Polygenic Score (PGS) ID: PGS003533

Predicted Trait
Reported Trait Glycated haemoglobin (HbA1c)
Mapped Trait(s) HbA1c measurement (EFO_0004541)
Released in PGS Catalog: April 12, 2023
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cont-decay-log_HbA1c
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
353,562 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 353,562 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 years		 — white British —

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) 		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
PPM017461 PSS010897|
European Ancestry|
19,078 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017545 PSS010813|
European Ancestry|
3,920 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017629 PSS010645|
European Ancestry|
6,172 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017713 PSS010561|
Greater Middle Eastern Ancestry|
1,100 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017797 PSS010225|
European Ancestry|
2,233 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017881 PSS010477|
South Asian Ancestry|
5,884 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017965 PSS010393|
East Asian Ancestry|
1,718 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018049 PSS010309|
African Ancestry|
2,089 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018133 PSS010729|
African Ancestry|
2,950 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Glycated haemoglobin (HbA1c) — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —

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
PSS010561 — — 1,100 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010309 — — 2,089 individuals,
37.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010729 — — 2,950 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010477 — — 5,884 individuals,
54.0 % Male samples
 Mean = 53.4 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010225 — — 2,233 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010897 — — 19,078 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 7.9 years		 European white British UKB —
PSS010645 — — 6,172 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010393 — — 1,718 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010813 — — 3,920 individuals,
38.0 % Male samples
 Mean = 54.4 years
Sd = 7.5 years		 European Polish UKB —