Trait: hearing loss

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004238
Description A partial or complete loss of hearing in one or both ears. It is classified as conductive, sensory, or central. [NCIT: C35731]
Trait category
Neurological disorder
Synonyms 8 synonyms
  • deafness
  • hearing impairment
  • hearing loss
  • hearing loss disorder
  • hypoacuses
  • hypoacusis
  • loss of hearing
  • loss, hearing
Mapped terms 15 mapped terms
  • ICD10:H91
  • ICD10CM:H90
  • ICD9:389
  • ICD9:389.8
  • ICD9:389.9
  • MEDGEN:235586
  • MESH:D034381
  • MONDO:0005365
  • MeSH:D034381
  • MedDRA:10019246
  • NCIT:C35731
  • NCIt:C35731
  • SCTID:15188001
  • SNOMEDCT:15188001
  • UMLS:C1384666
Child trait(s) 2 child traits

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
Note: This table shows all PGS for "hearing loss" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS000762
(PRS_HD)
 PGP000165 |
Cherny SS et al. Eur J Hum Genet (2020)
 Hearing difficulty age-related hearing impairment 100,325
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000762/ScoringFiles/PGS000762.txt.gz
PGS000763
(PRS_HAID)
 PGP000165 |
Cherny SS et al. Eur J Hum Genet (2020)
 Hearing aid use age-related hearing impairment 4,270
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000763/ScoringFiles/PGS000763.txt.gz
PGS001252
(GBE_BIN_FC3002247)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Hearing difficulty and deafness deafness,
hearing loss		 3,731
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001252/ScoringFiles/PGS001252.txt.gz
PGS001253
(GBE_BIN_FC1002247)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Hearing difficulty hearing loss 3,098
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001253/ScoringFiles/PGS001253.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
PPM001938 PGS000762
(PRS_HD)
 PSS000972|
European Ancestry|
3,636 individuals
 PGP000165 |
Cherny SS et al. Eur J Hum Genet (2020)
 Reported Trait: Hearing difficulties — — R²: 0.0911 Age, sex —
PPM001937 PGS000763
(PRS_HAID)
 PSS000971|
European Ancestry|
2,912 individuals
 PGP000165 |
Cherny SS et al. Eur J Hum Genet (2020)
 Reported Trait: Hearing aid use — — R²: 0.1923 Age, sex —
PPM008769 PGS001252
(GBE_BIN_FC3002247)
 PSS003899|
African Ancestry|
6,123 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.58635 [0.56411, 0.60859] R²: 0.01752
Incremental AUROC (full-covars): -0.00041
PGS R2 (no covariates): 0.00138
PGS AUROC (no covariates): 0.52307 [0.50054, 0.54561]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008770 PGS001252
(GBE_BIN_FC3002247)
 PSS003900|
East Asian Ancestry|
1,568 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62777 [0.58865, 0.66688] R²: 0.04973
Incremental AUROC (full-covars): 0.00284
PGS R2 (no covariates): 0.00305
PGS AUROC (no covariates): 0.53516 [0.49316, 0.57716]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008771 PGS001252
(GBE_BIN_FC3002247)
 PSS003901|
European Ancestry|
23,697 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62252 [0.61446, 0.63058] R²: 0.05132
Incremental AUROC (full-covars): 0.00531
PGS R2 (no covariates): 0.00527
PGS AUROC (no covariates): 0.53867 [0.53034, 0.54699]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008772 PGS001252
(GBE_BIN_FC3002247)
 PSS003902|
South Asian Ancestry|
7,266 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.61586 [0.5994, 0.63232] R²: 0.04282
Incremental AUROC (full-covars): 0.00304
PGS R2 (no covariates): 0.00345
PGS AUROC (no covariates): 0.53204 [0.5154, 0.54867]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008773 PGS001252
(GBE_BIN_FC3002247)
 PSS003903|
European Ancestry|
65,065 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62548 [0.62074, 0.63023] R²: 0.05558
Incremental AUROC (full-covars): 0.00728
PGS R2 (no covariates): 0.00646
PGS AUROC (no covariates): 0.54216 [0.53723, 0.54709]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008774 PGS001253
(GBE_BIN_FC1002247)
 PSS003755|
African Ancestry|
6,121 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.58714 [0.56491, 0.60938] R²: 0.01786
Incremental AUROC (full-covars): 0.00082
PGS R2 (no covariates): 0.00162
PGS AUROC (no covariates): 0.52504 [0.50255, 0.54753]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008775 PGS001253
(GBE_BIN_FC1002247)
 PSS003756|
East Asian Ancestry|
1,568 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.62831 [0.58912, 0.6675] R²: 0.04992
Incremental AUROC (full-covars): 0.00338
PGS R2 (no covariates): 0.003
PGS AUROC (no covariates): 0.53605 [0.49383, 0.57827]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008776 PGS001253
(GBE_BIN_FC1002247)
 PSS003757|
European Ancestry|
23,689 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.62276 [0.6147, 0.63082] R²: 0.0516
Incremental AUROC (full-covars): 0.00532
PGS R2 (no covariates): 0.00515
PGS AUROC (no covariates): 0.53825 [0.52992, 0.54658]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008777 PGS001253
(GBE_BIN_FC1002247)
 PSS003758|
South Asian Ancestry|
7,257 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.61668 [0.60019, 0.63317] R²: 0.04334
Incremental AUROC (full-covars): 0.00291
PGS R2 (no covariates): 0.00324
PGS AUROC (no covariates): 0.53126 [0.51459, 0.54793]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008778 PGS001253
(GBE_BIN_FC1002247)
 PSS003759|
European Ancestry|
65,054 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.62552 [0.62077, 0.63026] R²: 0.05561
Incremental AUROC (full-covars): 0.00726
PGS R2 (no covariates): 0.00632
PGS AUROC (no covariates): 0.54175 [0.53682, 0.54668]		 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
PSS003900 — —
[
  • 214 cases
  • , 1,354 controls
]
 — East Asian — UKB —
PSS003901 — —
[
  • 6,214 cases
  • , 17,483 controls
]
 — European non-white British ancestry UKB —
PSS003902 — —
[
  • 1,425 cases
  • , 5,841 controls
]
 — South Asian — UKB —
PSS003903 — —
[
  • 18,231 cases
  • , 46,834 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS000971 Hearing aid use cases responded ‘Yes’ to either ‘Do you wear a hearing aid?’ or ‘Wearing a hearing aid’ while controls responded ‘No’. —
[
  • 216 cases
  • , 2,696 controls
]
,
8.0 % Male samples
 Mean = 59.32 years
Sd = 9.69 years		 European
(British)		 — TwinsUK —
PSS000972 Hearing difficulty cases were defined as responding either ‘Yes, diagnosed by doctor or health professional’ or ‘Yes, not diagnosed by health professional’ to ‘Do you suffer from hearing loss?’ while participants that responded ‘No’ were assigned as controls. —
[
  • 970 cases
  • , 2,666 controls
]
,
8.5 % Male samples
 Mean = 60.34 years
Sd = 10.18 years		 European
(British)		 — TwinsUK —
PSS003755 — —
[
  • 697 cases
  • , 5,424 controls
]
 — African unspecified — UKB —
PSS003756 — —
[
  • 214 cases
  • , 1,354 controls
]
 — East Asian — UKB —
PSS003757 — —
[
  • 6,205 cases
  • , 17,484 controls
]
 — European non-white British ancestry UKB —
PSS003758 — —
[
  • 1,416 cases
  • , 5,841 controls
]
 — South Asian — UKB —
PSS003759 — —
[
  • 18,220 cases
  • , 46,834 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003899 — —
[
  • 699 cases
  • , 5,424 controls
]
 — African unspecified — UKB —