Polygenic Score (PGS) ID: PGS000026

Predicted Trait
Reported Trait Alzheimer’s Disease
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Released in PGS Catalog: Oct. 14, 2019
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Score Details

Score Construction
PGS Name PHS
Development Method
Name Hazard model with stepwise selection of SNP inclusion
Parameters SNPs eligible for inclusion had a significane of p < 10−5
Variants
Original Genome Build NR
Number of Variants 31
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000016
Citation (link to publication) Desikan RS et al. PLoS Med (2017)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
54,162 individuals (100%)
Score Development/Training
European: 100%
15,795 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002245
Europe PMC: 24162737
[
  • 17,008 cases
  • , 37,154 controls
]
European ADGC, CHARGE, EADI, GERAD
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
[
  • 6,409 cases
  • , 9,386 controls
]
,
40.19 % Male samples
European ADGC Cases are patients with clinically diagnosed AD and compared to cognitively normal older individuals ADGC Phase 1

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
PPM000053 PSS000036|
European Ancestry|
17,956 individuals
PGP000016 |
Desikan RS et al. PLoS Med (2017)
Reported Trait: Alzheimer disease r (correlation between between binned quantiles of PHS-predicted and empirical age of AD onset): 0.9 APOE risk alleles (e2 and e4), age, sex, genetic PCs 1-5
PPM002504 PSS001127|
European Ancestry|
8,415 individuals
PGP000222 |
Leonenko G et al. Ann Clin Transl Neurol (2019)
|Ext.
Reported Trait: Age at Alzheimer's disease onset β: 0.11 (0.02) Gender, PCs (1-3), APOE(ε2 + ε4) Due to SNP availability issues in the dataset, only 25 out of the 31 variants in Desikan et al's polygenic hazard score (PGS000026) were used. No APOE alleles were included

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
PSS000036 Cases are patients with clinically diagnosed AD and compared to cognitively normal older individuals
[
  • 6,984 cases
  • , 10,972 controls
]
,
40.51 % Male samples
European ADGC ADGC Phase 2
PSS001127 Cases included individuals with Alzheimer's disease.
[
  • 2,384 cases
  • , 6,031 controls
]
European 11 cohorts
  • ART
  • ,B58C
  • ,Bonn
  • ,GERAD
  • ,HNR
  • ,KORA
  • ,MRC
  • ,NIMH
  • ,UCL-LASER
  • ,UCL-PRION
  • ,WASHU