Polygenic Score (PGS) ID: PGS004870

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 27, 2024
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name INTERVENE_MegaPRS_T2D
Development Method
Name megaprs.auto
Parameters bolt, p=0.05, f2=0.15
Variants
Original Genome Build GRCh37
Number of Variants 930,506
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000618
Citation (link to publication) Jermy B et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
898,130 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
7 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST009379
Europe PMC: 30297969
 898,130 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
— 404 individuals European 1000G — — — non-Finnish Europeans —

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
PPM021142 PSS011650|
European Ancestry|
38,343 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.42 [1.38, 1.45] C-index: 0.61 [0.6, 0.62] — PCs 1-10 —
PPM021143 PSS011649|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.86 [1.79, 1.93] C-index: 0.69 [0.68, 0.7] — PCs 1-10 —
PPM021144 PSS011648|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.87 [1.79, 1.95] C-index: 0.68 [0.67, 0.69] — PCs 1-10 —
PPM021145 PSS011646|
European Ancestry|
44,183 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.56 [1.51, 1.6] — — PCs 1-10 —
PPM021146 PSS011647|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.68 [1.55, 1.83] C-index: 0.64 [0.62, 0.67] — PCs 1-10 —
PPM021147 PSS011645|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.7 [1.69, 1.71] C-index: 0.66 [0.66, 0.66] — PCs 1-10 —
PPM021148 PSS011644|
European Ancestry|
148,312 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T2D HR: 1.78 [1.74, 1.82] C-index: 0.67 [0.66, 0.67] — 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
PSS011645 — —
[
  • 62,413 cases
  • , 349,677 controls
]
 — European — FinnGen —
PSS011646 — —
[
  • 6,537 cases
  • , 37,646 controls
]
 — European — G&H —
PSS011647 — —
[
  • 613 cases
  • , 6,405 controls
]
 — European — GS:SFHS —
PSS011648 — —
[
  • 2,423 cases
  • , 27,004 controls
]
 — European — GEL —
PSS011649 — —
[
  • 3,129 cases
  • , 66,586 controls
]
 — European — HUNT —
PSS011650 — —
[
  • 5,430 cases
  • , 32,913 controls
]
 — European — MGBB —
PSS011644 — —
[
  • 6,813 cases
  • , 141,499 controls
]
 — European — EB —