Polygenic Score (PGS) ID: PGS004063

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: Dec. 19, 2023
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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 megaprs.auto.GCST90013445.T1D
Development Method
Name megaprs.auto
Parameters Model:Model150,Type:bolt,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:0.01,Bolt_f2:0.1,BayesR_p1:NA,BayesR_p2:NA,BayesR_p3:NA,BayesR_p4:NA
Variants
Original Genome Build GRCh38
Number of Variants 56,288
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: 89.3%
African: 7.1%
Additional Diverse Ancestries: 3.6%
59,527 individuals (100%)
Score Development/Training
European: 100%
804 individuals (100%)
PGS Evaluation
European: 80%
South Asian: 20%
5 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
— 804 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
PPM019970 PSS011224|
European Ancestry|
199,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: T1D OR: 1.96796 [1.8152611, 2.13351315]
β: 0.677 [0.59622931, 0.75776999]		 AUROC: 0.68845 [0.66493994, 0.71195684] R²: 0.06145 [0.0466906, 0.07846122] 0 beta = log(or)/sd_pgs
PPM019971 PSS011235|
European Ancestry|
322,349 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: T1D OR: 1.98877 [1.93780812, 2.04107353]
β: 0.68752 [0.6615575, 0.71347591]		 AUROC: 0.71357 [0.70595937, 0.72117434] R²: 0.0733 [0.06778529, 0.07934817] 0 beta = log(or)/sd_pgs
PPM019972 PSS011248|
South Asian Ancestry|
44,057 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: T1D OR: 0.99583 [0.90679351, 1.09360849]
β: -0.00418 [-0.0978405, 0.08948277]		 AUROC: 0.50552 [0.47751517, 0.53351676] R²: 2.41e-06 [0.0, 0.00132293] 0 beta = log(or)/sd_pgs
PPM019973 PSS011264|
European Ancestry|
66,865 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: T1D OR: 1.34209 [1.2160386, 1.48119754]
β: 0.29422 [0.19559853, 0.39285091]		 AUROC: 0.57505 [0.54588165, 0.60422019] R²: 0.00983 [0.00444222, 0.01812082] 0 beta = log(or)/sd_pgs
PPM019974 PSS011277|
European Ancestry|
90,274 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: T1D OR: 2.32027 [2.05513583, 2.61961025]
β: 0.84168 [0.72034195, 0.96302555]		 AUROC: 0.73583 [0.6992247, 0.77242674] R²: 0.10657 [0.0731231, 0.14722601] 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
PSS011277 — —
[
  • 201 cases
  • , 90,073 controls
]
 — European — UKB —
PSS011248 — —
[
  • 443 cases
  • , 43,614 controls
]
 — South Asian — G&H —
PSS011224 — —
[
  • 501 cases
  • , 198,773 controls
]
 — European — EB —
PSS011264 — —
[
  • 396 cases
  • , 66,469 controls
]
 — European — HUNT —
PSS011235 T1D, ICD10: E10, ICD9: 250[0|1]1 (exclude E11) —
[
  • 4,286 cases
  • , 318,063 controls
]
 — European — FinnGen —