Polygenic Score (PGS) ID: PGS004052

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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Terms and Licenses
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Score Details

Score Construction
PGS Name megaprs.auto.GCST004773.T2D
Development Method
Name megaprs.auto
Parameters Model:Model164,Type:bayesr,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:0.795,BayesR_p2:0.2,BayesR_p3:0.005,BayesR_p4:0
Variants
Original Genome Build GRCh38
Number of Variants 800,598
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
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
PPM019335 PSS011225|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Type 2 Diabetes OR: 1.51227 [1.48473504, 1.54032011]
β: 0.41361 [0.39523633, 0.43199026]		 AUROC: 0.61519 [0.61009733, 0.62027538] R²: 0.03887 [0.03526361, 0.04197686] 0 beta = log(or)/sd_pgs
PPM019337 PSS011249|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Type 2 Diabetes OR: 1.2863 [1.25264347, 1.32086195]
β: 0.25177 [0.2252561, 0.27828451]		 AUROC: 0.57001 [0.56255968, 0.57745664] R²: 0.01979 [0.01571473, 0.02380638] 0 beta = log(or)/sd_pgs
PPM019338 PSS011265|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Type 2 Diabetes β: 0.43541 [0.40237992, 0.46844556]
OR: 1.5456 [1.49537934, 1.59750903]		 AUROC: 0.6216 [0.61275773, 0.63044257] R²: 0.04245 [0.0366842, 0.04862483] 0 beta = log(or)/sd_pgs
PPM019339 PSS011291|
South Asian Ancestry|
9,326 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Type 2 Diabetes OR: 1.4232 [1.35315323, 1.49688143]
β: 0.35291 [0.30243759, 0.4033839]		 AUROC: 0.59803 [0.58420574, 0.61184824] R²: 0.03821 [0.02906588, 0.04987531] 0 beta = log(or)/sd_pgs
PPM019340 PSS011278|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Type 2 Diabetes OR: 1.64766 [1.60386839, 1.69264683]
β: 0.49936 [0.47241846, 0.52629348]		 AUROC: 0.63712 [0.62999838, 0.6442459] R²: 0.05548 [0.04987829, 0.06115078] 0 beta = log(or)/sd_pgs
PPM019336 PSS011236|
European Ancestry|
377,408 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Type 2 Diabetes OR: 1.53613 [1.5222648, 1.55012285]
β: 0.42927 [0.42019923, 0.43833419]		 AUROC: 0.61808 [0.61563838, 0.62051629] R²: 0.04083 [0.03909121, 0.04252571] 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 —