Polygenic Score (PGS) ID: PGS001781

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Feb. 23, 2022
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Score Details

Score Construction
PGS Name T2D_PRSCS
Development Method
Name PRS-CS
Parameters PRS-CS-auto, 1000G European sample (N = 503) as the external LD reference panel
Variants
Original Genome Build GRCh38
Number of Variants 1,091,673
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000261
Citation (link to publication) Tamlander M et al. Commun Biol (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
PGS Evaluation
European: 100%
6 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

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
PPM009277 PSS007684|
European Ancestry|
309,154 individuals
 PGP000261 |
Tamlander M et al. Commun Biol (2022)
 Reported Trait: Type 2 diabetes (incident and prevalent) OR: 1.59 [1.57, 1.61] AUROC: 0.758 [0.756, 0.761] — year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array —
PPM009281 PSS007685|
European Ancestry|
279,879 individuals
 PGP000261 |
Tamlander M et al. Commun Biol (2022)
 Reported Trait: Incident type 2 diabetes OR: 1.52 [1.49, 1.55] AUROC: 0.852 [0.849, 0.855] — year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array —
PPM009287 PSS007692|
European Ancestry|
343,672 individuals
 PGP000261 |
Tamlander M et al. Commun Biol (2022)
 Reported Trait: Prevalent type 2 diabetes OR: 1.75 [1.72, 1.78] AUROC: 0.725 [0.721, 0.729] — year of birth, sex —
PPM009283 PSS007691|
European Ancestry|
328,115 individuals
 PGP000261 |
Tamlander M et al. Commun Biol (2022)
 Reported Trait: Incident type 2 diabetes OR: 1.51 [1.48, 1.54] AUROC: 0.669 [0.664, 0.675] — year of birth, sex —
PPM009285 PSS007686|
European Ancestry|
309,154 individuals
 PGP000261 |
Tamlander M et al. Commun Biol (2022)
 Reported Trait: Prevalent type 2 diabetes OR: 1.59 [1.57, 1.61] AUROC: 0.81 [0.808, 0.813] — year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array —
PPM009279 PSS007690|
European Ancestry|
343,672 individuals
 PGP000261 |
Tamlander M et al. Commun Biol (2022)
 Reported Trait: Type 2 diabetes (incident and prevalent) OR: 1.68 [1.65, 1.7] AUROC: 0.708 [0.705, 0.711] — year of birth, sex —

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
PSS007684 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2019, whichever came first. Median = 13.0 years
IQR = [7.5, 19.7] years
[
  • 44,266 cases
  • , 264,888 controls
]
,
43.8 % Male samples
 Mean (Age At Baseline) = 53.2 years
Sd = 17.4 years		 European
(Finnish)		 — FinnGen —
PSS007685 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2019, whichever came first. —
[
  • 14,991 cases
  • , 264,888 controls
]
,
42.9 % Male samples
 Mean (Age At Baseline) = 51.8 years
Sd = 17.4 years		 European
(Finnish)		 — FinnGen —
PSS007686 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2019, whichever came first. —
[
  • 29,275 cases
  • , 279,879 controls
]
,
43.8 % Male samples
 Mean (Age At Baseline) = 53.2 years
Sd = 17.4 years		 European
(Finnish)		 — FinnGen —
PSS007690 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. Median = 10.4 years
IQR = [8.3, 11.3] years
[
  • 24,192 cases
  • , 319,480 controls
]
,
46.3 % Male samples
 Mean (Age At Baseline) = 57.4 years
Sd = 8.0 years		 European
(British)		 UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB —
PSS007691 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. —
[
  • 8,635 cases
  • , 319,480 controls
]
,
45.5 % Male samples
 Mean (Age At Baseline) = 57.2 years
Sd = 8.0 years		 European
(British)		 UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB —
PSS007692 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. —
[
  • 15,557 cases
  • , 328,115 controls
]
,
46.3 % Male samples
 Mean (Age At Baseline) = 57.4 years
Sd = 8.0 years		 European
(British)		 UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB —