PGS Publication: PGP000742

Publication Information (EuropePMC)
Title Polygenic risk score for type 2 diabetes shows context-dependent effects across populations.
PubMed ID 41034193(Europe PMC)
doi 10.1038/s41467-025-63546-4
Publication Date June 25, 2025
Journal Nat Commun
Author(s) Guo B, Cai Y, Kim D, Smit RAJ, Wang Z, Iyer KR, Hilliard AT, Haessler J, Tao R, Broadaway KA, Wang Y, Pozdeyev N, Stæger FF, Yang C, Vanderwerff B, Patki AD, Stalbow L, Lin M, Rafaels N, Shortt J, Wiley L, Stanislawski M, Pattee J, Davis L, Straub PS, Shuey MM, Cox NJ, Lee NR, Jørgensen ME, Bjerregaard P, Larsen C, Hansen T, Moltke I, Meigs JB, Stram DO, Yin X, Zhou X, Chang KM, Clarke SL, Guarischi-Sousa R, Lankester J, Tsao PS, Buyske S, Graff M, Raffield LM, Sun Q, Wilkens LR, Carlson CS, Easton CB, Liu S, Manson JE, Marchand LL, Haiman CA, Mohlke KL, Gordon-Larsen P, Albrechtsen A, Boehnke M, Rich SS, Manichaikul A, Rotter JI, Yousri NA, Irvin RM; biobank at the Colorado Center for Personalized Medicine (CCPM); VA Million Veteran Program (MVP); Gignoux C, North KE, Loos RJF, Assimes TL, Peters U, Kooperberg C, Raghavan S, Highland HM, Darst BF.
Released in PGS Catalog: Oct. 6, 2025

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)
PGS005243
(T2D_PRS_PRS_CSx_META_F_AFR)
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,183,017
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005243/ScoringFiles/PGS005243.txt.gz
PGS005244
(T2D_PRS_PRS_CSx_META_F_AMR)
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 960,470
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005244/ScoringFiles/PGS005244.txt.gz
PGS005246
(T2D_PRS_PRS_CSx_META_F_EUR)
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,111,848
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005246/ScoringFiles/PGS005246.txt.gz
PGS005247
(T2D_PRS_PRS_CSx_META_F_SAS)
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,126,657
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005247/ScoringFiles/PGS005247.txt.gz
PGS005242
(T2D_PRS_PRS_CSx_META_T)
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,257,036
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005242/ScoringFiles/PGS005242.txt.gz
PGS005245
(T2D_PRS_PRS_CSx_META_F_EAS)
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Type 2 diabetes (T2D) type 2 diabetes mellitus 1,021,829
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005245/ScoringFiles/PGS005245.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
PPM022720 PGS005242
(T2D_PRS_PRS_CSx_META_T)
 PSS012058|
African Ancestry|
13,161 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.56 [1.51, 1.61] AUROC: 0.687 [0.68, 0.693] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022721 PGS005242
(T2D_PRS_PRS_CSx_META_T)
 PSS012061|
Hispanic or Latin American Ancestry|
22,647 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.86 [1.8, 1.92] AUROC: 0.753 [0.747, 0.759] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022722 PGS005242
(T2D_PRS_PRS_CSx_META_T)
 PSS012059|
Additional Asian Ancestries|
7,498 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.9 [1.79, 2.02] AUROC: 0.768 [0.758, 0.779] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022723 PGS005242
(T2D_PRS_PRS_CSx_META_T)
 PSS012060|
European Ancestry|
22,063 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.78 [1.7, 1.87] AUROC: 0.761 [0.754, 0.769] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022724 PGS005243
(T2D_PRS_PRS_CSx_META_F_AFR)
 PSS012058|
African Ancestry|
13,161 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.23 [1.19, 1.26] AUROC: 0.664 [0.657, 0.671] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022725 PGS005244
(T2D_PRS_PRS_CSx_META_F_AMR)
 PSS012061|
Hispanic or Latin American Ancestry|
22,647 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.27 [1.24, 1.31] AUROC: 0.715 [0.708, 0.722] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022726 PGS005245
(T2D_PRS_PRS_CSx_META_F_EAS)
 PSS012059|
Additional Asian Ancestries|
7,498 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.71 [1.62, 1.8] AUROC: 0.758 [0.747, 0.769] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022727 PGS005246
(T2D_PRS_PRS_CSx_META_F_EUR)
 PSS012060|
European Ancestry|
22,063 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 2.01 [1.94, 2.09] AUROC: 0.786 [0.779, 0.793] — age, sex, BMI, sub-study, and first 10 PCs —
PPM022728 PGS005247
(T2D_PRS_PRS_CSx_META_F_SAS)
 PSS012059|
Additional Asian Ancestries|
7,498 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.25 [1.19, 1.31] AUROC: 0.73 [0.719, 0.741] — age, sex, BMI, sub-study, and first 10 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
PSS012060 — —
[
  • 4,076 cases
  • , 17,987 controls
]
,
17.1 % Male samples
 Mean = 62.0 years
Sd = 8.96 years		 European
(European)		 — PAGE —
PSS012061 — —
[
  • 9,441 cases
  • , 13,206 controls
]
,
36.8 % Male samples
 Mean = 57.0 years
Sd = 10.3 years		 Hispanic or Latin American — PAGE —
PSS012058 — —
[
  • 5,429 cases
  • , 7,732 controls
]
,
43.8 % Male samples
 Mean = 58.9 years
Sd = 9.99 years		 African unspecified
(African American)		 — PAGE —
PSS012059 — —
[
  • 3,185 cases
  • , 4,313 controls
]
,
49.0 % Male samples
 Mean = 60.5 years
Sd = 8.67 years		 Asian unspecified — PAGE —