

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
PSS001167 Cases were individuals with pathologically or clinically diagnosed Alzheimer's disease (AD). Of the 1008 AD cases, 332 had been confirmed pathologically whilst 676 had been confirmed clinically. Pathological AD was confirmed by the Biobanc Hospital Clínic–IDIBAPS, whilst clinical diagnosis of AD was based on clinical criteria from Fundació ACE. —
[
  • 1,008 cases
  • , 1,386 controls
]
,
29.2 % Male samples
 — European
(Spanish)		 — EADB —