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(Variants and weights)

Polygenic Score (PGS) ID: PGS000026

Predicted Trait

Reported Trait: Alzheimer’s Disease
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): Alzheimer's disease

Score Details

Name: PHS

Original Genome Build: NR
Number of Variants: 31

PGS Development Method: Hazard model with stepwise selection of SNP inclusion
PGS Development Details/Relevant Parameters: SNPs eligible for inclusion had a significane of p < 10−5

Citation: Desikan RS et al. PLoS Med (2017) | PGS Catalog Publication ID: PGP000016

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002245
PubMed: 24162737.0
54,162 individuals
[ 17,008 cases, 37,154 controls]
European
Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
Cases are patients with clinically diagnosed AD and compared to cognitively normal older individuals 15,795 individuals
[ 6,409 cases, 9,386 controls]
40.18847736625514 % Male samples
European ADGC 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000053 PSS000036 Desikan RS et al. (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

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers 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 17,956 individuals
[ 6,984 cases, 10,972 controls]
40.50574738249053 % Male samples
European ADGC ADGC Phase 2