Polygenic Score (PGS) ID: PGS002046

Predicted Trait
Reported Trait Otosclerosis
Mapped Trait(s) otosclerosis (EFO_0004213)
Additional Trait Information sense organs
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_383
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 570,308
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM011232 PSS009309|
European Ancestry|
19,770 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Otosclerosis Partial Correlation (partial-r): 0.0182 [0.0043, 0.0321] sex, age, birth date, deprivation index, 16 PCs
PPM011233 PSS009083|
European Ancestry|
4,097 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Otosclerosis Partial Correlation (partial-r): 0.0328 [0.0021, 0.0634] sex, age, birth date, deprivation index, 16 PCs
PPM011234 PSS008637|
European Ancestry|
6,611 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Otosclerosis Partial Correlation (partial-r): -0.0025 [-0.0266, 0.0217] sex, age, birth date, deprivation index, 16 PCs
PPM011235 PSS008411|
Greater Middle Eastern Ancestry|
1,182 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Otosclerosis Partial Correlation (partial-r): 0.0315 [-0.026, 0.0889] sex, age, birth date, deprivation index, 16 PCs
PPM011236 PSS008191|
South Asian Ancestry|
6,238 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Otosclerosis Partial Correlation (partial-r): 0.0251 sex, age, birth date, deprivation index, 16 PCs
PPM011237 PSS007756|
African Ancestry|
2,469 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Otosclerosis Partial Correlation (partial-r): 0.0104 [-0.0293, 0.0499] 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
PSS007756 2,469 individuals African American or Afro-Caribbean Carribean UKB
PSS008637 6,611 individuals European Italy (South Europe) UKB
PSS009083 4,097 individuals European Poland (NE Europe) UKB
PSS008411 1,182 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009309 19,770 individuals European UK (+ Ireland) UKB
PSS008191 6,238 individuals South Asian India (South Asia) UKB