PGS Publication: PGP000222

Publication Information (EuropePMC)
Title Polygenic risk and hazard scores for Alzheimer's disease prediction.
PubMed ID 30911569(Europe PMC)
doi 10.1002/acn3.716
Publication Date Feb. 18, 2019
Journal Ann Clin Transl Neurol
Author(s) Leonenko G, Sims R, Shoai M, Frizzati A, Bossù P, Spalletta G, Fox NC, Williams J, GERAD consortium, Hardy J, Escott-Price V.
Released in PGS Catalog: Aug. 26, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000876
(PRS31_AD)
 PGP000222 |
Leonenko G et al. Ann Clin Transl Neurol (2019)
 Alzheimer's disease Alzheimer disease 31
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000876/ScoringFiles/PGS000876.txt.gz

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000026
(PHS)
 PGP000016 |
Desikan RS et al. PLoS Med (2017)
 Alzheimer's disease Alzheimer disease 33
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000026/ScoringFiles/PGS000026.txt.gz

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) 		Evaluated Score 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
PPM002504 PGS000026
(PHS)
 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
PPM002505 PGS000876
(PRS31_AD)
 PSS001127|
European Ancestry|
8,415 individuals
 PGP000222 |
Leonenko G et al. Ann Clin Transl Neurol (2019)
 Reported Trait: Age at Alzheimer's disease onset β: 0.13 (0.02) — — Gender, PCs (1-3), APOE(ε2 + ε4) Due to SNP availability issues in the dataset, only 25 out of the 31 variants used to construct the polygenic risk score were used.
PPM002506 PGS000876
(PRS31_AD)
 PSS001125|
European Ancestry|
9,903 individuals
 PGP000222 |
Leonenko G et al. Ann Clin Transl Neurol (2019)
 Reported Trait: Age at Alzheimer's disease onset β: 0.28 (0.04) — — Gender, PCs (1-3), APOE ε2, APOE ε4 —
PPM002507 PGS000876
(PRS31_AD)
 PSS001126|
European Ancestry|
4,100 individuals
 PGP000222 |
Leonenko G et al. Ann Clin Transl Neurol (2019)
 Reported Trait: Age at Alzheimer's disease onset in individuals above the age of 55 β: 0.29 (0.03) — — Gender, PCs (1-3), APOE ε2, APOE ε4 —

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
PSS001125 Cases included individuals with Alzheimer's disease. —
[
  • 2,626 cases
  • , 7,277 controls
]
 — European — 11 cohorts
  • ART
  • ,B58C
  • ,Bonn
  • ,GERAD
  • ,HNR
  • ,KORA
  • ,MRC
  • ,NIMH
  • ,UCL-LASER
  • ,UCL-PRION
  • ,WASHU
 —
PSS001126 All individuals were aged 55 and above. Cases include individuals with Alzheimer's disease. —
[
  • 2,575 cases
  • , 1,525 controls
]
 — European — 11 cohorts
  • ART
  • ,B58C
  • ,Bonn
  • ,GERAD
  • ,HNR
  • ,KORA
  • ,MRC
  • ,NIMH
  • ,UCL-LASER
  • ,UCL-PRION
  • ,WASHU
 —
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
 —