PGS Catalog - Loesch DP, medRxiv (2024) (Publication)

PGS Preprint: PGP000701

Publication Information (EuropePMC)
Title	Identification of plasma proteomic markers underlying polygenic risk of type 2 diabetes and related comorbidities
doi	10.1101/2024.03.15.24304200
Publication Date	March 19, 2024
Journal	*medRxiv* Preprint
Author(s)	Loesch DP, Garg M, Matelska D, Vitsios D, Jiang X, Ritchie SC, Sun BB, Runz H, Whelan CD, Holman RR, Mentz RJ, Moura FA, Wiviott SD, Sabatine MS, Udler MS, Gause-Nilsson IA, Petrovski S, Oscarsson J, Nag A, Paul DS, Inouye M.

Released in PGS Catalog: Feb. 4, 2025

Associated Polygenic Score(s)

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)
PGS005115 (PGS_T2D_beta_cell)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	30	- -	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005115/ScoringFiles/PGS005115.txt.gz
PGS005110 (PGS_T2D_gw)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	1,114,950	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005110/ScoringFiles/PGS005110.txt.gz
PGS005112 (PGS_CAD)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Coronary artery disease	coronary artery disease	1,106,628	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005112/ScoringFiles/PGS005112.txt.gz
PGS005114 (PGS_BMI)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Body mass index (BMI)	body mass index	1,022,364	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005114/ScoringFiles/PGS005114.txt.gz
PGS005117 (PGS_T2D_liver_lipid)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	5	- -	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005117/ScoringFiles/PGS005117.txt.gz
PGS005118 (PGS_T2D_obesity)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	5	- -	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005118/ScoringFiles/PGS005118.txt.gz
PGS005111 (PGS_T2D_gwas)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	150	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005111/ScoringFiles/PGS005111.txt.gz
PGS005113 (PGS_CKD)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Chronic kidney disease	chronic kidney disease	1,116,379	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005113/ScoringFiles/PGS005113.txt.gz
PGS005116 (PGS_T2D_lipodystrophy)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	20	- -	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005116/ScoringFiles/PGS005116.txt.gz
PGS005119 (PGS_T2D_proinsulin)	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Type 2 diabetes (T2D)	type 2 diabetes mellitus	7	- -	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005119/ScoringFiles/PGS005119.txt.gz

External PGS Evaluated 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)
PGS002732 (GRS_77)	PGP000341 \| Vujkovic M et al. Nat Genet (2022)	Chronic elevation of alanine aminotransferase	serum alanine aminotransferase measurement	77	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002732/ScoringFiles/PGS002732.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
PPM022302	PGS005111 (PGS_T2D_gwas)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.45 [1.41, 1.5]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022303	PGS005112 (PGS_CAD)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: coronary artery disease	OR: 1.45 [1.41, 1.49]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022304	PGS005113 (PGS_CKD)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: chronic kidney disease	OR: 1.35 [1.29, 1.41]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022305	PGS005114 (PGS_BMI)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: body mass index	β: 1.32 [1.28, 1.36]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022306	PGS005115 (PGS_T2D_beta_cell)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.27 [1.23, 1.31]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022307	PGS005116 (PGS_T2D_lipodystrophy)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.18 [1.14, 1.22]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022308	PGS005117 (PGS_T2D_liver_lipid)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.06 [1.03, 1.1]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022309	PGS005118 (PGS_T2D_obesity)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.1 [1.07, 1.14]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022311	PGS002732 (GRS_77)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Ext.\|Pre	Reported Trait: non-alcoholic fattly liver disease	OR: 1.31 [1.21, 1.41]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022312	PGS005110 (PGS_T2D_gw)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 2.42 [2.33, 2.51]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022313	PGS005111 (PGS_T2D_gwas)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.46 [1.41, 1.51]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022314	PGS005112 (PGS_CAD)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: coronary artery disease	OR: 1.46 [1.42, 1.5]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022315	PGS005113 (PGS_CKD)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: chronic kidney disease	OR: 1.35 [1.29, 1.42]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022316	PGS005114 (PGS_BMI)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: body mass index	β: 1.34 [1.3, 1.39]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022317	PGS005115 (PGS_T2D_beta_cell)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.27 [1.23, 1.31]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022318	PGS005116 (PGS_T2D_lipodystrophy)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.18 [1.14, 1.22]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022319	PGS005117 (PGS_T2D_liver_lipid)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.07 [1.04, 1.11]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022320	PGS005118 (PGS_T2D_obesity)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.11 [1.07, 1.14]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022322	PGS002732 (GRS_77)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Ext.\|Pre	Reported Trait: non-alcoholic fattly liver disease	OR: 1.31 [1.21, 1.42]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022301	PGS005110 (PGS_T2D_gw)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 2.33 [2.25, 2.41]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022310	PGS005119 (PGS_T2D_proinsulin)	PSS011911\| Multi-ancestry (including European)\| 48,603 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.09 [1.05, 1.12]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—
PPM022321	PGS005119 (PGS_T2D_proinsulin)	PSS011912\| European Ancestry\| 45,356 individuals	PGP000701 \| Loesch DP et al. medRxiv (2024) \|Pre	Reported Trait: type 2 diabetes	OR: 1.09 [1.06, 1.13]	—	—	age, age^2, sex, UKB centre, array, genetic PCS 1-20	—

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
PSS011911	ICD10: E11 for T2D, N18 for CKD, first occurence of I20-125 for CAD. BMI: baseline body mass index	Median = 14.8 years	48,603 individuals, 46.0 % Male samples	Mean = 56.8 years Sd = 8.2 years	European, East Asian, South Asian, Hispanic or Latin American, African unspecified	—	UKB	—
PSS011912	ICD10: E11 for T2D, N18 for CKD, first occurence of I20-125 for CAD, K76.0 for NAFLD. BMI: baseline body mass index	Median = 14.8 years	45,356 individuals, 46.0 % Male samples	Mean = 57.1 years Sd = 8.1 years	European	—	UKB	—