Polygenic Score (PGS) ID: PGS004225

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Dec. 15, 2023
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Score Details

Score Construction
PGS Name PRS46_T2DEastAsia
Development Method
Name Genome-wide significant SNPs
Parameters MAF>0.5, r2 < 0.8
Variants
Original Genome Build NR
Number of Variants 46
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000526
Citation (link to publication) Liu J et al. Nutrients (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 99.6%
Additional Asian Ancestries: 0.4%
974,507 individuals (100%)
PGS Evaluation
East Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000383
Europe PMC: 19401414
 1,022 individuals East Asian NR
Europe PMC: 19937226
[
  • 1,892 cases
  • , 1,808 controls
]
 East Asian
(Chinese)		 NR
GWAS Catalog: GCST000601
Europe PMC: 20174558
 1,889 individuals East Asian NR
GWAS Catalog: GCST000787
Europe PMC: 20818381
 7,541 individuals East Asian NR
GWAS Catalog: GCST000796
Europe PMC: 20862305
 2,729 individuals East Asian NR
GWAS Catalog: GCST001351
Europe PMC: 22158537
 15,000 individuals East Asian NR
GWAS Catalog: GCST001351
Europe PMC: 22158537
 2,034 individuals South East Asian NR
GWAS Catalog: GCST001351
Europe PMC: 22158537
 1,783 individuals Asian unspecified NR
Europe PMC: 22437209
[
  • 2,925 cases
  • , 3,281 controls
]
 East Asian
(Chinese)		 NR
Europe PMC: 22506066
[
  • 1,200 cases
  • , 1,200 controls
]
 East Asian
(Chinese)		 NR
GWAS Catalog: GCST001666
Europe PMC: 22961080
 3,712 individuals East Asian NR
GWAS Catalog: GCST001919
Europe PMC: 23532257
 1,639 individuals East Asian NR
GWAS Catalog: GCST002128
Europe PMC: 23945395
 26,805 individuals East Asian NR
Europe PMC: 24053193
[
  • 2,925 cases
  • , 3,281 controls
]
 East Asian
(Han Chinese)		 NR
GWAS Catalog: GCST003400
Europe PMC: 26818947
 41,646 individuals East Asian NR
GWAS Catalog: GCST007847
Europe PMC: 30718926
 191,764 individuals East Asian NR
GWAS Catalog: GCST010118
Europe PMC: 32499647
 433,540 individuals East Asian NR
GWAS Catalog: GCST90013693
Europe PMC: 32514122
 210,865 individuals East Asian NR
GWAS Catalog: GCST010436
Europe PMC: 32794382
 14,026 individuals East Asian NR

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
PPM020217 PSS011306|
East Asian Ancestry|
5,024 individuals
 PGP000526 |
Liu J et al. Nutrients (2023)
 Reported Trait: Type 2 diabetes with lifestyle group — — Hazard ratio (HR, poor lifestyle and high PRS vs. ideal lifestyle and low PRS): 3.93 [2.07, 7.44] — —
PPM020215 PSS011306|
East Asian Ancestry|
5,024 individuals
 PGP000526 |
Liu J et al. Nutrients (2023)
 Reported Trait: Type 2 diabetes — — Hazard ratio (HR, high vs low quintile): 2.06 [1.42, 2.97] age, gender, SBP, DBP, FBG, TC, TG, HDLC, and diabetes family history —

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
PSS011306 — — 5,024 individuals,
40.0 % Male samples
 — East Asian
(Chinese)		 — Wuxi NCDs —