Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0001365 |
Description | Age-related loss of vision in the central portion of the retina (macula), secondary to retinal degeneration. [NCIT: P378] | Trait category |
Neurological disorder
|
Synonyms |
47 synonyms
|
Mapped terms |
33 mapped terms
|
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) |
---|---|---|---|---|---|---|
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 |
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 |
---|---|---|---|---|---|---|---|---|---|
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 | — |
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 | — |
PSS011783 | — | — | [
|
— | European | — | AugUR | — |
PSS011784 | — | — | [
|
— | European | — | AugUR | — |
PSS011785 | — | — | [
|
— | European | — | AugUR | — |
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 | — |
PSS011398 | ICD-9-CM codes 362.51 or 362.52; ICD-10-CM codes H35.31 or H35.32 | — | [ ,
97.0 % Male samples |
— | European | — | MVP | — |
PSS011786 | — | — | [
|
— | European | — | AugUR | — |
PSS011787 | — | — | [
|
— | European | — | AugUR | — |
PSS011788 | — | — | [
|
— | European | — | AugUR | — |
PSS009078 | — | — | 4,043 individuals | — | European | Poland (NE Europe) | UKB | — |
PSS008406 | — | — | 1,165 individuals | — | Greater Middle Eastern (Middle Eastern, North African or Persian) | Iran (Middle East) | UKB | — |
PSS008632 | — | — | 6,470 individuals | — | European | Italy (South Europe) | UKB | — |
PSS008856 | — | — | 3,723 individuals | — | African unspecified | Nigeria (West Africa) | UKB | — |
PSS008186 | — | — | 6,037 individuals | — | South Asian | India (South Asia) | UKB | — |
PSS009304 | — | — | 19,413 individuals | — | European | UK (+ Ireland) | UKB | — |
PSS007970 | — | — | 1,775 individuals | — | East Asian | China (East Asia) | UKB | — |