Polygenic Score (PGS) ID: PGS001357

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Nov. 4, 2021
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Score Details

Score Construction
PGS Name T2D_AnnoPred_PRS
Development Method
Name AnnoPred
Parameters Tier3, pT, p=0.003
Variants
Original Genome Build hg19
Number of Variants 2,996,761
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000252
Citation (link to publication) Ye Y et al. Circ Genom Precis Med (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
Score Development/Training
European: 100%
92,928 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: GCST004773
Europe PMC: 10.2337/db16-1253
[
  • 26,676 cases
  • , 132,532 controls
]
 European 17 cohorts
  • ARIC
  • ,BioMe
  • ,DGDG
  • ,DGI
  • ,EGCUT
  • ,EPIC
  • ,FHS
  • ,FUSION
  • ,GoDARTS
  • ,HPFS
  • ,KORA
  • ,NHS
  • ,PIVUS
  • ,RS
  • ,ULSAM
  • ,WTCCC
  • ,deCODE
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
—
[
  • 4,639 cases
  • , 88,289 controls
]
 European UKB — Mean = 56.81 years — — —

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
PPM005189 PSS003606|
European Ancestry|
178,138 individuals
 PGP000252 |
Ye Y et al. Circ Genom Precis Med (2021)
 Reported Trait: Type 2 diabetes — AUROC: 0.6446 — Age, sex, PCs(1-10) —

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
PSS003606 — —
[
  • 4,659 cases
  • , 173,479 controls
]
 Mean = 56.81 years European — UKB —