Trait: macular degeneration

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009606
Description Loss of vision in the central portion of the retina (macula), secondary to retinal degeneration. [NCIT: P378]
Trait category
Neurological disorder
Synonyms 5 synonyms
  • macula lutea retinal degeneration
  • macula retinal degeneration
  • macular degeneration
  • macular degeneration of retina
  • retinal degeneration of macula lutea
Mapped terms 7 mapped terms
  • DOID:4448
  • MESH:D008268
  • MONDO:0003004
  • MedDRA:10025409
  • NCIT:C123330
  • SCTID:422338006
  • UMLS:C0024437

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)
PGS001013
(GBE_BIN_FC5006148)
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Macular degeneration macular degeneration 53
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001013/ScoringFiles/PGS001013.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
PPM007828 PGS001013
(GBE_BIN_FC5006148)
PSS003974|
African Ancestry|
3,196 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Eye problems/disorders Macular degeneration AUROC: 0.7052 [0.63504, 0.77537] : 0.07369
Incremental AUROC (full-covars): -0.00271
PGS R2 (no covariates): 6e-05
PGS AUROC (no covariates): 0.50582 [0.43466, 0.57699]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007829 PGS001013
(GBE_BIN_FC5006148)
PSS003975|
East Asian Ancestry|
711 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Eye problems/disorders Macular degeneration AUROC: 0.90123 [0.8354, 0.96707] : 0.32752
Incremental AUROC (full-covars): -0.00016
PGS R2 (no covariates): 0.01068
PGS AUROC (no covariates): 0.59339 [0.45683, 0.72996]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007830 PGS001013
(GBE_BIN_FC5006148)
PSS003976|
European Ancestry|
9,755 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Eye problems/disorders Macular degeneration AUROC: 0.72878 [0.69745, 0.76011] : 0.07729
Incremental AUROC (full-covars): 0.00516
PGS R2 (no covariates): 0.00265
PGS AUROC (no covariates): 0.53845 [0.49847, 0.57843]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007831 PGS001013
(GBE_BIN_FC5006148)
PSS003977|
South Asian Ancestry|
3,327 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Eye problems/disorders Macular degeneration AUROC: 0.76624 [0.71098, 0.8215] : 0.10324
Incremental AUROC (full-covars): -0.00396
PGS R2 (no covariates): 0.00053
PGS AUROC (no covariates): 0.47169 [0.39626, 0.54712]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007832 PGS001013
(GBE_BIN_FC5006148)
PSS003978|
European Ancestry|
22,208 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Eye problems/disorders Macular degeneration AUROC: 0.70257 [0.6826, 0.72253] : 0.06704
Incremental AUROC (full-covars): 0.00573
PGS R2 (no covariates): 0.00599
PGS AUROC (no covariates): 0.55283 [0.52939, 0.57627]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003974
[
  • 68 cases
  • , 3,128 controls
]
African unspecified UKB
PSS003975
[
  • 18 cases
  • , 693 controls
]
East Asian UKB
PSS003976
[
  • 235 cases
  • , 9,520 controls
]
European non-white British ancestry UKB
PSS003977
[
  • 63 cases
  • , 3,264 controls
]
South Asian UKB
PSS003978
[
  • 637 cases
  • , 21,571 controls
]
European white British ancestry UKB Testing cohort (heldout set)