Polygenic Score (PGS) ID: PGS003444

Predicted Trait
Reported Trait type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: June 1, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name PRScsx_T2D_LAT_EASweights
Development Method
Name PRS-CSx
Parameters The polygenicity value that maximized the PRS performance in the score development cohort was 1e-02. To calculate a polygenic risk score in any genotyped individual, please follow the next steps. First, use the ancestry-specific weights (PRScsx_T2D_LAT_EURweights, PRScsx_T2D_LAT_EASweights and PRScsx_T2D_LAT_LATweights) to calculate 3 separate scores for each genotyped individual. Second, standardize each score (mean of zero and standard deviation of 1) and combine the three of them to calculate a single score value: metascore=(zscoreEUR* 0.531117)+(zscoreEAS*0.5690198)+(zscoreLAT*0.1465538). Third, standardize the metascore before applying. Evaluation of each ancestry-specific score separately is not the intended use of this PRS-CSx polygenic score. Note that performance reported is based on the combination of the 3 ancestry-specific scores (PRScsx_T2D_LAT_EURweights,PRScsx_T2D_LAT_EASweights,PRScsx_T2D_LAT_LATweights) as explained above.
Variants
Original Genome Build GRCh37
Number of Variants 1,001,579
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000445
Citation (link to publication) Huerta-Chagoya A et al. Diabetologia (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
433,540 individuals (100%)
Score Development/Training
Hispanic or Latin American: 100%
1,730 individuals (100%)
PGS Evaluation
Hispanic or Latin American: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010118
Europe PMC: 32499647
 433,540 individuals East Asian AGEN
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
[
  • 409 cases
  • , 1,321 controls
]
 Hispanic or Latin American
(Mexican)		 MXB — — — — —

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
PPM017183 PSS010157|
Hispanic or Latin American Ancestry|
1,484 individuals
 PGP000445 |
Huerta-Chagoya A et al. Diabetologia (2023)
 Reported Trait: type 2 diabetes OR: 1.9 [1.65, 2.19] AUROC: 0.7475 R²: 0.207 sex, age, PCs(1-10), PRScsx_T2D_LAT_EURweights, PRScsx_T2D_LAT_LATweights NOTE: Performance is based on a linear combination of this PGS with PRScsx_T2D_LAT_EASweights and PRScsx_T2D_LAT_LATweights (metascore=(zscoreEUR* 0.531117)+(zscoreEAS*0.5690198)+(zscoreLAT*0.1465538)). See score development details for how to apply

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
PSS010157 — —
[
  • 399 cases
  • , 1,085 controls
]
 Mean = 42.3 years Hispanic or Latin American
(Mexican)		 — METSB —