Polygenic Score (PGS) ID: PGS005399

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Additional Trait Information Polygenic score trained on male individuals only
Released in PGS Catalog: Feb. 26, 2026
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Terms and Licenses
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Score Details

Score Construction
PGS Name T1D_PRS_male
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD clumping was performed using PLINK v1.9 with a 1 Mb window, step size of 50 SNPs, and r² > 0.2. SNPs were selected from the male-only GWAS using a p-value threshold of P < 1e-4. Effect alleles and weights were extracted from the respective GWAS summary statistics. Polygenic risk scores were calculated using PLINK's scoring function.
Variants
Original Genome Build GRCh38
Number of Variants 264,227
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000781
Citation (link to publication) Qu HQ et al. Diabetes Res Clin Pract (2026)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
8,767 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90633790
[
  • 3,109 cases
  • , 5,658 controls
]
,
100.0 % Male samples
 European CHOP

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
PPM023442 PSS012188|
European Ancestry|
1,435 individuals
 PGP000781 |
Qu HQ et al. Diabetes Res Clin Pract (2026)
 Reported Trait: Type 1 diabetes diagnosis OR: 1.896 [1.627, 2.21] AUROC: 0.668 [0.629, 0.707] delta AUC (sex‑specific-all‑samples): 0.0444 [0.0341, 0.0546] — DeLong's test (2‑correlated ROC curves): Z = -8.4547, p < 2.2 × 10⁻¹⁶ ; Bootstrap test (2,000 stratified replicates): D = -8.3838, p < 2.2 × 10⁻¹⁶

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
PSS012188 Type 1 diabetes, diagnosed by physician; cases confirmed through clinical criteria at CHOP. ICD-10 code E10 used where available. —
[
  • 242 cases
  • , 1,193 controls
]
,
100.0 % Male samples
 — European — CHOP Independent validation cohort recruited through the Children's Hospital of Philadelphia (CHOP). No overlap with discovery GWAS samples.