Polygenic Score (PGS) ID: PGS000125

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: March 27, 2020
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Score Details

Score Construction
PGS Name Qi_T2D_2017
Development Method
Name Genome-wide significant variants
Parameters Unweighted allele count
Variants
Original Genome Build NR
Number of Variants 80
Effect Weight Type Dosage
PGS Source
PGS Catalog Publication (PGP) ID PGP000062
Citation (link to publication) Qi Q et al. Diabetes (2017)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 40.8%
East Asian: 26.9%
African: 14.1%
South Asian: 11.8%
Hispanic or Latin American: 6.4%
169,298 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: GCST002317
Europe PMC: 24390345
 8,214 individuals Hispanic or Latin American NR
GWAS Catalog: GCST002560
Europe PMC: 2510218
 23,827 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST002352
Europe PMC: 2450948
 2,583 individuals Hispanic or Latin American NR
GWAS Catalog: GCST002352
Europe PMC: 2450948
 20,019 individuals South Asian NR
GWAS Catalog: GCST002352
Europe PMC: 2450948
 69,033 individuals European NR
GWAS Catalog: GCST002352
Europe PMC: 2450948
 18,817 individuals East Asian NR
GWAS Catalog: GCST002128
Europe PMC: 23945395
 26,805 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
PPM000404 PSS000232|
Hispanic or Latin American Ancestry|
7,746 individuals
 PGP000062 |
Qi Q et al. Diabetes (2017)
 Reported Trait: Type 2 Diabetes — — OR (Odds Ratio, per risk allele): 1.07 [1.06, 1.08] center, age, sex, 5 PCs of ancestry Covariance matrices corresponding to genetic relatedness (kinship), household, and census block group were included as random effects in the mixed model analysis

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
PSS000232 Individuals with T2D were defined as those with fasting time >8 h and fasting glucose levels ≥126 mg/dL, fasting ≤8 h and fasting glucose ≥200 mg/dL, post–oral glucose tolerance test glucose ≥200 mg/dL, HbA1c ≥6.5% (48 mmol/mol), or on current treatment with antihyperglycemia medications. —
[
  • 2,499 cases
  • , 5,247 controls
]
,
39.65 % Male samples
 — Hispanic or Latin American
(Central American, Cuban, Dominican, Mexican, Puerto Rican, South American)		 Ancestry groups were defined based on a combination of self-identified Hispanic/Latino background and genetic similarity HCHS, SOL —