PGS Publication: PGP000299

Publication Information (EuropePMC)
Title Photoreceptor Layer Thinning Is an Early Biomarker for Age-Related Macular Degeneration: Epidemiologic and Genetic Evidence from UK Biobank OCT Data.
PubMed ID 35149155(Europe PMC)
doi 10.1016/j.ophtha.2022.02.001
Publication Date Feb. 8, 2022
Journal Ophthalmology
Author(s) Zekavat SM, Sekimitsu S, Ye Y, Raghu V, Zhao H, Elze T, Segrè AV, Wiggs JL, Natarajan P, Del Priore L, Zebardast N, Wang JC.
Released in PGS Catalog: April 1, 2022

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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)
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

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
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 —

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
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 —