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 8 mapped terms
  • DOID:4448
  • MEDGEN:7434
  • MESH:D008268
  • MONDO:0003004
  • MedDRA:10025409
  • NCIT:C123330
  • SCTID:422338006
  • UMLS:C0024437
Child trait(s) age-related macular degeneration

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
Note: This table shows all PGS for "macular degeneration" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001013
(GBE_BIN_FC5006148)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Macular degeneration macular degeneration 53
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001013/ScoringFiles/PGS001013.txt.gz
PGS001834
(portability-PLR_362.29)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Macular degeneration (senile) of retina NOS age-related macular degeneration 157
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001834/ScoringFiles/PGS001834.txt.gz
PGS002041
(portability-ldpred2_362.29)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Macular degeneration (senile) of retina NOS age-related macular degeneration 116,538
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002041/ScoringFiles/PGS002041.txt.gz
PGS002269
(PRS47_AMD)
 PGP000299 |
Zekavat SM et al. Ophthalmology (2022)
 Age-related macular degeneration age-related macular degeneration 47
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002269/ScoringFiles/PGS002269.txt.gz
PGS004606
(AMD-IAMDGC-EUR)
 PGP000582 |
Gorman BR et al. medRxiv (2022)
|Pre		 Age-related macular degeneration age-related macular degeneration 1,000,946
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004606/ScoringFiles/PGS004606.txt.gz
PGS004607
(AMD-MVP-AFR)
 PGP000582 |
Gorman BR et al. medRxiv (2022)
|Pre		 Age-related macular degeneration age-related macular degeneration 1,067,520
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004607/ScoringFiles/PGS004607.txt.gz
PGS004952
(PRS52_AMD)
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Age-related macular degeneration age-related macular degeneration 52
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004952/ScoringFiles/PGS004952.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. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.7052 [0.63504, 0.77537] R²: 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. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.90123 [0.8354, 0.96707] R²: 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. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.72878 [0.69745, 0.76011] R²: 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. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.76624 [0.71098, 0.8215] R²: 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. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Macular degeneration — AUROC: 0.70257 [0.6826, 0.72253] R²: 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
PPM009565 PGS001834
(portability-PLR_362.29)
 PSS009078|
European Ancestry|
4,043 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0258 [-0.0051, 0.0567] sex, age, birth date, deprivation index, 16 PCs —
PPM009566 PGS001834
(portability-PLR_362.29)
 PSS008632|
European Ancestry|
6,470 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0177 [-0.0067, 0.0421] sex, age, birth date, deprivation index, 16 PCs —
PPM009567 PGS001834
(portability-PLR_362.29)
 PSS008406|
Greater Middle Eastern Ancestry|
1,165 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): -0.03 [-0.0877, 0.028] sex, age, birth date, deprivation index, 16 PCs —
PPM009568 PGS001834
(portability-PLR_362.29)
 PSS008186|
South Asian Ancestry|
6,037 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0368 [0.0116, 0.062] sex, age, birth date, deprivation index, 16 PCs —
PPM009569 PGS001834
(portability-PLR_362.29)
 PSS007970|
East Asian Ancestry|
1,775 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): -0.0304 [-0.0771, 0.0164] sex, age, birth date, deprivation index, 16 PCs —
PPM009570 PGS001834
(portability-PLR_362.29)
 PSS007752|
African Ancestry|
2,374 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0015 [-0.0389, 0.0419] sex, age, birth date, deprivation index, 16 PCs —
PPM009571 PGS001834
(portability-PLR_362.29)
 PSS008856|
African Ancestry|
3,723 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0144 [-0.0178, 0.0466] sex, age, birth date, deprivation index, 16 PCs —
PPM009564 PGS001834
(portability-PLR_362.29)
 PSS009304|
European Ancestry|
19,413 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0175 [0.0034, 0.0315] sex, age, birth date, deprivation index, 16 PCs —
PPM011195 PGS002041
(portability-ldpred2_362.29)
 PSS009078|
European Ancestry|
4,043 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0248 [-0.0061, 0.0556] sex, age, birth date, deprivation index, 16 PCs —
PPM011196 PGS002041
(portability-ldpred2_362.29)
 PSS008632|
European Ancestry|
6,470 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0179 [-0.0065, 0.0423] sex, age, birth date, deprivation index, 16 PCs —
PPM011197 PGS002041
(portability-ldpred2_362.29)
 PSS008406|
Greater Middle Eastern Ancestry|
1,165 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): -0.0344 [-0.0921, 0.0236] sex, age, birth date, deprivation index, 16 PCs —
PPM011198 PGS002041
(portability-ldpred2_362.29)
 PSS008186|
South Asian Ancestry|
6,037 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0372 [0.0119, 0.0624] sex, age, birth date, deprivation index, 16 PCs —
PPM011199 PGS002041
(portability-ldpred2_362.29)
 PSS007970|
East Asian Ancestry|
1,775 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): -0.0312 [-0.0779, 0.0156] sex, age, birth date, deprivation index, 16 PCs —
PPM011200 PGS002041
(portability-ldpred2_362.29)
 PSS007752|
African Ancestry|
2,374 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0038 [-0.0366, 0.0442] sex, age, birth date, deprivation index, 16 PCs —
PPM011201 PGS002041
(portability-ldpred2_362.29)
 PSS008856|
African Ancestry|
3,723 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.018 [-0.0143, 0.0501] sex, age, birth date, deprivation index, 16 PCs —
PPM011194 PGS002041
(portability-ldpred2_362.29)
 PSS009304|
European Ancestry|
19,413 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Macular degeneration (senile) of retina NOS — — Partial Correlation (partial-r): 0.0159 [0.0018, 0.0299] sex, age, birth date, deprivation index, 16 PCs —
PPM012920 PGS002269
(PRS47_AMD)
 PSS009618|
Multi-ancestry (including European)|
44,823 individuals
 PGP000299 |
Zekavat SM et al. Ophthalmology (2022)
 Reported Trait: Rentinal layer thickness (photoreceptor inner and outer segments) β: -0.21 [-0.23, -0.19] — — Age, age2 (to adjust for non-linear relationships with age), sex, smoking status, and the first ten principal components of genetic ancestry —
PPM012921 PGS002269
(PRS47_AMD)
 PSS009618|
Multi-ancestry (including European)|
44,823 individuals
 PGP000299 |
Zekavat SM et al. Ophthalmology (2022)
 Reported Trait: Rentinal layer thickness (retinal pigment epithelium and Bruch’s membrane complex) β: -0.14 [-0.16, -0.12] — — Age, age2 (to adjust for non-linear relationships with age), sex, smoking status, and the first ten principal components of genetic ancestry —
PPM012922 PGS002269
(PRS47_AMD)
 PSS009618|
Multi-ancestry (including European)|
44,823 individuals
 PGP000299 |
Zekavat SM et al. Ophthalmology (2022)
 Reported Trait: Rentinal layer thickness (choroid-sclera interface) β: -0.03 [-0.06, -0.01] — — Age, age2 (to adjust for non-linear relationships with age), sex, smoking status, and the first ten principal components of genetic ancestry —
PPM020767 PGS004606
(AMD-IAMDGC-EUR)
 PSS011398|
European Ancestry|
163,011 individuals
 PGP000582 |
Gorman BR et al. medRxiv (2022)
|Pre		 Reported Trait: Age-related macular degeneration OR: 1.76 [1.73, 1.78] AUROC: 0.71 — age, sex, principal components 1-10 —
PPM020768 PGS004607
(AMD-MVP-AFR)
 PSS011398|
European Ancestry|
163,011 individuals
 PGP000582 |
Gorman BR et al. medRxiv (2022)
|Pre		 Reported Trait: Age-related macular degeneration OR: 1.48 [1.34, 1.63] AUROC: 0.65 — age, sex, principal components 1-10 —
PPM021759 PGS004952
(PRS52_AMD)
 PSS011783|
European Ancestry|
1,575 individuals
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Reported Trait: Early age-related macular degeneration (Clinical Classification) OR: 1.13 [1.09, 1.16] AUROC: 64.2 — Age, sex, survey membership, 10 PCs —
PPM021760 PGS004952
(PRS52_AMD)
 PSS011784|
European Ancestry|
1,511 individuals
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Reported Trait: Intermediate age-related macular degeneration (Clinical Classification) OR: 1.25 [1.2, 1.29] AUROC: 73.3 — Age, sex, survey membership, 10 PCs —
PPM021761 PGS004952
(PRS52_AMD)
 PSS011785|
European Ancestry|
1,232 individuals
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Reported Trait: Late age-related macular degeneration (Clinical Classification) OR: 1.41 [1.32, 1.5] AUROC: 84.2 — Age, sex, survey membership, 10 PCs —
PPM021762 PGS004952
(PRS52_AMD)
 PSS011786|
European Ancestry|
1,780 individuals
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Reported Trait: Mild early age-related macular degeneration (3CACSS) OR: 1.08 [1.04, 1.13] AUROC: 59.9 — Age, sex, survey membership, 10 PCs —
PPM021763 PGS004952
(PRS52_AMD)
 PSS011787|
European Ancestry|
1,696 individuals
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Reported Trait: Moderate early age-related macular degeneration (3CACSS) OR: 1.29 [1.22, 1.37] AUROC: 76.3 — Age, sex, survey membership, 10 PCs —
PPM021764 PGS004952
(PRS52_AMD)
 PSS011788|
European Ancestry|
1,699 individuals
 PGP000673 |
Herold JM et al. Invest Ophthalmol Vis Sci (2023)
 Reported Trait: Severe early age-related macular degeneration (3CACSS) OR: 1.38 [1.29, 1.47] AUROC: 80.95 — Age, sex, survey membership, 10 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
PSS007752 — — 2,374 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008406 — — 1,165 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009304 — — 19,413 individuals — European UK (+ Ireland) UKB —
PSS011783 — —
[
  • 510 cases
  • , 1,065 controls
]
 — European — AugUR —
PSS011784 — —
[
  • 446 cases
  • , 1,065 controls
]
 — European — AugUR —
PSS011785 — —
[
  • 167 cases
  • , 1,065 controls
]
 — European — AugUR —
PSS011786 — —
[
  • 203 cases
  • , 1,577 controls
]
 — European — AugUR —
PSS011787 — —
[
  • 119 cases
  • , 1,577 controls
]
 — European — AugUR —
PSS011398 ICD-9-CM codes 362.51 or 362.52; ICD-10-CM codes H35.31 or H35.32 —
[
  • 32,567 cases
  • , 130,444 controls
]
,
97.0 % Male samples
 — European — MVP —
PSS011788 — —
[
  • 122 cases
  • , 1,577 controls
]
 — European — AugUR —
PSS009078 — — 4,043 individuals — European Poland (NE Europe) UKB —
PSS008186 — — 6,037 individuals — South Asian India (South Asia) UKB —
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)
PSS008856 — — 3,723 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007970 — — 1,775 individuals — East Asian China (East Asia) UKB —
PSS009618 AMD phenotype was defined using a combination of main and secondary ICD-10 (Field IDs 41202, 41204: Code H35.3) and ICD-9 (Field IDs 41203, 41205: Code 3625) diagnoses for macular degeneration, self-reported macular degeneration (Field ID 20002: Code 1528), and macular degeneration from the available general practice data. Prevalent AMD cases were defined as individuals who had AMD first diagnosed at or before enrollment. Incident AMD cases were defined as individuals who had AMD first diagnosed after enrollment — 44,253 individuals — European — UKB —
PSS009618 AMD phenotype was defined using a combination of main and secondary ICD-10 (Field IDs 41202, 41204: Code H35.3) and ICD-9 (Field IDs 41203, 41205: Code 3625) diagnoses for macular degeneration, self-reported macular degeneration (Field ID 20002: Code 1528), and macular degeneration from the available general practice data. Prevalent AMD cases were defined as individuals who had AMD first diagnosed at or before enrollment. Incident AMD cases were defined as individuals who had AMD first diagnosed after enrollment — 40 individuals — South Asian — UKB —
PSS009618 AMD phenotype was defined using a combination of main and secondary ICD-10 (Field IDs 41202, 41204: Code H35.3) and ICD-9 (Field IDs 41203, 41205: Code 3625) diagnoses for macular degeneration, self-reported macular degeneration (Field ID 20002: Code 1528), and macular degeneration from the available general practice data. Prevalent AMD cases were defined as individuals who had AMD first diagnosed at or before enrollment. Incident AMD cases were defined as individuals who had AMD first diagnosed after enrollment — 530 individuals — Not reported — UKB —
PSS008632 — — 6,470 individuals — European Italy (South Europe) UKB —