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 25 synonyms
  • 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 terms 26 mapped terms
  • DOID:8923
  • EFO:0000389
  • 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
  • MEDGEN:57486
  • MONDO:0005012
  • NCIT:C3510
  • OMIM:155600
  • OMIM:615848
  • ONCOTREE:SKCM
  • SCTID: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
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000339
(PRS22_CM)
 PGP000106 |
Law MH et al. Hum Mol Genet (2020)
 Cutaneous melanoma cutaneous melanoma 22
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000339/ScoringFiles/PGS000339.txt.gz
PGS000766
(PRS56_CM)
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Cutaneous melanoma cutaneous melanoma 56
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000766/ScoringFiles/PGS000766.txt.gz
PGS003382
(best_SKCM)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Skin cutaneous melanoma cutaneous melanoma 672
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003382/ScoringFiles/PGS003382.txt.gz
PGS003745
(PRS57_SM)
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Skin Melanoma cutaneous melanoma 57
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003745/ScoringFiles/PGS003745.txt.gz
PGS004247
(PRS65_melanoma)
 PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
 Melanoma cutaneous melanoma 65
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004247/ScoringFiles/PGS004247.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
PPM001963 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma — — Hazard Ratio (HR, top 20% vs bottom 20%): 2.51 [1.28, 4.92] — Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001964 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma (males) — — Hazard Ratio (HR, top 20% vs bottom 20%): 3.7 [1.37, 9.98] — Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001965 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma (males) — — Hazard Ratio (HR, middle 60% vs bottom 20%): 2.61 [1.03, 6.63] — Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001966 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Prevalent cutaneous melanoma OR: 1.55 [1.42, 1.69] AUROC: 0.64 [0.62, 0.66] Odds Ratio (OR, top 20% vs bottom 20%): 3.66 [2.69, 5.05] Sex, family history Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001967 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Prevalent cutaneous melanoma (males) OR: 1.39 [1.23, 1.57] — — Family history Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001968 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Prevalent cutaneous melanoma (females) OR: 1.72 [1.53, 1.94] — — Family history Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM001962 PGS000766
(PRS56_CM)
 PSS000982|
European Ancestry|
12,712 individuals
 PGP000172 |
Bakshi A et al. J Natl Cancer Inst (2021)
 Reported Trait: Incident cutaneous melanoma HR: 1.46 [1.2, 1.77] C-index: 0.643 [0.584, 0.702] — Sex, melanoma family history, treatment (aspirin/placebo), age at enrolment, PRS*treatment Only 55 of the 56 SNPs within the PGS were utilised. Rs16891982 was not included as the SNP did not pass imputation quality control.
PPM016257 PGS003382
(best_SKCM)
 PSS010085|
European Ancestry|
273,786 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: skin cutaneous melanoma — AUROC: 0.682 R²: 0.0261 age, sex, top 20 genetic principal components —
PPM018501 PGS003745
(PRS57_SM)
 PSS010995|
European Ancestry|
448 individuals
 PGP000470 |
Xin J et al. EBioMedicine (2023)
 Reported Trait: Skin Melanoma OR: 1.49 [1.34, 1.66] — — — —
PPM020312 PGS004247
(PRS65_melanoma)
 PSS011329|
European Ancestry|
115,207 individuals
 PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
 Reported Trait: Melanoma HR: 1.71 [1.55, 1.89] — — first 10 genetic principal components —
PPM020304 PGS004247
(PRS65_melanoma)
 PSS011328|
European Ancestry|
133,830 individuals
 PGP000542 |
Kim ES et al. NPJ Precis Oncol (2023)
 Reported Trait: Melanoma HR: 1.78 [1.62, 1.96] — — first 10 genetic principal components —

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 —
PSS000982 Cases were individuals with cutaneous melanoma. Of the 628 cases, 528 were prevalent melanoma, whilst 98 were incident melanoma cases. Endpoints used were primary invasive cutaneous melanoma and metastatic melanoma with unknown primary location occurring during the trial (incident). Metastatic recurrence was excluded. Incident melanomas were confirmed by expert panel using histopathology, imaging of metastasis or other clinical evidence. If a participant had two events during the trial, the time of the first event was used. Prevalent melanomas occurring pre-trial were self-reported by participants but not confirmed by review of medical records and assumed to be invasive. Age at diagnosis for self-reported melanomas was reported as either before or after 50 years. Median = 4.7 years
[
  • 626 cases
  • , 12,086 controls
]
,
45.0 % Male samples
 Mean = 75.0 years
Sd = 4.23 years		 European — ASPREE —
PSS011328 — — 133,830 individuals,
0.0 % Male samples
 — European
(British)		 — UKB —
PSS011329 — — 115,207 individuals,
100.0 % Male samples
 — European
(British)		 — UKB —
PSS010085 C43 —
[
  • 4,242 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer
PSS010995 — — 448 individuals Mean = 58.23 years European — TCGA —
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 —