Trait: melanoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000756
Description A malignant, usually aggressive tumor composed of atypical, neoplastic melanocytes. Most often, melanomas arise in the skin (cutaneous melanomas) and include the following histologic subtypes: superficial spreading melanoma, nodular melanoma, acral lentiginous melanoma, and lentigo maligna melanoma. Cutaneous melanomas may arise from acquired or congenital melanocytic or dysplastic nevi. Melanomas may also arise in other anatomic sites including the gastrointestinal system, eye, urinary tract, and reproductive system. Melanomas frequently metastasize to lymph nodes, liver, lungs, and brain. [NCIT: C3224]
Trait category
Cancer
Synonyms 22 synonyms
  • MM - Malignant melanoma
  • Melanoma, Malignant
  • melanoma (disease)
  • Malignant melanoma, no ICD-O subtype
  • Melanomas
  • Malignant melanoma, NOS
  • melanoma
  • [M]Malignant melanoma NOS (morphologic abnormality)
  • melanoma, malignant
  • Malignant melanoma, no ICD-O subtype (morphologic abnormality)
  • Malignant Melanoma
  • [M]Malignant melanoma NOS
  • Naevocarcinoma
  • Malignant melanoma (morphologic abnormality)
  • malignant melanoma NOS (morphologic abnormality)
  • Malignant melanoma, morphology (morphologic abnormality)
  • malignant melanoma
  • malignant melanoma (disorder)
  • Melanosarcoma
  • Malignant Melanomas
  • Melanomas, Malignant
  • Melanoma, NOS
Mapped term(s) 17 mapped terms
  • MESH:D008545
  • HP:0002861
  • MSH:D008545
  • NCIT:C3224
  • DOID:1909
  • ICDO:8720/3
  • SNOMEDCT:2092003
  • UMLS:C0025202
  • SCTID:372244006
  • OMIM:155755
  • KEGG:05218
  • OMIM:155600
  • MONDO:0005105
  • SNOMEDCT:372244006
  • NCIt:C3224
  • UMLS:CN971653
  • ONCOTREE:MEL
Child trait(s) cutaneous melanoma

Associated Polygenic Score(s)

Note: This table shows all PGS for "melanoma" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000079 CC_Melanoma PGP000050 Graff RE et al. bioRxiv (2020) Pre Melanoma melanoma 24 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000079/ScoringFiles/PGS000079.txt.gz
PGS000118 MEL29 PGP000055 Fritsche LG et al. PLoS Genet (2019) Melanoma melanoma 29 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000118/ScoringFiles/PGS000118.txt.gz
PGS000157 cGRS_Melanoma PGP000075 Shi Z et al. Cancer Med (2019) Melanoma melanoma 17 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000157/ScoringFiles/PGS000157.txt.gz
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
PPM000199 PGS000079 (CC_Melanoma) PSS000118 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Melanoma OR: 1.44[1.41, 1.48] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000339 PGS000118 (MEL29) PSS000206 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Melanoma OR: 1.48[1.41, 1.56] AUROC: 0.61[0.59, 0.62] age, sex, batch, PC1-4
PPM000342 PGS000118 (MEL29) PSS000207 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.3[1.26, 1.34] AUROC: 0.57[0.56, 0.58] age, sex, batch, PC1-4
PPM000345 PGS000118 (MEL29) PSS000211 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.2[1.22, 1.36] age, sex, genotyping array, first 4 genotype PCs
PPM000348 PGS000118 (MEL29) PSS000210 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Melanoma OR: 1.5[1.44, 1.55] age, sex, genotyping array, first 4 genotype PCs
PPM000477 PGS000157 (cGRS_Melanoma) PSS000277 PGP000075
Shi Z et al. (2019)
Reported Trait: Melanoma Mean realative risk: 1.2[1.14, 1.26]
Wilcoxon test (case vs. control) p-value: 5.99e-11
PPM000488 PGS000157 (cGRS_Melanoma) PSS000277 PGP000075
Shi Z et al. (2019)
Reported Trait: Melanoma Odds Ratio (OR; high vs. average risk groups): 1.72[1.37, 2.16]
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
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

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
PSS000206 Melanomas of skin : ICD9- 172.0,172.1,172.2,172.3,172.4,172.5,172.6,172.7,172.8,172.9
[
  • 1,279 cases
  • , 19,189 controls
]
,
46.9 % Male samples
Mean = 54.2 years
Sd = 15.9 years
European MGI
PSS000207 PheCode 172
[
  • 3,002 cases
  • , 17,466 controls
]
,
46.9 % Male samples
Mean = 54.2 years
Sd = 15.9 years
European MGI
PSS000210 PheCode 172.11
[
  • 2,718 cases
  • , 27,180 controls
]
,
45.9 % Male samples
Mean = 57.7 years
Sd = 8.1 years
European White British Subset UKB
PSS000211 PheCode 172
[
  • 13,624 cases
  • , 136,233 controls
]
,
45.9 % Male samples
Mean = 57.7 years
Sd = 8.1 years
European White British Subset UKB
PSS000277 Primary tumor samples from TCGA
[
  • 450 cases
  • , 0 controls
]
Mean = 59.0 years
Sd = 16.0 years
European TCGA
PSS000277
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE
PSS000118 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 25010
[
  • 6,782 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
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