Trait: cutaneous melanoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000389
Description A primary melanoma arising from atypical melanocytes in the skin. Precursor lesions include acquired and congenital melanocytic nevi, and dysplastic nevi. Several histologic variants have been recognized, including superficial spreading melanoma, acral lentiginous melanoma, nodular melanoma, and lentigo maligna melanoma. [NCIT: C3510]
Trait category
Cancer
Synonyms 50 synonyms
  • cutaneous melanoma
  • Melanoma of the Skin
  • malignant melanoma (of skin), stage unspecified
  • [X]Malignant melanoma of skin, unspecified
  • Melanoma of skin, site unspecified
  • Malignant Melanoma of Skin
  • melanoma of the skin
  • Malignant melanoma of skin (disorder)
  • malignant scalp melanoma
  • Malignant melanoma of skin NOS
  • malignant melanoma of skin stage unspecified
  • MM - Malignant melanoma of skin
  • Malignant melanoma of other specified skin site
  • zone of skin melanoma (disease)
  • Malignant Melanoma (of Skin), Stage Unspecified
  • malignant lower limb melanoma
  • cancer of skin
  • Melanoma of Skin
  • malignant melanoma of skin
  • malignant neck melanoma
  • malignant melanoma of skin of trunk except scrotum
  • Cutaneous malignant melanoma
  • Malignant melanoma of skin NOS (disorder)
  • melanoma of skin
  • Malignant melanoma of skin of other and unspecified parts of face
  • malignant lip melanoma
  • malignant ear melanoma
  • Malignant Cutaneous Melanoma
  • Malignant melanoma of skin, NOS
  • malignant trunk melanoma
  • malignant melanoma of ear and/or external auricular canal
  • Malignant melanoma of other specified skin site (disorder)
  • zone of skin melanoma
  • MALIG MELANOMA SKIN NEC
  • cutaneous melanoma (disease)
  • malignant melanoma of skin of lower limb
  • melanoma (disease) of zone of skin
  • Malignant melanoma of other specified sites of skin
  • [X]Malignant melanoma of skin, unspecified (disorder)
  • MALIG MELANOMA SKIN NOS
  • Malignant Melanoma of Skin Stage Unspecified
  • cutaneous (skin) melanoma
  • malignant cutaneous melanoma
  • skin, melanoma
  • malignant melanoma of skin of upper limb
  • malignant upper limb melanoma
  • Skin Melanoma
  • Skin, Melanoma
  • skin melanoma
  • MAL MELANOM FACE NEC/NOS
Mapped term(s) 26 mapped terms
  • SNOMEDCT:93655004
  • OMIM:155600
  • ICD9:172.0
  • SCTID:93655004
  • ICD9:172.3
  • ICD9:172.4
  • ICD9:172.2
  • OMIM:615848
  • NCIt:C3510
  • ICD9:172.8
  • ICD9:172.5
  • ICD9:172.9
  • ICD9:172
  • NCIT:C3510
  • ICD10:C43
  • UMLS:C0151779
  • UMLS:C0153536
  • UMLS:C0153535
  • DOID:8923
  • ICD10:C43.0
  • HP:0012056
  • ICD10:C43.4
  • ICD10:C43.2
  • MONDO:0005012
  • ONCOTREE:SKCM
  • ICD10:C43.9

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)
PGS000339 PRS22_CM PGP000106 Law MH et al. Hum Mol Genet (2020) Cutaneous melanoma cutaneous melanoma 22 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000339/ScoringFiles/PGS000339.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
PPM000922 PGS000339 (PRS22_CM) PSS000464 PGP000106
Law MH et al. (2020)
Reported Trait: Cutaneous melanoma in multiplex melanoma families Difference of PRS (deltaPRS; unaffected melanoma family members vs. unrelated controls): 0.347 PCs (1-10) *Sample overlap between the controls used in this analysis and score development
PPM000921 PGS000339 (PRS22_CM) PSS000463 PGP000106
Law MH et al. (2020)
Reported Trait: Cutaneous melanoma in multiplex melanoma families Difference of PRS (deltaPRS; melanoma family cases vs. unrelated controls): 0.505 PCs (1-10) *Sample overlap between the controls used in this analysis and score development

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
PSS000464 Unaffected family members from families with increased melaona risk. Recruited families were ranked as low-, medium- or high-risk using a risk index (T) that factored in the number of confirmed cases of melanoma versus number of unaffected family members, ages and year of birth
[
  • 111 cases
  • , 1,774 controls
]
,
46.37 % Male samples
European Australia BATS, QFMP
PSS000463 Unaffected family members from families with increased melaona risk. Recruited families were ranked as low-, medium- or high-risk using a risk index (T) that factored in the number of confirmed cases of melanoma versus number of unaffected family members, ages and year of birth
[
  • 1,292 cases
  • , 1,774 controls
]
,
46.28 % Male samples
European Australia BATS, QFMP