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 malignant melanoma
  • MAL MELANOM FACE NEC/NOS
  • MALIG MELANOMA SKIN NEC
  • MALIG MELANOMA SKIN NOS
  • MM - Malignant melanoma of skin
  • Malignant Cutaneous Melanoma
  • Malignant Melanoma (of Skin), Stage Unspecified
  • Malignant Melanoma of Skin
  • Malignant Melanoma of Skin Stage Unspecified
  • Malignant melanoma of other specified sites of skin
  • Malignant melanoma of other specified skin site
  • Malignant melanoma of other specified skin site (disorder)
  • Malignant melanoma of skin (disorder)
  • Malignant melanoma of skin NOS
  • Malignant melanoma of skin NOS (disorder)
  • Malignant melanoma of skin of other and unspecified parts of face
  • Malignant melanoma of skin, NOS
  • Melanoma of Skin
  • Melanoma of skin, site unspecified
  • Melanoma of the Skin
  • Skin Melanoma
  • Skin, Melanoma
  • [X]Malignant melanoma of skin, unspecified
  • [X]Malignant melanoma of skin, unspecified (disorder)
  • cancer of skin
  • cutaneous (skin) melanoma
  • cutaneous melanoma
  • cutaneous melanoma (disease)
  • malignant cutaneous melanoma
  • malignant ear melanoma
  • malignant lip melanoma
  • malignant lower limb melanoma
  • malignant melanoma (of skin), stage unspecified
  • malignant melanoma of ear and/or external auricular canal
  • malignant melanoma of skin
  • malignant melanoma of skin of lower limb
  • malignant melanoma of skin of trunk except scrotum
  • malignant melanoma of skin of upper limb
  • malignant melanoma of skin stage unspecified
  • malignant neck melanoma
  • malignant scalp melanoma
  • malignant trunk melanoma
  • malignant upper limb melanoma
  • melanoma (disease) of zone of skin
  • melanoma of skin
  • melanoma of the skin
  • skin melanoma
  • skin, melanoma
  • zone of skin melanoma
  • zone of skin melanoma (disease)
Mapped term(s) 26 mapped terms
  • DOID:8923
  • HP:0012056
  • ICD10:C43
  • ICD10:C43.0
  • ICD10:C43.2
  • ICD10:C43.4
  • ICD10:C43.9
  • ICD9:172
  • ICD9:172.0
  • ICD9:172.2
  • ICD9:172.3
  • ICD9:172.4
  • ICD9:172.5
  • ICD9:172.8
  • ICD9:172.9
  • MONDO:0005012
  • NCIT:C3510
  • NCIt:C3510
  • OMIM:155600
  • OMIM:615848
  • ONCOTREE:SKCM
  • SCTID:93655004
  • SNOMEDCT:93655004
  • UMLS:C0151779
  • UMLS:C0153535
  • UMLS:C0153536

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 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

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
PPM000922 PGS000339
(PRS22_CM)
PSS000464|
European Ancestry|
1,885 individuals
PGP000106 |
Law MH et al. Hum Mol Genet (2020)
Reported Trait: Cutaneous melanoma in multiplex melanoma families Difference of PRS (deltaPRS; unaffected melanoma family members vs. unrelated controls): 0.347 (0.104) PCs (1-10) *Sample overlap between the controls used in this analysis and score development
PPM000921 PGS000339
(PRS22_CM)
PSS000463|
European Ancestry|
3,066 individuals
PGP000106 |
Law MH et al. Hum Mol Genet (2020)
Reported Trait: Cutaneous melanoma in multiplex melanoma families Difference of PRS (deltaPRS; melanoma family cases vs. unrelated controls): 0.505 (0.036) PCs (1-10) *Sample overlap between the controls used in this analysis and score development

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
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