PGS Preprint: PGP000514

Publication Information (EuropePMC)
Title Trans-ancestry polygenic models for the prediction of LDL blood levels: An analysis of the UK Biobank and Taiwan Biobank
doi 10.1101/2023.08.03.23293320
Publication Date Aug. 6, 2023
Journal medRxiv Preprint
Author(s) Hassanin E, Lee K, Hsieh T, Aldisi R, Lee Y, Bobbili D, Krawitz P, May P, Chen C, Maj C.
Released in PGS Catalog: Nov. 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)
PGS003974
(AFR_without-UKB_LDL)
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 LDL cholesterol low density lipoprotein cholesterol measurement 886,257
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003974/ScoringFiles/PGS003974.txt.gz
PGS003977
(SAS_without-UKB_LDL)
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 LDL cholesterol low density lipoprotein cholesterol measurement 826,248
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003977/ScoringFiles/PGS003977.txt.gz
PGS003975
(EAS_without-UKB_LDL)
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 LDL cholesterol low density lipoprotein cholesterol measurement 862,971
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003975/ScoringFiles/PGS003975.txt.gz
PGS003976
(EUR_without-UKB_LDL)
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 LDL cholesterol low density lipoprotein cholesterol measurement 821,134
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003976/ScoringFiles/PGS003976.txt.gz
PGS003978
(meta_without-UKB_LDL)
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 LDL cholesterol low density lipoprotein cholesterol measurement 348,056
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003978/ScoringFiles/PGS003978.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
PPM019138 PGS003976
(EUR_without-UKB_LDL)
 PSS011207|
European Ancestry|
423,596 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 10.6 % — —
PPM019139 PGS003978
(meta_without-UKB_LDL)
 PSS011207|
European Ancestry|
423,596 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 10.5 % — —
PPM019140 PGS003975
(EAS_without-UKB_LDL)
 PSS011203|
East Asian Ancestry|
1,480 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 8.6 % — —
PPM019141 PGS003978
(meta_without-UKB_LDL)
 PSS011203|
East Asian Ancestry|
1,480 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 7.8 % — —
PPM019142 PGS003975
(EAS_without-UKB_LDL)
 PSS011201|
East Asian Ancestry|
68,978 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 9.3 % — —
PPM019143 PGS003976
(EUR_without-UKB_LDL)
 PSS011201|
East Asian Ancestry|
68,978 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 4.5 % — —
PPM019144 PGS003978
(meta_without-UKB_LDL)
 PSS011201|
East Asian Ancestry|
68,978 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 6.7 % — —
PPM019145 PGS003974
(AFR_without-UKB_LDL)
 PSS011206|
African Ancestry|
3,802 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 9.2 % — —
PPM019146 PGS003977
(SAS_without-UKB_LDL)
 PSS011204|
South Asian Ancestry|
6,303 individuals
 PGP000514 |
Hassanin E et al. medRxiv (2023)
|Pre		 Reported Trait: LDL level — — R²: 5.6 % — —

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
PSS011201 — — 68,978 individuals,
31.2 % Male samples
 — East Asian — TWB —
PSS011203 — — 1,480 individuals,
36.8 % Male samples
 — East Asian — UKB —
PSS011204 — — 6,303 individuals,
54.1 % Male samples
 — South Asian — UKB —
PSS011206 — — 3,802 individuals,
45.9 % Male samples
 — African American or Afro-Caribbean — UKB —
PSS011207 — — 423,596 individuals,
45.9 % Male samples
 — European — UKB —