Trait: skin carcinoma in situ

Trait Information
Identifier MONDO_0004641
Description A in situ carcinoma that involves the zone of skin. [MONDO: patterns/location]
Trait category
Cancer
Synonyms 18 synonyms
  • carcinoma in situ of skin
  • carcinoma in situ of the skin
  • carcinoma in situ of zone of skin
  • carcinoma of skin stage 0
  • carcinoma of the skin stage 0
  • cutaneous carcinoma in situ
  • nonmelanoma carcinoma in situ
  • skin cancer stage 0
  • skin carcinoma in situ
  • skin carcinoma stage 0
  • stage 0 nonmelanoma skin carcinoma in situ
  • stage 0 skin cancer
  • stage 0 skin cancer aJCC v6
  • stage 0 skin cancer aJCC v7
  • stage 0 skin carcinoma
  • stage 0 zone of skin carcinoma
  • zone of skin carcinoma in situ
  • zone of skin in situ carcinoma
Mapped term(s) 23 mapped terms
  • COHD:138996
  • DOID:8687
  • ICD10:D04
  • ICD10:D04.0
  • ICD10:D04.2
  • ICD10:D04.3
  • ICD10:D04.4
  • ICD10:D04.6
  • ICD10:D04.7
  • ICD10:D04.9
  • ICD9:232
  • ICD9:232.0
  • ICD9:232.2
  • ICD9:232.3
  • ICD9:232.4
  • ICD9:232.5
  • ICD9:232.6
  • ICD9:232.7
  • ICD9:232.8
  • ICD9:232.9
  • NCIT:C3640
  • SCTID:92749008
  • UMLS:C0154073

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000469 PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Carcinoma in situ of skin skin carcinoma in situ 1,119,238 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000469/ScoringFiles/PGS000469.txt.gz
PGS000470 PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Carcinoma in situ of skin skin carcinoma in situ 5 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000470/ScoringFiles/PGS000470.txt.gz
PGS000471 PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Carcinoma in situ of skin skin carcinoma in situ 7 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000471/ScoringFiles/PGS000471.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001156 PGS000471 (PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608) PSS000547 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Carcinoma in situ of skin OR: 1.401 [1.297, 1.513]
β: 0.337 (0.0393)
AUROC: 0.569 [0.541, 0.595] Nagelkerke's Pseudo-R²: 0.0255
Brier score: 0.0923
Odds Ratio (OR, top 1% vs. Rest): 3.77 [2.24, 6.34]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608
PPM001155 PGS000470 (PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608) PSS000547 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Carcinoma in situ of skin OR: 1.308 [1.208, 1.417]
β: 0.269 (0.0407)
AUROC: 0.557 [0.531, 0.582] Nagelkerke's Pseudo-R²: 0.0154
Brier score: 0.093
Odds Ratio (OR, top 1% vs. Rest): 2.45 [1.34, 4.45]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PT_MGI_20200608
PPM001154 PGS000469 (PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PRS-CS_MGI_20200608) PSS000547 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Carcinoma in situ of skin OR: 1.09 [1.001, 1.188]
β: 0.0865 (0.0437)
AUROC: 0.524 [0.499, 0.549] Nagelkerke's Pseudo-R²: 0.00141
Brier score: 0.0939
Odds Ratio (OR, top 1% vs. Rest): 1.48 [0.703, 3.1]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_PRS-CS_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000547 PheCode:172.3; ICD9CM:232.0, 232.1, 232.2, 232.3, 232.4, 232.5, 232.6, 232.7, 232.8, 232.9; ICD10CM:D04, D04.0, D04.1, D04.10, D04.11, D04.12, D04.2, D04.20, D04.21, D04.22, D04.3, D04.30, D04.39, D04.4, D04.5, D04.6, D04.60, D04.61, D04.62, D04.7, D04.70, D04.71, D04.72, D04.8, D04.9
[
  • 585 cases
  • , 4,915 controls
]
European MGI