Polygenic Score (PGS) ID: PGS000330

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type II diabetes mellitus (EFO_0001360)
Released in PGS: Sept. 18, 2020
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Score Details

Score Construction
PGS Name PRS_T2D
Variants
Original Genome Build hg19
Number of Variants 6,437,380
Development Method
Name LDpred
Parameters ρ = 0.3; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only]
PGS Source
PGS Catalog Publication (PGP) ID PGP000100
Citation (link to publication) Mars N et al. Nat Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST009379
EuropePMC: 30297969
898,130 individuals European
Score Development/Training
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
National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. 21,813 individuals,
47.3 % Male samples
Mean (Age At Baseline) = 48.0 years European
(Finnish)
FINRISK Used to select optimal threshold of ρ for all subsequent analyses. FINRISK surveys from 1992, 1997, 2002 and 2007

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000887 PSS000448 PGP000100
Mars N et al. (2020)
Reported Trait: Type 2 diabetes (incident and prevalent cases) HR: 1.74[1.72, 1.77] genotyping array/batch, 10 ancestry PCs, stratified by sex
PPM000892 PSS000441 PGP000100
Mars N et al. (2020)
Reported Trait: Incident type 2 diabetes HR: 1.7[1.63, 1.78] C-index: 0.763 age, sex, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000897 PSS000441 PGP000100
Mars N et al. (2020)
Reported Trait: Incident type 2 diabetes C-index: 0.845 age, sex, BMI, history of stroke or CHD, parental history of diabetes, SBP, DBP, HDL, triglycerides, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000448 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 17,519 cases
  • , 117,781 controls
]
,
43.7 % Male samples
Mean (Age At Baseline) = 59.2 years
Sd = 16.6 years
European
(Finnish)
FinnGen
PSS000441 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 1,346 cases
  • , 19,684 controls
]
,
47.3 % Male samples
Mean (Age At Baseline) = 48.0 years European
(Finnish)
FINRISK FINRISK surveys from 1992, 1997, 2002 and 2007