Polygenic Score (PGS) ID: PGS001890

Predicted Trait
Reported Trait avMSE
Mapped Trait(s) visual acuity measurement (EFO_0008385)
Additional Trait Information physical measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_avMSE
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 44,864
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
PPM010004 PSS009386|
European Ancestry|
4,208 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.3416 [0.3146, 0.3681] sex, age, birth date, deprivation index, 16 PCs
PPM010005 PSS009160|
European Ancestry|
1,144 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.3333 [0.2803, 0.3843] sex, age, birth date, deprivation index, 16 PCs
PPM010006 PSS008714|
European Ancestry|
2,005 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.3002 [0.2596, 0.3397] sex, age, birth date, deprivation index, 16 PCs
PPM010007 PSS008488|
Greater Middle Eastern Ancestry|
440 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.2562 [0.1645, 0.3434] sex, age, birth date, deprivation index, 16 PCs
PPM010008 PSS008266|
South Asian Ancestry|
2,632 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.2318 [0.1952, 0.2677] sex, age, birth date, deprivation index, 16 PCs
PPM010009 PSS008044|
East Asian Ancestry|
634 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.1646 [0.0866, 0.2406] sex, age, birth date, deprivation index, 16 PCs
PPM010010 PSS007830|
African Ancestry|
1,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.1066 [0.0527, 0.1598] sex, age, birth date, deprivation index, 16 PCs
PPM010011 PSS008934|
African Ancestry|
1,910 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.0914 [0.0465, 0.1359] 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
PSS008934 1,910 individuals African unspecified Nigeria (West Africa) UKB
PSS008488 440 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009160 1,144 individuals European Poland (NE Europe) UKB
PSS008714 2,005 individuals European Italy (South Europe) UKB
PSS008266 2,632 individuals South Asian India (South Asia) UKB
PSS009386 4,208 individuals European UK (+ Ireland) UKB
PSS008044 634 individuals East Asian China (East Asia) UKB
PSS007830 1,331 individuals African American or Afro-Caribbean Carribean UKB