Trait: visual acuity measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0008385
Description quantification of visual acuity
Trait category
Other measurement
Mapped term PMID:28835685

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
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001890
(portability-PLR_avMSE)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
avMSE visual acuity measurement 44,864
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001890/ScoringFiles/PGS001890.txt.gz
PGS001985
(portability-PLR_logMAR)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
logMAR in round (left/right) visual acuity measurement 223
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001985/ScoringFiles/PGS001985.txt.gz
PGS002103
(portability-ldpred2_avMSE)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
avMSE visual acuity measurement 833,170
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002103/ScoringFiles/PGS002103.txt.gz
PGS003493
(cont-decay-avMSE)
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
avMSE visual acuity measurement 979,739
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003493/ScoringFiles/PGS003493.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
PPM010004 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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 PGS001890
(portability-PLR_avMSE)
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
PPM010755 PGS001985
(portability-PLR_logMAR)
PSS009425|
European Ancestry|
4,973 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0683 [0.0405, 0.0959] sex, age, birth date, deprivation index, 16 PCs
PPM010757 PGS001985
(portability-PLR_logMAR)
PSS008753|
European Ancestry|
2,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0178 [-0.0242, 0.0598] sex, age, birth date, deprivation index, 16 PCs
PPM010758 PGS001985
(portability-PLR_logMAR)
PSS008527|
Greater Middle Eastern Ancestry|
473 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0533 [-0.039, 0.1447] sex, age, birth date, deprivation index, 16 PCs
PPM010759 PGS001985
(portability-PLR_logMAR)
PSS008305|
South Asian Ancestry|
2,803 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): -0.0076 [-0.0447, 0.0296] sex, age, birth date, deprivation index, 16 PCs
PPM010760 PGS001985
(portability-PLR_logMAR)
PSS008082|
East Asian Ancestry|
698 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): -0.0376 [-0.1126, 0.0378] sex, age, birth date, deprivation index, 16 PCs
PPM010761 PGS001985
(portability-PLR_logMAR)
PSS007869|
African Ancestry|
1,407 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0259 [-0.0268, 0.0784] sex, age, birth date, deprivation index, 16 PCs
PPM010762 PGS001985
(portability-PLR_logMAR)
PSS008973|
African Ancestry|
2,025 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): -0.0189 [-0.0627, 0.0249] sex, age, birth date, deprivation index, 16 PCs
PPM010756 PGS001985
(portability-PLR_logMAR)
PSS009199|
European Ancestry|
1,340 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: logMAR in round (left/right) Partial Correlation (partial-r): 0.0299 [-0.0241, 0.0837] sex, age, birth date, deprivation index, 16 PCs
PPM011680 PGS002103
(portability-ldpred2_avMSE)
PSS009386|
European Ancestry|
4,208 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.3473 [0.3203, 0.3736] sex, age, birth date, deprivation index, 16 PCs
PPM011681 PGS002103
(portability-ldpred2_avMSE)
PSS009160|
European Ancestry|
1,144 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.3219 [0.2685, 0.3734] sex, age, birth date, deprivation index, 16 PCs
PPM011682 PGS002103
(portability-ldpred2_avMSE)
PSS008714|
European Ancestry|
2,005 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.2905 [0.2497, 0.3303] sex, age, birth date, deprivation index, 16 PCs
PPM011683 PGS002103
(portability-ldpred2_avMSE)
PSS008488|
Greater Middle Eastern Ancestry|
440 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.2346 [0.1421, 0.3231] sex, age, birth date, deprivation index, 16 PCs
PPM011684 PGS002103
(portability-ldpred2_avMSE)
PSS008266|
South Asian Ancestry|
2,632 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.2366 [0.2001, 0.2725] sex, age, birth date, deprivation index, 16 PCs
PPM011685 PGS002103
(portability-ldpred2_avMSE)
PSS008044|
East Asian Ancestry|
634 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.1513 [0.073, 0.2277] sex, age, birth date, deprivation index, 16 PCs
PPM011687 PGS002103
(portability-ldpred2_avMSE)
PSS008934|
African Ancestry|
1,910 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.0959 [0.051, 0.1404] sex, age, birth date, deprivation index, 16 PCs
PPM011686 PGS002103
(portability-ldpred2_avMSE)
PSS007830|
African Ancestry|
1,331 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: avMSE Partial Correlation (partial-r): 0.0923 [0.0384, 0.1457] sex, age, birth date, deprivation index, 16 PCs
PPM017421 PGS003493
(cont-decay-avMSE)
PSS010892|
European Ancestry|
4,334 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.12 sex, age, deprivation index, PC1-16
PPM017505 PGS003493
(cont-decay-avMSE)
PSS010808|
European Ancestry|
1,138 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.1 sex, age, deprivation index, PC1-16
PPM017589 PGS003493
(cont-decay-avMSE)
PSS010640|
European Ancestry|
1,952 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.08 sex, age, deprivation index, PC1-16
PPM017673 PGS003493
(cont-decay-avMSE)
PSS010556|
Greater Middle Eastern Ancestry|
432 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.05 sex, age, deprivation index, PC1-16
PPM017757 PGS003493
(cont-decay-avMSE)
PSS010220|
European Ancestry|
467 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.11 sex, age, deprivation index, PC1-16
PPM017841 PGS003493
(cont-decay-avMSE)
PSS010472|
South Asian Ancestry|
2,604 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.06 sex, age, deprivation index, PC1-16
PPM017925 PGS003493
(cont-decay-avMSE)
PSS010388|
East Asian Ancestry|
631 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.03 sex, age, deprivation index, PC1-16
PPM018009 PGS003493
(cont-decay-avMSE)
PSS010304|
African Ancestry|
1,322 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE partial-R2: 0.01 sex, age, deprivation index, PC1-16
PPM018093 PGS003493
(cont-decay-avMSE)
PSS010724|
African Ancestry|
1,891 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: avMSE 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
PSS009160 1,144 individuals European Poland (NE Europe) UKB
PSS008266 2,632 individuals South Asian India (South Asia) UKB
PSS008527 473 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009425 4,973 individuals European UK (+ Ireland) UKB
PSS010808 1,138 individuals,
36.0 % Male samples
Mean = 54.7 years
Sd = 8.0 years
European Polish UKB
PSS010556 432 individuals,
56.0 % Male samples
Mean = 52.8 years
Sd = 8.2 years
Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB
PSS008934 1,910 individuals African unspecified Nigeria (West Africa) UKB
PSS010304 1,322 individuals,
37.0 % Male samples
Mean = 52.8 years
Sd = 7.9 years
African American or Afro-Caribbean Caribbean UKB
PSS008044 634 individuals East Asian China (East Asia) UKB
PSS009199 1,340 individuals European Poland (NE Europe) UKB
PSS008305 2,803 individuals South Asian India (South Asia) UKB
PSS008714 2,005 individuals European Italy (South Europe) UKB
PSS010724 1,891 individuals,
43.0 % Male samples
Mean = 52.2 years
Sd = 8.1 years
African unspecified Nigerian UKB
PSS008973 2,025 individuals African unspecified Nigeria (West Africa) UKB
PSS010472 2,604 individuals,
54.0 % Male samples
Mean = 53.6 years
Sd = 8.4 years
South Asian Indian UKB
PSS008082 698 individuals East Asian China (East Asia) UKB
PSS010220 467 individuals,
43.0 % Male samples
Mean = 58.9 years
Sd = 6.9 years
European Ashkenazi UKB
PSS007830 1,331 individuals African American or Afro-Caribbean Carribean UKB
PSS008488 440 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009386 4,208 individuals European UK (+ Ireland) UKB
PSS008753 2,200 individuals European Italy (South Europe) UKB
PSS010892 4,334 individuals,
48.0 % Male samples
Mean = 57.1 years
Sd = 8.0 years
European white British UKB
PSS010640 1,952 individuals,
44.0 % Male samples
Mean = 54.5 years
Sd = 8.6 years
European Italian UKB
PSS010388 631 individuals,
31.0 % Male samples
Mean = 53.8 years
Sd = 8.1 years
East Asian Chinese UKB
PSS007869 1,407 individuals African American or Afro-Caribbean Carribean UKB