PGS Publication: PGP000469

Publication Information (EuropePMC)
Title The utility of a type 2 diabetes polygenic score in addition to clinical variables for prediction of type 2 diabetes incidence in birth, youth and adult cohorts in an Indigenous study population.
PubMed ID 36862161(Europe PMC)
doi 10.1007/s00125-023-05870-2
Publication Date March 2, 2023
Journal Diabetologia
Author(s) Wedekind LE, Mahajan A, Hsueh WC, Chen P, Olaiya MT, Kobes S, Sinha M, Baier LJ, Knowler WC, McCarthy MI, Hanson RL.
Released in PGS Catalog: June 1, 2023

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS003733
(PS_T2D_287-EUR-DIAMANTE)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 287
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003733/ScoringFiles/PGS003733.txt.gz
PGS003731
(PS_T2D_282-SAS-DIAMANTE)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 282
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003731/ScoringFiles/PGS003731.txt.gz
PGS003729
(PS_T2D_293-DIAGRAM)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 293
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003729/ScoringFiles/PGS003729.txt.gz
PGS003730
(PS_T2D_287-DIAMANTE)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 287
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003730/ScoringFiles/PGS003730.txt.gz
PGS003732
(PS_T2D_287-HIS-DIAMANTE)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 287
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003732/ScoringFiles/PGS003732.txt.gz
PGS003728
(PS_T2D_183-AGEN)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 183
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003728/ScoringFiles/PGS003728.txt.gz
PGS003734
(PS_T2D_280-EAS-DIAMANTE)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 280
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003734/ScoringFiles/PGS003734.txt.gz
PGS003735
(PS_T2D_276-AFR-DIAMANTE)
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 276
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003735/ScoringFiles/PGS003735.txt.gz

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) 		Evaluated Score 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
PPM018469 PGS003729
(PS_T2D_293-DIAGRAM)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.27 [1.17, 1.38] AUROC: 0.735 Net reclassification improvement: 0.27 [0.149, 0.392]
∆AUC: 0.007 [0.001, 0.014]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018470 PGS003735
(PS_T2D_276-AFR-DIAMANTE)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.13 [1.04, 1.22] — ∆AUC: 0.003 [0.0, 0.007]
Net reclassification improvement: 0.181 [0.047, 0.316]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018471 PGS003730
(PS_T2D_287-DIAMANTE)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.2 [1.1, 1.3] — Net reclassification improvement: 0.216 [0.094, 0.338]
∆AUC: 0.004 [-0.001, 0.009]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018472 PGS003734
(PS_T2D_280-EAS-DIAMANTE)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.13 [1.04, 1.23] — Net reclassification improvement: 0.115 [-0.014, 0.244]
∆AUC: 0.001 [-0.002, 0.005]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018473 PGS003733
(PS_T2D_287-EUR-DIAMANTE)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.21 [1.12, 1.32] — Net reclassification improvement: 0.277 [0.156, 0.397]
∆AUC: 0.005 [0.0, 0.011]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018474 PGS003732
(PS_T2D_287-HIS-DIAMANTE)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.18 [1.09, 1.29] — Net reclassification improvement: 0.219 [0.097, 0.34]
∆AUC: 0.004 [-0.001, 0.008]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018475 PGS003731
(PS_T2D_282-SAS-DIAMANTE)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.19 [1.09, 1.29] — Net reclassification improvement: 0.181 [0.054, 0.308]
∆AUC: 0.004 [-0.001, 0.009]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —
PPM018476 PGS003728
(PS_T2D_183-AGEN)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.28 [1.12, 1.46] — Net reclassification improvement: 0.331 [0.141, 0.521]
∆AUC: 0.005 [-0.003, 0.012]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018477 PGS003729
(PS_T2D_293-DIAGRAM)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.49 [1.29, 1.72] AUROC: 0.812 Net reclassification improvement: 0.268 [0.072, 0.464]
∆AUC: 0.007 [-0.003, 0.017]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018478 PGS003735
(PS_T2D_276-AFR-DIAMANTE)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.21 [1.06, 1.38] — Net reclassification improvement: 0.185 [-0.017, 0.388]
∆AUC: 0.005 [-0.001, 0.01]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018479 PGS003730
(PS_T2D_287-DIAMANTE)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.34 [1.17, 1.54] — Net reclassification improvement: 0.314 [0.116, 0.512]
∆AUC: 0.004 [-0.001, 0.009]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018480 PGS003734
(PS_T2D_280-EAS-DIAMANTE)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.19 [1.04, 1.36] — Net reclassification improvement: 0.182 [-0.019, 0.383]
∆AUC: 0.001 [-0.004, 0.007]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018481 PGS003733
(PS_T2D_287-EUR-DIAMANTE)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.37 [1.19, 1.58] — Net reclassification improvement: 0.296 [0.09, 0.502]
∆AUC: 0.008 [-0.001, 0.017]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018482 PGS003732
(PS_T2D_287-HIS-DIAMANTE)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.32 [1.15, 1.51] — Net reclassification improvement: 0.15 [-0.054, 0.354]
∆AUC: 0.006 [-0.001, 0.014]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018483 PGS003731
(PS_T2D_282-SAS-DIAMANTE)
 PSS010984|
Additional Diverse Ancestries|
2,229 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (youth cohort at 10 year follow-up) HR: 1.35 [1.18, 1.56] — Net reclassification improvement: 0.302 [0.089, 0.515]
∆AUC: 0.002 [-0.007, 0.012]		 age, sex, parental diabetes, modified BMI z score, fasting plasma glucose —
PPM018484 PGS003728
(PS_T2D_183-AGEN)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.27 [1.15, 1.39] — Net reclassification improvement: 0.164 [0.025, 0.303]
∆AUC: 0.037 [0.013, 0.06]		 sex, parental diabetes, and birth weight —
PPM018485 PGS003729
(PS_T2D_293-DIAGRAM)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.48 [1.35, 1.63] AUROC: 0.685 Net reclassification improvement: 0.362 [0.222, 0.502]
∆AUC: 0.072 [0.045, 0.099]		 sex, parental diabetes, and birth weight —
PPM018486 PGS003735
(PS_T2D_276-AFR-DIAMANTE)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.28 [1.16, 1.41] — Net reclassification improvement: 0.231 [0.091, 0.376]
∆AUC: 0.042 [0.019, 0.065]		 sex, parental diabetes, and birth weight —
PPM018487 PGS003730
(PS_T2D_287-DIAMANTE)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.45 [1.32, 1.6] — Net reclassification improvement: 0.259 [0.115, 0.403]
∆AUC: 0.073		 sex, parental diabetes, and birth weight —
PPM018488 PGS003734
(PS_T2D_280-EAS-DIAMANTE)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.33 [1.22, 1.46] — Net reclassification improvement: 0.176 [0.029, 0.323]
∆AUC: 0.052 [0.026, 0.077]		 sex, parental diabetes, and birth weight —
PPM018489 PGS003733
(PS_T2D_287-EUR-DIAMANTE)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.47 [1.33, 1.62] — Net reclassification improvement: 0.328 [0.183, 0.474]
∆AUC: 0.075 [0.048, 0.102]		 sex, parental diabetes, and birth weight —
PPM018490 PGS003732
(PS_T2D_287-HIS-DIAMANTE)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.4 [1.28, 1.55] — Net reclassification improvement: 0.277 [0.125, 0.428]
∆AUC: 0.072 [0.046, 0.099]		 sex, parental diabetes, and birth weight —
PPM018491 PGS003731
(PS_T2D_282-SAS-DIAMANTE)
 PSS010983|
Additional Diverse Ancestries|
2,894 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (birth cohort at 30 year follow-up) HR: 1.32 [1.2, 1.45] — Net reclassification improvement: 0.201 [0.057, 0.306]
∆AUC: 0.054 [0.031, 0.077]		 sex, parental diabetes, and birth weight —
PPM018468 PGS003728
(PS_T2D_183-AGEN)
 PSS010982|
Additional Diverse Ancestries|
2,333 individuals
 PGP000469 |
Wedekind LE et al. Diabetologia (2023)
 Reported Trait: Incident type 2 diabetes (adult cohort at 10 year follow-up) HR: 1.14 [1.06, 1.24] — Net reclassification improvement: 0.115 [-0.014, 0.244]
∆AUC: 0.001 [-0.003, 0.005]		 age, sex, parental diabetes, BMI, fasting plasma glucose and HbA1c. —

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
PSS010983 — Mean = 21.28 years
[
  • 438 cases
  • , 2,456 controls
]
 — Native American — NR —
PSS010984 — Mean = 7.99 years
[
  • 228 cases
  • , 2,001 controls
]
 Mean = 12.05 years
Sd = 3.73 years		 Native American — NR —
PSS010982 — Mean = 7.15 years
[
  • 640 cases
  • , 1,693 controls
]
 Mean = 31.04 years
Sd = 10.43 years		 Native American — NR —