Polygenic Score (PGS) ID: PGS000014

Predicted Trait
Reported Trait Type 2 diabetes
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_T2D
Development Method
Name LDpred
Parameters ρ = 0.01; LD panel = 503 1000G Europeans
Variants
Original Genome Build hg19
Number of Variants 6,917,436
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
318,416 individuals (100%)
Score Development/Training
European: 100%
120,280 individuals (100%)
PGS Evaluation
European: 66.7%
Multi-ancestry (including European): 33.3%
  • African
  • Additional Asian Ancestries
  • Additional Diverse Ancestries
  • European
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European DIAGRAM, EPIC, GERA
GWAS Catalog: GCST004774
Europe PMC: 28566273
 159,208 individuals European DIAGRAM, EPIC, GERA
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
—
[
  • 2,785 cases
  • , 117,495 controls
]
 European UKB Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. — — — UKB Phase 1

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
PPM000023 PSS000017|
European Ancestry|
288,978 individuals
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Reported Trait: Type 2 diabetes — AUROC: 0.73 [0.72, 0.73] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.029 age; sex; Ancestry PC 1-4; genotyping chip —
PPM002477 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.709 [0.696, 0.722] Hazard ratio (HR, top 10% vs. remaining 90%): 2.0 [1.73, 2.31] Sex, age, principal components, assessment center —
PPM002478 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.68 [0.663, 0.697] — Age, principal components and assessment center —
PPM002479 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.705 [0.682, 0.728] — Age, principal components and assessment center —
PPM002480 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.776 [0.764, 0.788] — Sex, age, principal components, assessment center, polyexposure score —
PPM002481 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.844 [0.834, 0.854] — Sex, age, principal components, assessment center, clinical risk score —
PPM002482 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes — C-index: 0.855 [0.845, 0.865] — Sex, age, principal components, assessment center, polyexposure socre, clinical risk score —
PPM002483 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.786 [0.765, 0.807] — Age, principal components, assessment center, polyexposure score —
PPM002485 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.859 [0.842, 0.876] — Sex, age, principal components, assessment center, clinical risk score —
PPM002486 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.749 [0.734, 0.764] — Age, principal components, assessment center, polyexposure score —
PPM002487 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.821 [0.808, 0.834] — Age, principal components, assessment center, polyexposure socre, clinical risk score —
PPM002488 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in males — C-index: 0.834 [0.821, 0.847] — Sex, age, principal components, assessment center, clinical risk score —
PPM002484 PSS001117|
European Ancestry|
68,229 individuals
 PGP000218 |
He Y et al. Diabetes Care (2021)
|Ext.		 Reported Trait: Incident type II diabetes in females — C-index: 0.869 [0.853, 0.885] — Age, principal components, assessment center, polyexposure socre, clinical risk score —
PPM015522 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Type 2 diabetes mellitus OR: 1.75 [1.57, 1.95] — — 4 genetic PCs —

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
PSS000017 Type 2 diabetes ascertainment was based on self-report in an interview with a trained nurse or an ICD-10 code of E11.X in hospitalization records. —
[
  • 5,853 cases
  • , 283,125 controls
]
 — European — UKB UKB Phase 2
PSS001117 T2D cases were defined as having an ICD-10 code of E11.X or having self-reported T2D in the in- terview. Only cases in which the individuals did not have T2D during the first assessment visit period (2006–2010) but were subsequently fol- lowed up for incident T2D events were considered. Median = 3.58 years
[
  • 1,281 cases
  • , 66,948 controls
]
,
47.81 % Male samples
 — European — UKB —
PSS009971 — — 30,716 individuals — European — MGBB —
PSS009971 — — 1,807 individuals — African unspecified
(Black)		 — MGBB —
PSS009971 — — 786 individuals — Asian unspecified — MGBB —
PSS009971 — — 3,113 individuals — Other — MGBB —