Polygenic Score (PGS) ID: PGS004014

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Dec. 19, 2023
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Score Details

Score Construction
PGS Name lassosum.CV.GCST004773.T2D
Development Method
Name lassosum.CV
Parameters s0.9,lambda0.00428133239871939
Variants
Original Genome Build GRCh38
Number of Variants 95,649
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti M R et al. medRxiv (2023) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
Score Development/Training
European: 100%
23,748 individuals (100%)
PGS Evaluation
European: 66.7%
South Asian: 33.3%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European NR
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
— 23,748 individuals European UKB — — — — —

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
PPM019359 PSS011225|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Type 2 Diabetes OR: 1.48322
β: 0.39422		 AUROC: 0.61 — 0 beta = log(or)/sd_pgs
PPM019360 PSS011236|
European Ancestry|
377,408 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Type 2 Diabetes OR: 1.47356
β: 0.38768		 AUROC: 0.61 — 0 beta = log(or)/sd_pgs
PPM019361 PSS011249|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Type 2 Diabetes OR: 1.25868
β: 0.23007		 AUROC: 0.56 — 0 beta = log(or)/sd_pgs
PPM019362 PSS011265|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Type 2 Diabetes OR: 1.49153
β: 0.3998		 AUROC: 0.61 — 0 beta = log(or)/sd_pgs
PPM019364 PSS011278|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Type 2 Diabetes OR: 1.57088
β: 0.45164		 AUROC: 0.62 — 0 beta = log(or)/sd_pgs
PPM019363 PSS011291|
South Asian Ancestry|
9,326 individuals
 PGP000517 |
Monti M R et al. medRxiv (2023)
|Pre		 Reported Trait: Type 2 Diabetes OR: 1.34108
β: 0.29348		 AUROC: 0.58 — 0 beta = log(or)/sd_pgs

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
PSS011278 — —
[
  • 5,937 cases
  • , 84,337 controls
]
 — European — UKB —
PSS011249 — —
[
  • 6,630 cases
  • , 37,427 controls
]
 — South Asian — G&H —
PSS011225 — —
[
  • 12,344 cases
  • , 186,930 controls
]
 — European — EB —
PSS011291 — —
[
  • 2,066 cases
  • , 7,260 controls
]
 — South Asian — UKB —
PSS011265 — —
[
  • 3,861 cases
  • , 63,004 controls
]
 — European — HUNT —
PSS011236 T2D, ICD10: E11, ICD9: 250[0|1]0 (exclude E10) —
[
  • 59,345 cases
  • , 318,063 controls
]
 — European — FinnGen —