Polygenic Score (PGS) ID: PGS000779

Predicted Trait
Reported Trait Alzheimer's disease
Mapped Trait(s) Alzheimer disease (MONDO_0004975)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name PGS7_AD
Development Method
Name LASSO
Parameters 5-fold cross-validation, p<0.05
Variants
Original Genome Build NR
Number of Variants 7
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000183
Citation (link to publication) Zhou X et al. Alzheimers Dement (Amst) (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 91.4%
Multi-ancestry (excluding European): 8.6%
  • East Asian
  • Not Reported
147,484 individuals (100%)
Score Development/Training
East Asian: 100%
674 individuals (100%)
PGS Evaluation
East Asian: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 17434289
[
  • 318 cases
  • , 232 controls
]
 European WASHU
GWAS Catalog: GCST007319
Europe PMC: 30617256
 79,145 individuals European ADSP, IGAP, PGC
Europe PMC: 31346172
[
  • 7,799 cases
  • , 4,856 controls
]
,
42.09 % Male samples
 East Asian, NR
(Chinese, NR)		 ADC, ADNI, LOAD
GWAS Catalog: GCST002245
Europe PMC: 24162737
 55,134 individuals European 19 cohorts
  • ACT
  • ,ADC
  • ,ADNI
  • ,AGES
  • ,CHS
  • ,EADI
  • ,FHS
  • ,GERAD
  • ,GSK
  • ,LOAD
  • ,MAYO
  • ,MIRAGE
  • ,OHSU
  • ,ROSMAP
  • ,RS
  • ,TGEN
  • ,UMVUMSS
  • ,UPITT
  • ,WASHU
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
—
[
  • 341 cases
  • , 333 controls
]
,
36.19 % Male samples
 East Asian
(Chinese)		 NR Cases include individuals with Alzheimer's disease. Patients with AD were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM‐5). — — — Participants recruited from the Specialist Outpatient Department of Prince of Wales Hospital.

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
PPM002022 PSS001005|
East Asian Ancestry|
112 individuals
 PGP000183 |
Zhou X et al. Alzheimers Dement (Amst) (2020)
 Reported Trait: Alzheimer's disease — AUROC: 0.612 Beta (β, top 33.3% vs bottom 33.3%): 1.485 (0.602) Age, sex —
PPM002023 PSS001006|
European Ancestry|
2,696 individuals
 PGP000183 |
Zhou X et al. Alzheimers Dement (Amst) (2020)
 Reported Trait: Alzheimer's disease — AUROC: 0.717 Beta (β, top 33.3% vs bottom 33.3%): 2.283 (1.021) Age, sex, PCs(1-5) —

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
PSS001005 Cases include individuals with Alzheimer's disease (AD) The phenotypes of the participants were determined on the basis of the most recent diagnostic records (until December 2019). —
[
  • 33 cases
  • , 79 controls
]
,
54.29 % Male samples
 — East Asian
(Chinese)		 — NR Participants recruited from the Specialist Outpatient Department of Prince of Wales Hospital.
PSS001006 Cases include individuals with Alzheimer's disease (AD). Patients with definite AD have been diagnosed according to established neuropathological criteria (CERAD, Braak, Khachaturian, NIA-RI, or other established criteria). —
[
  • 464 cases
  • , 2,232 controls
]
,
37.62 % Male samples
 — European — LOAD —