PGS Publication: PGP000405

Publication Information (EuropePMC)
Title The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians.
PubMed ID 36333282(Europe PMC)
doi 10.1038/s41467-022-34163-2
Publication Date Nov. 4, 2022
Journal Nat Commun
Author(s) Kim YJ, Moon S, Hwang MY, Han S, Jang HM, Kong J, Shin DM, Yoon K, Kim SM, Lee JE, Mahajan A, Park HY, McCarthy MI, Cho YS, Kim BJ.
Released in PGS Catalog: Dec. 20, 2022

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 Scoring File (FTP Link)
PGS003339
(CVGRS_LDL)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
LDL cholesterol level low density lipoprotein cholesterol measurement 65
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003339/ScoringFiles/PGS003339.txt.gz
PGS003344
(CVGRS_GGT)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Gamma glutamyl transferase level serum gamma-glutamyl transferase measurement 82
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003344/ScoringFiles/PGS003344.txt.gz
PGS003350
(ALLGRS_TC)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Total cholesterol total cholesterol measurement 102
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003350/ScoringFiles/PGS003350.txt.gz
PGS003338
(CVGRS_HDL)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
HDL cholesterol level high density lipoprotein cholesterol measurement 79
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003338/ScoringFiles/PGS003338.txt.gz
PGS003337
(CVGRS_HbA1c)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Hemoglobin A1c level HbA1c measurement 68
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003337/ScoringFiles/PGS003337.txt.gz
PGS003340
(CVGRS_TG)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Triglyceride level triglyceride measurement 65
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003340/ScoringFiles/PGS003340.txt.gz
PGS003341
(CVGRS_TC)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Total cholesterol total cholesterol measurement 91
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003341/ScoringFiles/PGS003341.txt.gz
PGS003342
(CVGRS_ALT)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Alanine aminotransferase level serum alanine aminotransferase measurement 51
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003342/ScoringFiles/PGS003342.txt.gz
PGS003343
(CVGRS_AST)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Aspartate aminotransferase level aspartate aminotransferase measurement 54
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003343/ScoringFiles/PGS003343.txt.gz
PGS003345
(ALLGRS_FPG)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Fasting plasma glucose fasting blood glucose measurement 60
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003345/ScoringFiles/PGS003345.txt.gz
PGS003346
(ALLGRS_HbA1c)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Hemoglobin A1c level HbA1c measurement 74
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003346/ScoringFiles/PGS003346.txt.gz
PGS003347
(ALLGRS_HDL)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
HDL cholesterol level high density lipoprotein cholesterol measurement 92
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003347/ScoringFiles/PGS003347.txt.gz
PGS003348
(ALLGRS_LDL)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
LDL cholesterol level low density lipoprotein cholesterol measurement 78
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003348/ScoringFiles/PGS003348.txt.gz
PGS003349
(ALLGRS_TG)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Triglyceride level triglyceride measurement 76
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003349/ScoringFiles/PGS003349.txt.gz
PGS003352
(ALLGRS_AST)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Aspartate aminotransferase level aspartate aminotransferase measurement 56
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003352/ScoringFiles/PGS003352.txt.gz
PGS003353
(GRS_T2D)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Type 2 diabetes type 2 diabetes mellitus 287
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003353/ScoringFiles/PGS003353.txt.gz
PGS003351
(ALLGRS_ALT)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Alanine aminotransferase level serum alanine aminotransferase measurement 57
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003351/ScoringFiles/PGS003351.txt.gz
PGS003336
(CVGRS_FPG)
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Fasting plasma glucose fasting blood glucose measurement 56
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003336/ScoringFiles/PGS003336.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
PPM016175 PGS003336
(CVGRS_FPG)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Fasting plasma glucose β: 0.20444
PPM016176 PGS003337
(CVGRS_HbA1c)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Hemoglobin A1c level β: 0.27528
PPM016177 PGS003338
(CVGRS_HDL)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: HDL cholesterol level β: 0.32033
PPM016178 PGS003339
(CVGRS_LDL)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: LDL cholesterol level β: 0.31083
PPM016179 PGS003340
(CVGRS_TG)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Triglyceride level β: 0.2506
PPM016180 PGS003341
(CVGRS_TC)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Total cholesterol β: 0.28536
PPM016181 PGS003342
(CVGRS_ALT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Alanine aminotransferase level β: 0.1213
PPM016182 PGS003343
(CVGRS_AST)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Aspartate aminotransferase level β: 0.13654
PPM016183 PGS003344
(CVGRS_GGT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Gamma glutamyl transferase level β: 0.24364
PPM016184 PGS003345
(ALLGRS_FPG)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Fasting plasma glucose β: 0.20689
PPM016185 PGS003346
(ALLGRS_HbA1c)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Hemoglobin A1c level β: 0.28295
PPM016186 PGS003347
(ALLGRS_HDL)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: HDL cholesterol level β: 0.32811
PPM016187 PGS003348
(ALLGRS_LDL)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: LDL cholesterol level β: 0.31961
PPM016188 PGS003349
(ALLGRS_TG)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Triglyceride level β: 0.25635
PPM016189 PGS003350
(ALLGRS_TC)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Total cholesterol β: 0.29361
PPM016190 PGS003351
(ALLGRS_ALT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Alanine aminotransferase level β: 0.16161
PPM016191 PGS003352
(ALLGRS_AST)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Aspartate aminotransferase level β: 0.14314
PPM016192 PGS003336
(CVGRS_FPG)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.46435
PPM016193 PGS003337
(CVGRS_HbA1c)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.35007
PPM016194 PGS003338
(CVGRS_HDL)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.03795
PPM016195 PGS003339
(CVGRS_LDL)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 0.99947
PPM016196 PGS003340
(CVGRS_TG)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.01294
PPM016197 PGS003341
(CVGRS_TC)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 0.98882
PPM016198 PGS003342
(CVGRS_ALT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.04754
PPM016199 PGS003343
(CVGRS_AST)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 0.99256
PPM016200 PGS003344
(CVGRS_GGT)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 1.04096
PPM016201 PGS003353
(GRS_T2D)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Fasting plasma glucose OR: 1.83 [1.59, 2.11]
PPM016202 PGS003353
(GRS_T2D)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Hemoglobin A1c level OR: 1.68 [1.46, 1.93]
PPM016203 PGS003353
(GRS_T2D)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Type 2 diabetes OR: 2.99 [2.61, 3.44]
PPM016204 PGS003353
(GRS_T2D)
PSS010055|
East Asian Ancestry|
22,608 individuals
PGP000405 |
Kim YJ et al. Nat Commun (2022)
Reported Trait: Fasting plasma glucose and Type 2 diabetes OR: 3.52 [2.69, 4.61]

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
PSS010055 22,608 individuals East Asian KBA, KoGES