Polygenic Score (PGS) ID: PGS000020

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 14, 2019
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name dGRS1000
Development Method
Name Pruning and Thresholding (P+T)
Parameters P < 0.05, r2 < 0.05, betas are weighted by the probability that they are in the top 1000 signals
Variants
Original Genome Build NCBI36
Number of Variants 7,502
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000010
Citation (link to publication) Läll K et al. Genet Med (2016)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
69,033 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST005047
Europe PMC: 22885922
 69,033 individuals European 30 cohorts
  • AMC-PAS
  • ,ARIC
  • ,BHS
  • ,DGDG
  • ,DGI
  • ,DILGOM
  • ,DUNDEE
  • ,EAS
  • ,EMIL
  • ,EPIC
  • ,EUROSPAN
  • ,FHS
  • ,FUSION
  • ,GMetS
  • ,HNR
  • ,HPFS
  • ,HSIEA
  • ,IMPROVE
  • ,KORA
  • ,NHS
  • ,PIVUS
  • ,PMB
  • ,PROMIS
  • ,RS
  • ,SCARFSHEEP
  • ,STR
  • ,ULSAM
  • ,W2C
  • ,WTCCC
  • ,deCODE

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
PPM000040 PSS000025|
European Ancestry|
6,280 individuals
 PGP000010 |
Läll K et al. Genet Med (2016)
 Reported Trait: Incident type 2 diabetes HR: 1.48 [1.32, 1.66] C-index: 0.79 [0.771, 0.812] — BMI category, smoking level, waist-to-hip ratio, waist circumference, physical activity level, history of high blood glucose, fruit and vegetable consumption, and sex. Cox age-as-time-scale

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
PSS000025 Incident cases of Type 2 Diabetes in 5.63 years follow-up —
[
  • 302 cases
  • , 5,978 controls
]
,
55.0 % Male samples
 — European
(Estonian)		 — EB —