Polygenic Score (PGS) ID: PGS004602

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Jan. 26, 2024
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Score Details

Score Construction
PGS Name PRS424_T2D
Development Method
Name Genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 424
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000580
Citation (link to publication) Zhuang P et al. Diabetes Care (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,114,458 individuals (100%)
PGS Evaluation
European: 66.7%
Multi-ancestry (including European): 33.3%
  • European
  • Not Reported
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010555
Europe PMC: 32541925
 1,114,458 individuals European 6 cohorts
  • DIAMANTE
  • ,MDC
  • ,MVP
  • ,MedSTAR
  • ,PMB
  • ,PennCATH

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
PPM020759 PSS011395|
European Ancestry|
357,419 individuals
 PGP000580 |
Zhuang P et al. Diabetes Care (2021)
 Reported Trait: Type 2 diabetes HR: 1.54 [1.5, 1.58]
β: 0.431 (0.014)		 — — Age, sex, center, BMI, education, Townsend deprivation index, household income, smoking, alcohol consumption, physical activity, history of hypertension, history of high cholesterol, vitamin supplement use, mineral supplement use, aspirin use, and lipid-lowering medication —
PPM020760 PSS011395|
European Ancestry|
357,419 individuals
 PGP000580 |
Zhuang P et al. Diabetes Care (2021)
 Reported Trait: HbA1c β: 0.544 (0.007) — — Age, sex, center, BMI, education, Townsend deprivation index, household income, smoking, alcohol consumption, physical activity, history of hypertension, history of high cholesterol, vitamin supplement use, mineral supplement use, aspirin use, and lipid-lowering medication —
PPM020779 PSS011407|
Multi-ancestry (including European)|
59,325 individuals
 PGP000587 |
Luo M et al. Br J Sports Med (2023)
|Ext.		 Reported Trait: Incident type 2 diabetes — — Hazard ratio (HR, high vs low PRS tertile): 2.43 [2.04, 2.9] Age as the underlying timescale, gender, genotyping array, the first 10 principal components of ancestry, ethnicity, educational attainment, household income, Townsend deprivation index, employment status, assessment center, moking status, alcohol consumption, healthy diet score, hypertension, dyslipidemia, depression, total wear time, seasonality, and total volume of physical activity —
PPM021336 PSS011692|
European Ancestry|
433,150 individuals
 PGP000634 |
Chen JX et al. J Clin Endocrinol Metab (2023)
|Ext.		 Reported Trait: Age at onset of type 2 diabetes ≤ 50 years HR: 1.26 [1.13, 1.41] — — Sex, ethnicity, education, Townsend deprivation index, 4 age groups, follow-up time category, HbA1c, BMI, systolic blood pressure, smoking status, physical activity, diet, use of antihypertensive drugs, use of lipid-lowering drugs, cardiovascular disease, parental history of diabetes —

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
PSS011407 — Mean = 6.8 years
IQR = [6.3, 7.3] years
[
  • 884 cases
  • , 58,441 controls
]
,
44.0 % Male samples
 Mean = 61.1 years
Sd = 7.8 years		 European, Not reported White European (97.1%) UKB —
PSS011692 ICD-10 code, E11 — 433,150 individuals — European
(British)		 — UKB —
PSS011395 — Mean = 8.1 years 357,419 individuals — European
(White British)		 — UKB —