Polygenic Score (PGS) ID: PGS000125

Predicted Trait
Reported Trait Type 2 Diabetes
Mapped Trait(s) type II diabetes mellitus (EFO_0001360)
Released in PGS: March 27, 2020

Score Details

Score Construction
PGS Name Qi_T2D_2017
Variants
Original Genome Build NR
Number of Variants 80
Development Method
Name GWAS-significant SNPs
Parameters Unweighted allele count
PGS Source
PGS Catalog Publication (PGP) ID PGP000062
Citation (link to publication) Qi Q et al. Diabetes (2017)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002317
EuropePMC: 24390345
8,214 individuals Hispanic or Latin American
GWAS Catalog: GCST002560
EuropePMC: 2510218
23,827 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002352
EuropePMC: 2450948
2,583 individuals Hispanic or Latin American
GWAS Catalog: GCST002352
EuropePMC: 2450948
20,019 individuals South Asian
GWAS Catalog: GCST002352
EuropePMC: 2450948
69,033 individuals European
GWAS Catalog: GCST002352
EuropePMC: 2450948
18,817 individuals East Asian
GWAS Catalog: GCST002128
EuropePMC: 23945395
26,805 individuals East Asian

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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000404 PSS000232 PGP000062
Qi Q et al. (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 ID)
Detailed Phenotype Description 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