Polygenic Score (PGS) ID: PGS002243

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: April 13, 2022
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Terms and Licenses
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Score Details

Score Construction
PGS Name ldpred_t2d
Development Method
Name LDpred
Parameters p = 0.003, LD radius = 2000, LD reference panel: European ancestry in 1000 Genomes
Variants
Original Genome Build GRCh37
Number of Variants 6,431,973
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000271
Citation (link to publication) Mars N et al. Cell Genom (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
Score Development/Training
European: 100%
175,364 individuals (100%)
PGS Evaluation
European: 55.6%
African: 22.2%
East Asian: 11.1%
South Asian: 11.1%
9 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 NR
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
—
[
  • 24,226 cases
  • , 151,138 controls
]
 European
(Finnish)		 FinnGen — — — — —

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
PPM012733 PSS009522|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.58 [1.56, 1.6] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012737 PSS009518|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.55 [1.51, 1.59] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012741 PSS009514|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.37 [1.36, 1.39] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012745 PSS009526|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.64 [1.6, 1.69] — — birth year, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012749 PSS009534|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.46 [1.41, 1.51] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012753 PSS009530|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.24 [1.09, 1.42] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012757 PSS009542|
European Ancestry|
343,676 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.78 [1.75, 1.81] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012762 PSS009538|
African Ancestry|
7,618 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.46 [1.32, 1.62] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —
PPM012767 PSS009546|
South Asian Ancestry|
7,628 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Type 2 diabetes OR: 1.66 [1.55, 1.79] — — age, sex, 10 PCs (+/- dataset-specific technical covariates) —

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
PSS009534 — —
[
  • 5,182 cases
  • , 20,514 controls
]
 — European — MGBB —
PSS009538 — —
[
  • 691 cases
  • , 6,927 controls
]
 — African unspecified — UKB —
PSS009542 — —
[
  • 13,616 cases
  • , 330,060 controls
]
 — European British UKB —
PSS009514 — —
[
  • 40,121 cases
  • , 138,605 controls
]
 — East Asian
(Japanese)		 — BBJ —
PSS009546 — —
[
  • 1,120 cases
  • , 6,508 controls
]
 — South Asian — UKB —
PSS009518 — —
[
  • 7,066 cases
  • , 103,531 controls
]
 — European
(Estonian)		 — EB —
PSS009522 — —
[
  • 37,001 cases
  • , 221,401 controls
]
 — European
(Finnish)		 — FinnGen —
PSS009526 — —
[
  • 5,228 cases
  • , 64,194 controls
]
 — European Norwegian HUNT —
PSS009530 — —
[
  • 660 cases
  • , 875 controls
]
 — African American or Afro-Caribbean — MGBB —