Polygenic Score (PGS) ID: PGS001953

Predicted Trait
Reported Trait Glycated haemoglobin (HbA1c)
Mapped Trait(s) HbA1c measurement (EFO_0004541)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_HbA1c
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 46,566
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010500 PSS009208|
European Ancestry|
3,930 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.3374 [0.3093, 0.3649] sex, age, birth date, deprivation index, 16 PCs
PPM010501 PSS008762|
European Ancestry|
6,326 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.3092 [0.2867, 0.3314] sex, age, birth date, deprivation index, 16 PCs
PPM010502 PSS008536|
Greater Middle Eastern Ancestry|
1,128 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.329 [0.2755, 0.3806] sex, age, birth date, deprivation index, 16 PCs
PPM010503 PSS008314|
South Asian Ancestry|
5,936 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.2406 [0.2164, 0.2644] sex, age, birth date, deprivation index, 16 PCs
PPM010504 PSS008091|
East Asian Ancestry|
1,731 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.2506 [0.2057, 0.2945] sex, age, birth date, deprivation index, 16 PCs
PPM010505 PSS007878|
African Ancestry|
2,100 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.1217 [0.0792, 0.1639] sex, age, birth date, deprivation index, 16 PCs
PPM010506 PSS008982|
African Ancestry|
2,976 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.087 [0.0511, 0.1226] sex, age, birth date, deprivation index, 16 PCs
PPM010499 PSS009434|
European Ancestry|
19,060 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Glycated haemoglobin (HbA1c) Partial Correlation (partial-r): 0.3405 [0.3279, 0.353] sex, age, birth date, deprivation index, 16 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
PSS007878 2,100 individuals African American or Afro-Caribbean Carribean UKB
PSS008091 1,731 individuals East Asian China (East Asia) UKB
PSS008982 2,976 individuals African unspecified Nigeria (West Africa) UKB
PSS008536 1,128 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009208 3,930 individuals European Poland (NE Europe) UKB
PSS008314 5,936 individuals South Asian India (South Asia) UKB
PSS008762 6,326 individuals European Italy (South Europe) UKB
PSS009434 19,060 individuals European UK (+ Ireland) UKB