Trait: otosclerosis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004213
Description Formation of spongy bone in the labyrinth capsule which can progress toward the stapes (stapedial fixation) or anteriorly toward the cochlea leading to conductive, sensorineural, or mixed hearing loss. Several genes are associated with familial otosclerosis with varied clinical signs. [MESH: D010040]
Trait category
Neurological disorder
Synonyms 3 synonyms
  • otosclerosis
  • otosclerosis (disease)
  • otospongiosis
Mapped terms 17 mapped terms
  • DOID:12185
  • HP:0000362
  • ICD10:H80
  • ICD9:387
  • ICD9:387.8
  • ICD9:387.9
  • MESH:D010040
  • MONDO:0005349
  • MeSH:D010040
  • MedDRA:10033103
  • MedDRA:10033107
  • MedDRA:10033108
  • OMIMPS:166800
  • Orphanet:2794
  • SCTID:11543004
  • SNOMEDCT:11543004
  • UMLS:C0029899

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
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001255
(GBE_HC914)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Otosclerosis (time-to-event) otosclerosis 213
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001255/ScoringFiles/PGS001255.txt.gz
PGS002046
(portability-ldpred2_383)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Otosclerosis otosclerosis 570,308
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002046/ScoringFiles/PGS002046.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
PPM011237 PGS002046
(portability-ldpred2_383)
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
PPM011236 PGS002046
(portability-ldpred2_383)
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
PPM011235 PGS002046
(portability-ldpred2_383)
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
PPM011234 PGS002046
(portability-ldpred2_383)
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
PPM011233 PGS002046
(portability-ldpred2_383)
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
PPM011232 PGS002046
(portability-ldpred2_383)
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
PPM008784 PGS001255
(GBE_HC914)
PSS004705|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE otosclerosis AUROC: 0.6532 [0.60975, 0.69665] : 0.02085
Incremental AUROC (full-covars): 0.05946
PGS R2 (no covariates): 0.01341
PGS AUROC (no covariates): 0.6319 [0.58724, 0.67656]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008783 PGS001255
(GBE_HC914)
PSS004704|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE otosclerosis AUROC: 0.71231 [0.61511, 0.80951] : 0.04349
Incremental AUROC (full-covars): 0.03275
PGS R2 (no covariates): 0.00824
PGS AUROC (no covariates): 0.59763 [0.48884, 0.70642]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008782 PGS001255
(GBE_HC914)
PSS004703|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE otosclerosis AUROC: 0.66807 [0.58985, 0.74629] : 0.03365
Incremental AUROC (full-covars): 0.05467
PGS R2 (no covariates): 0.01522
PGS AUROC (no covariates): 0.62631 [0.54794, 0.70468]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008781 PGS001255
(GBE_HC914)
PSS004702|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE otosclerosis AUROC: 0.91156 [0.77281, 1.0] : 0.29139
Incremental AUROC (full-covars): 0.03981
PGS R2 (no covariates): 0.06779
PGS AUROC (no covariates): 0.7376 [0.46621, 1.0]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS009309 19,770 individuals European UK (+ Ireland) UKB
PSS004703
[
  • 53 cases
  • , 24,852 controls
]
European non-white British ancestry UKB
PSS004704
[
  • 20 cases
  • , 7,811 controls
]
South Asian UKB
PSS004705
[
  • 156 cases
  • , 67,269 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004702
[
  • 4 cases
  • , 6,493 controls
]
African unspecified UKB
PSS007756 2,469 individuals African American or Afro-Caribbean Carribean UKB
PSS009083 4,097 individuals European Poland (NE Europe) UKB
PSS008637 6,611 individuals European Italy (South Europe) UKB
PSS008191 6,238 individuals South Asian India (South Asia) UKB
PSS008411 1,182 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB