Polygenic Score (PGS) ID: PGS004874

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: June 27, 2024
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Score Details

Score Construction
PGS Name INTERVENE_MegaPRS_T1D
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.75, p2=0.2, p3=0.05, p4=0
Variants
Original Genome Build GRCh37
Number of Variants 56,916
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: 89.3%
African: 7.1%
Additional Diverse Ancestries: 3.6%
59,527 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90013445
Europe PMC: 34127860
 53,130 individuals European NR
GWAS Catalog: GCST90013445
Europe PMC: 34127860
 2,148 individuals Other admixed ancestry NR
GWAS Catalog: GCST90013445
Europe PMC: 34127860
 4,249 individuals African unspecified 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
PPM021179 PSS011637|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 2.37 [2.31, 2.44] C-index: 0.77 [0.77, 0.78] — PCs 1-10 —
PPM021173 PSS011643|
European Ancestry|
447,332 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 2.11 [1.98, 2.24] — — PCs 1-10 —
PPM021174 PSS011642|
European Ancestry|
32,779 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 1.41 [1.17, 1.69] C-index: 0.69 [0.64, 0.74] — PCs 1-10 —
PPM021175 PSS011641|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 1.43 [1.28, 1.59] C-index: 0.64 [0.61, 0.67] — PCs 1-10 —
PPM021176 PSS011640|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 2.09 [1.91, 2.29] C-index: 0.75 [0.72, 0.78] — PCs 1-10 —
PPM021177 PSS011638|
European Ancestry|
44,187 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 1.05 [0.95, 1.15] — — PCs 1-10 —
PPM021178 PSS011639|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 1.56 [1.14, 2.12] C-index: 0.73 [0.67, 0.78] — PCs 1-10 —
PPM021180 PSS011636|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident T1D HR: 1.64 [1.5, 1.79] C-index: 0.68 [0.65, 0.7] — 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
PSS011636 — —
[
  • 497 cases
  • , 199,371 controls
]
 — European — EB —
PSS011637 — —
[
  • 4,310 cases
  • , 407,780 controls
]
 — European — FinnGen —
PSS011638 — —
[
  • 434 cases
  • , 43,753 controls
]
 — European — G&H —
PSS011639 — —
[
  • 78 cases
  • , 6,940 controls
]
 — European — GS:SFHS —
PSS011640 — —
[
  • 397 cases
  • , 29,030 controls
]
 — European — GEL —
PSS011641 — —
[
  • 342 cases
  • , 69,373 controls
]
 — European — HUNT —
PSS011642 — —
[
  • 103 cases
  • , 32,676 controls
]
 — European — MGBB —
PSS011643 — —
[
  • 992 cases
  • , 446,340 controls
]
 — European — UKB —