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)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (excluding European)
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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 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

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
PPM001156 PGS000471
(PRSWEB_PHECODE172.3_UKBB-SAIGE-HRC-X172.3_LASSOSUM_MGI_20200608)
PSS000547|
European Ancestry|
5,500 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,500 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
5,500 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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)
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