Polygenic Score (PGS) ID: PGS002277

Predicted Trait
Reported Trait Type 2 diabetes (based on SNPs associated with insulin secretion)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Additional Trait Information Insulin secretion 1
Released in PGS Catalog: April 13, 2022
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Score Details

Score Construction
PGS Name pPS_Insulin_secretion_1
Development Method
Name Partitioned polygenic score
Parameters cluster consisting of eight variants classified as ‘Insulin secretion 1’ in PMID:29632382, weights from PMID:20081858
Variants
Original Genome Build NR
Number of Variants 8
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000305
Citation (link to publication) Siddiqui MK et al. Diabetologia (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 68.6%
Multi-ancestry (excluding European): 31.4%
  • South Asian
  • East Asian
  • African
  • Hispanic or Latin American
488,710 individuals (100%)
PGS Evaluation
South Asian: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST005180
Europe PMC: 20081858
36,466 individuals European NR
GWAS Catalog: GCST007515
Europe PMC: 29632382
298,957 individuals European NR
GWAS Catalog: GCST007515
Europe PMC: 29632382
153,287 individuals South Asian,East Asian,African American or Afro-Caribbean,Hispanic or Latin American 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
PPM012949 PSS009629|
South Asian Ancestry|
5,806 individuals
PGP000305 |
Siddiqui MK et al. Diabetologia (2022)
Reported Trait: Age at diagnosis (overweight BMI) β: 32.68 (20.7) : 0.0097
PPM012950 PSS009629|
South Asian Ancestry|
5,806 individuals
PGP000305 |
Siddiqui MK et al. Diabetologia (2022)
Reported Trait: Age at diagnosis (obese BMI) β: 18.9 (10.76) : 0.0036
PPM012947 PSS009629|
South Asian Ancestry|
5,806 individuals
PGP000305 |
Siddiqui MK et al. Diabetologia (2022)
Reported Trait: Age at diagnosis Z: 5.2 Z-score p-value < 0.0001
PPM012948 PSS009629|
South Asian Ancestry|
5,806 individuals
PGP000305 |
Siddiqui MK et al. Diabetologia (2022)
Reported Trait: Age at diagnosis (normal BMI) β: 37.31 (16.7) : 0.012

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
PSS009629 5,806 individuals South Asian
(Indian)
INSPIRED Dr. Mohan’s Diabetes Specialities Centre (INSPIRED - DMDSC)