Polygenic Score (PGS) ID: PGS002042

Predicted Trait
Reported Trait Corneal dystrophy
Mapped Trait(s) corneal dystrophy (MONDO_0018102)
Additional Trait Information sense organs
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_364.5
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 59,944
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 50%
African: 16.7%
Greater Middle Eastern: 16.7%
South Asian: 16.7%
6 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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) 		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
PPM011202 PSS009305|
European Ancestry|
19,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0471 [0.033, 0.0611] sex, age, birth date, deprivation index, 16 PCs —
PPM011203 PSS009079|
European Ancestry|
4,029 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0812 [0.0504, 0.1119] sex, age, birth date, deprivation index, 16 PCs —
PPM011204 PSS008633|
European Ancestry|
6,462 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0519 [0.0275, 0.0762] sex, age, birth date, deprivation index, 16 PCs —
PPM011205 PSS008407|
Greater Middle Eastern Ancestry|
1,162 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): 0.0275 [-0.0306, 0.0853] sex, age, birth date, deprivation index, 16 PCs —
PPM011206 PSS008187|
South Asian Ancestry|
6,052 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): -0.0133 [-0.0385, 0.0119] sex, age, birth date, deprivation index, 16 PCs —
PPM011207 PSS008857|
African Ancestry|
3,718 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Corneal dystrophy — — Partial Correlation (partial-r): -0.0084 [-0.0406, 0.0238] sex, age, birth date, deprivation index, 16 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
PSS008407 — — 1,162 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009079 — — 4,029 individuals — European Poland (NE Europe) UKB —
PSS008633 — — 6,462 individuals — European Italy (South Europe) UKB —
PSS009305 — — 19,321 individuals — European UK (+ Ireland) UKB —
PSS008187 — — 6,052 individuals — South Asian India (South Asia) UKB —
PSS008857 — — 3,718 individuals — African unspecified Nigeria (West Africa) UKB —