Trait: seborrheic keratosis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005584
Description A common benign skin neoplasm usually affecting older individuals. The lesions usually are multiple and arise in the face, chest, and shoulders. They appear as black or brown, slightly elevated skin lesions. [NCIT: P378]
Trait category
Other disease
Synonyms 7 synonyms
  • basal cell papilloma
  • keratosis Seborrheica
  • keratosis, seborrheic
  • keratosis, seborrheic, somatic
  • seborrheic keratosis
  • seborrheic verruca
  • senile wart
Mapped terms 16 mapped terms
  • DOID:6498
  • ICD10:L82
  • ICD10CM:L82
  • ICD9:702.1
  • MESH:D017492
  • MONDO:0008420
  • MeSH:D017492
  • MedDRA:10039791
  • NCIT:C9006
  • NCIt:C9006
  • OMIM:182000
  • SCTID:398838000
  • SNOMEDCT:25499005
  • SNOMEDCT:398838000
  • UMLS:C0022603
  • Wikipedia:Seborrheic_keratosis

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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001140
(GBE_HC1190)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Seborrheic keratosis (time-to-event) seborrheic keratosis 1,368
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001140/ScoringFiles/PGS001140.txt.gz
PGS002085
(portability-ldpred2_702.2)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Seborrheic keratosis seborrheic keratosis 481,233
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002085/ScoringFiles/PGS002085.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
PPM008427 PGS001140
(GBE_HC1190)
 PSS004178|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.69791 [0.62772, 0.7681] R²: 0.0531
Incremental AUROC (full-covars): 0.01676
PGS R2 (no covariates): 0.01004
PGS AUROC (no covariates): 0.5859 [0.50622, 0.66558]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008428 PGS001140
(GBE_HC1190)
 PSS004179|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.74674 [0.66312, 0.83035] R²: 0.10541
Incremental AUROC (full-covars): -0.00457
PGS R2 (no covariates): 0.01744
PGS AUROC (no covariates): 0.62007 [0.51848, 0.72165]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008429 PGS001140
(GBE_HC1190)
 PSS004180|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.63238 [0.61781, 0.64695] R²: 0.03162
Incremental AUROC (full-covars): 0.01328
PGS R2 (no covariates): 0.00595
PGS AUROC (no covariates): 0.55636 [0.54088, 0.57185]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008430 PGS001140
(GBE_HC1190)
 PSS004181|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.65125 [0.6056, 0.6969] Incremental AUROC (full-covars): 0.00972
R²: 0.03155
PGS R2 (no covariates): 0.00354
PGS AUROC (no covariates): 0.54802 [0.49607, 0.59996]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008431 PGS001140
(GBE_HC1190)
 PSS004182|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.62735 [0.61905, 0.63565] R²: 0.03214
Incremental AUROC (full-covars): 0.01502
PGS R2 (no covariates): 0.00744
PGS AUROC (no covariates): 0.56248 [0.55356, 0.57141]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM011540 PGS002085
(portability-ldpred2_702.2)
 PSS009349|
European Ancestry|
19,837 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0237 [0.0098, 0.0376] sex, age, birth date, deprivation index, 16 PCs —
PPM011541 PGS002085
(portability-ldpred2_702.2)
 PSS009123|
European Ancestry|
4,111 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.03 sex, age, birth date, deprivation index, 16 PCs —
PPM011542 PGS002085
(portability-ldpred2_702.2)
 PSS008677|
European Ancestry|
6,626 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0128 [-0.0113, 0.0369] sex, age, birth date, deprivation index, 16 PCs —
PPM011543 PGS002085
(portability-ldpred2_702.2)
 PSS008451|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0512 [-0.006, 0.108] sex, age, birth date, deprivation index, 16 PCs —
PPM011544 PGS002085
(portability-ldpred2_702.2)
 PSS008231|
South Asian Ancestry|
6,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): -0.0097 [-0.0344, 0.015] sex, age, birth date, deprivation index, 16 PCs —
PPM011545 PGS002085
(portability-ldpred2_702.2)
 PSS008011|
East Asian Ancestry|
1,807 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): -0.0149 [-0.0612, 0.0315] sex, age, birth date, deprivation index, 16 PCs —
PPM011546 PGS002085
(portability-ldpred2_702.2)
 PSS007796|
African Ancestry|
2,483 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0158 [-0.0237, 0.0553] sex, age, birth date, deprivation index, 16 PCs —
PPM011547 PGS002085
(portability-ldpred2_702.2)
 PSS008900|
African Ancestry|
3,922 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): -0.0283 [-0.0596, 0.0031] 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
PSS008900 — — 3,922 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009349 — — 19,837 individuals — European UK (+ Ireland) UKB —
PSS008677 — — 6,626 individuals — European Italy (South Europe) UKB —
PSS008231 — — 6,321 individuals — South Asian India (South Asia) UKB —
PSS008451 — — 1,197 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008011 — — 1,807 individuals — East Asian China (East Asia) UKB —
PSS007796 — — 2,483 individuals — African American or Afro-Caribbean Carribean UKB —
PSS004178 — —
[
  • 54 cases
  • , 6,443 controls
]
 — African unspecified — UKB —
PSS004179 — —
[
  • 37 cases
  • , 1,667 controls
]
 — East Asian — UKB —
PSS004180 — —
[
  • 1,295 cases
  • , 23,610 controls
]
 — European non-white British ancestry UKB —
PSS004181 — —
[
  • 113 cases
  • , 7,718 controls
]
 — South Asian — UKB —
PSS004182 — —
[
  • 4,266 cases
  • , 63,159 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS009123 — — 4,111 individuals — European Poland (NE Europe) UKB —