PGS Catalog - PGS004035 / Type 1 diabetes (T1D) (Polygenic Score)

Polygenic Score (PGS) ID: PGS004035

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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Score Details

Score Construction
PGS Name	ldpred2.auto.GCST90013445.T1D
Development Method
Name	LDpred2-auto
Parameters	auto
Variants
Original Genome Build	GRCh38
Number of Variants	56,562
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	PGS Performance: Other Relevant Information
PPM019965	PSS011224\| European Ancestry\| 199,274 individuals	PGP000517 \| Monti R et al. Am J Hum Genet (2024)	Reported Trait: T1D	OR: 2.32281 [2.13168407, 2.53107946] β: 0.84278 [0.75691231, 0.92864588]	AUROC: 0.71195 [0.68696399, 0.73694375]	R²: 0.0847 [0.06629693, 0.10703174]	beta = log(or)/sd_pgs
PPM019966	PSS011235\| European Ancestry\| 322,349 individuals	PGP000517 \| Monti R et al. Am J Hum Genet (2024)	Reported Trait: T1D	OR: 2.04799 [1.98592622, 2.11200077] β: 0.71686 [0.68608541, 0.74763573]	AUROC: 0.69176 [0.68386243, 0.69965429]	R²: 0.05646 [0.05209086, 0.06140139]	beta = log(or)/sd_pgs
PPM019967	PSS011248\| South Asian Ancestry\| 44,057 individuals	PGP000517 \| Monti R et al. Am J Hum Genet (2024)	Reported Trait: T1D	OR: 1.00124 [0.9117887, 1.09947388] β: 0.00124 [-0.092347, 0.09483178]	AUROC: 0.50968 [0.48325371, 0.53611056]	R²: 2.13e-07 [0.0, 0.00104871]	beta = log(or)/sd_pgs
PPM019968	PSS011264\| European Ancestry\| 66,865 individuals	PGP000517 \| Monti R et al. Am J Hum Genet (2024)	Reported Trait: T1D	OR: 1.41811 [1.28793383, 1.56143556] β: 0.34932 [0.25303925, 0.44560563]	AUROC: 0.5837 [0.55391495, 0.61347751]	R²: 0.01451 [0.00709685, 0.02594541]	beta = log(or)/sd_pgs
PPM019969	PSS011277\| European Ancestry\| 90,274 individuals	PGP000517 \| Monti R et al. Am J Hum Genet (2024)	Reported Trait: T1D	OR: 2.67223 [2.33127749, 3.06303713] β: 0.98291 [0.8464164, 1.11940695]	AUROC: 0.74858 [0.71080109, 0.78636453]	R²: 0.11349 [0.08057329, 0.1513995]	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	—	—	90,274 individuals [ 201 cases , 90,073 controls ]	—	European	—	UKB	—
PSS011248	—	—	44,057 individuals [ 443 cases , 43,614 controls ]	—	South Asian	—	G&H	—
PSS011224	—	—	199,274 individuals [ 501 cases , 198,773 controls ]	—	European	—	EB	—
PSS011264	—	—	66,865 individuals [ 396 cases , 66,469 controls ]	—	European	—	HUNT	—
PSS011235	T1D, ICD10: E10, ICD9: 250[0\|1]1 (exclude E11)	—	322,349 individuals [ 4,286 cases , 318,063 controls ]	—	European	—	FinnGen	—