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
  • Malignant Melanoma
  • Malignant Melanomas
  • Malignant melanoma (morphologic abnormality)
  • Malignant melanoma, NOS
  • Malignant melanoma, morphology (morphologic abnormality)
  • Malignant melanoma, no ICD-O subtype
  • Malignant melanoma, no ICD-O subtype (morphologic abnormality)
  • Melanoma, Malignant
  • Melanoma, NOS
  • Melanomas
  • Melanomas, Malignant
  • Melanosarcoma
  • Naevocarcinoma
  • [M]Malignant melanoma NOS
  • [M]Malignant melanoma NOS (morphologic abnormality)
  • malignant melanoma
  • malignant melanoma (disorder)
  • malignant melanoma NOS (morphologic abnormality)
  • melanoma
  • melanoma (disease)
  • melanoma, malignant
Mapped term(s) 17 mapped terms
  • DOID:1909
  • HP:0002861
  • ICDO:8720/3
  • KEGG:05218
  • MESH:D008545
  • MONDO:0005105
  • MeSH:D008545
  • NCIT:C3224
  • NCIt:C3224
  • OMIM:155600
  • OMIM:155755
  • ONCOTREE:MEL
  • SCTID:372244006
  • SNOMEDCT:2092003
  • SNOMEDCT:372244006
  • UMLS:C0025202
  • UMLS:CN971653
Child trait(s) cutaneous melanoma

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
Note: This table shows all PGS for "melanoma" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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
PGS000408
(PRSWEB_PHECODE172.1_20001-1059_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 10
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000408/ScoringFiles/PGS000408.txt.gz
PGS000409
(PRSWEB_PHECODE172.1_20001-1059_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 1,111,490
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000409/ScoringFiles/PGS000409.txt.gz
PGS000410
(PRSWEB_PHECODE172.1_20001-1059_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 7
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000410/ScoringFiles/PGS000410.txt.gz
PGS000411
(PRSWEB_PHECODE172.1_20001-1059_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 185
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000411/ScoringFiles/PGS000411.txt.gz
PGS000412
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 16
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000412/ScoringFiles/PGS000412.txt.gz
PGS000413
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 1,111,490
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000413/ScoringFiles/PGS000413.txt.gz
PGS000414
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 21
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000414/ScoringFiles/PGS000414.txt.gz
PGS000415
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 505
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000415/ScoringFiles/PGS000415.txt.gz
PGS000416
(PRSWEB_PHECODE172.1_C43_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 9
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000416/ScoringFiles/PGS000416.txt.gz
PGS000417
(PRSWEB_PHECODE172.1_C43_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 1,109,519
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000417/ScoringFiles/PGS000417.txt.gz
PGS000418
(PRSWEB_PHECODE172.1_C43_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 9
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000418/ScoringFiles/PGS000418.txt.gz
PGS000419
(PRSWEB_PHECODE172.1_C43_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 436
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000419/ScoringFiles/PGS000419.txt.gz
PGS000420
(PRSWEB_PHECODE172.1_D03_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 147
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000420/ScoringFiles/PGS000420.txt.gz
PGS000421
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 18
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000421/ScoringFiles/PGS000421.txt.gz
PGS000422
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_P_5e-08_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 18
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000422/ScoringFiles/PGS000422.txt.gz
PGS000423
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 29
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000423/ScoringFiles/PGS000423.txt.gz
PGS000424
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 27
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000424/ScoringFiles/PGS000424.txt.gz
PGS000425
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 20
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000425/ScoringFiles/PGS000425.txt.gz
PGS000426
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_P_5e-08_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 20
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000426/ScoringFiles/PGS000426.txt.gz
PGS000427
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 20
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000427/ScoringFiles/PGS000427.txt.gz
PGS000428
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_UKB_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 20
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000428/ScoringFiles/PGS000428.txt.gz
PGS000429
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_P_5e-08_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 12
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000429/ScoringFiles/PGS000429.txt.gz
PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 1,119,238
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000430/ScoringFiles/PGS000430.txt.gz
PGS000431
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PT_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 15
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000431/ScoringFiles/PGS000431.txt.gz
PGS000432
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_LASSOSUM_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history) melanoma 296
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000432/ScoringFiles/PGS000432.txt.gz
PGS000732
(PRS_Melanoma)
PGP000138 |
Fontanillas P et al. Nat Commun (2021)
Melanoma melanoma 18
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000732/ScoringFiles/PGS000732.txt.gz - Check Terms/Licenses
PGS000743
(PRS_melanoma)
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Melanoma melanoma 45
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000743/ScoringFiles/PGS000743.txt.gz
PGS000744
(PRS_melanoma_pigment.pathway)
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Melanoma melanoma 31
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000744/ScoringFiles/PGS000744.txt.gz
PGS000745
(PRS_melanoma_telomere.pathway)
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Melanoma melanoma 9
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000745/ScoringFiles/PGS000745.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
PPM000199 PGS000079
(CC_Melanoma)
PSS000118|
European Ancestry|
417,136 individuals
PGP000050 |
Graff RE et al. bioRxiv (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
PPM001672 PGS000732
(PRS_Melanoma)
PSS000872|
European Ancestry|
88,924 individuals
PGP000138 |
Fontanillas P et al. Nat Commun (2021)
Reported Trait: Melanoma OR: 1.33 [1.29, 1.37] AUROC: 0.579
PPM000348 PGS000118
(MEL29)
PSS000210|
European Ancestry|
29,898 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Melanoma OR: 1.5 [1.44, 1.55] age, sex, genotyping array, first 4 genotype PCs
PPM000345 PGS000118
(MEL29)
PSS000211|
European Ancestry|
149,857 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Skin cancer OR: 1.2 [1.22, 1.36] age, sex, genotyping array, first 4 genotype PCs
PPM000342 PGS000118
(MEL29)
PSS000207|
European Ancestry|
20,468 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Skin cancer OR: 1.3 [1.26, 1.34] AUROC: 0.57 [0.56, 0.58] age, sex, batch, PC1-4
PPM000339 PGS000118
(MEL29)
PSS000206|
European Ancestry|
20,468 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Melanoma OR: 1.48 [1.41, 1.56] AUROC: 0.61 [0.59, 0.62] age, sex, batch, PC1-4
PPM000488 PGS000157
(cGRS_Melanoma)
PSS000277|
European Ancestry|
13,877 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Melanoma Odds Ratio (OR; high vs. average risk groups): 1.72 [1.37, 2.16]
PPM000477 PGS000157
(cGRS_Melanoma)
PSS000277|
European Ancestry|
13,877 individuals
PGP000075 |
Shi Z et al. Cancer Med (2019)
Reported Trait: Melanoma Mean realative risk: 1.2 [1.14, 1.26]
Wilcoxon test (case vs. control) p-value: 5.99e-11
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
PPM001095 PGS000410
(PRSWEB_PHECODE172.1_20001-1059_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.399 [1.327, 1.476]
β: 0.336 (0.0272)
AUROC: 0.578 [0.562, 0.594] Nagelkerke's Pseudo-R²: 0.0239
Brier score: 0.0956
Odds Ratio (OR, top 1% vs. Rest): 2.65 [1.79, 3.93]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_20001-1059_PT_MGI_20200608
PPM001098 PGS000413
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_PRS-CS_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.27 [1.199, 1.346]
β: 0.239 (0.0294)
AUROC: 0.568 [0.552, 0.584] Nagelkerke's Pseudo-R²: 0.0109
Brier score: 0.0964
Odds Ratio (OR, top 1% vs. Rest): 2.09 [1.35, 3.22]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_PRS-CS_MGI_20200608
PPM001101 PGS000416
(PRSWEB_PHECODE172.1_C43_P_5e-08_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.473 [1.394, 1.557]
β: 0.388 (0.0282)
AUROC: 0.598 [0.582, 0.613] Nagelkerke's Pseudo-R²: 0.0297
Brier score: 0.0952
Odds Ratio (OR, top 1% vs. Rest): 2.88 [1.96, 4.21]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C43_P_5e-08_MGI_20200608
PPM001103 PGS000418
(PRSWEB_PHECODE172.1_C43_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.473 [1.394, 1.557]
β: 0.388 (0.0282)
AUROC: 0.598 [0.582, 0.613] Nagelkerke's Pseudo-R²: 0.0297
Brier score: 0.0952
Odds Ratio (OR, top 1% vs. Rest): 2.88 [1.96, 4.21]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C43_PT_MGI_20200608
PPM001106 PGS000421
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_P_5e-08_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.453 [1.37, 1.541]
β: 0.374 (0.03)
AUROC: 0.6 [0.584, 0.616] Nagelkerke's Pseudo-R²: 0.0257
Brier score: 0.0955
Odds Ratio (OR, top 1% vs. Rest): 2.39 [1.58, 3.61]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_P_5e-08_MGI_20200608
PPM001110 PGS000425
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_P_5e-08_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.453 [1.369, 1.542]
β: 0.374 (0.0304)
AUROC: 0.601 [0.585, 0.617] Nagelkerke's Pseudo-R²: 0.0255
Brier score: 0.0955
Odds Ratio (OR, top 1% vs. Rest): 2.54 [1.7, 3.8]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_Melanoma-Ransohoff_P_5e-08_MGI_20200608
PPM001093 PGS000408
(PRSWEB_PHECODE172.1_20001-1059_P_5e-08_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.384 [1.311, 1.461]
β: 0.325 (0.0276)
AUROC: 0.576 [0.561, 0.593] Nagelkerke's Pseudo-R²: 0.0217
Brier score: 0.0957
Odds Ratio (OR, top 1% vs. Rest): 2.25 [1.48, 3.42]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_20001-1059_P_5e-08_MGI_20200608
PPM001096 PGS000411
(PRSWEB_PHECODE172.1_20001-1059_LASSOSUM_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.378 [1.308, 1.451]
β: 0.32 (0.0265)
AUROC: 0.571 [0.555, 0.587] Nagelkerke's Pseudo-R²: 0.0222
Brier score: 0.0957
Odds Ratio (OR, top 1% vs. Rest): 2.0 [1.29, 3.09]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_20001-1059_LASSOSUM_MGI_20200608
PPM001099 PGS000414
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.44 [1.363, 1.522]
β: 0.365 (0.0283)
AUROC: 0.593 [0.576, 0.609] Nagelkerke's Pseudo-R²: 0.026
Brier score: 0.0954
Odds Ratio (OR, top 1% vs. Rest): 2.97 [2.02, 4.36]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_PT_MGI_20200608
PPM001100 PGS000415
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_LASSOSUM_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.391 [1.318, 1.467]
β: 0.33 (0.0272)
AUROC: 0.578 [0.562, 0.595] Nagelkerke's Pseudo-R²: 0.0227
Brier score: 0.0957
Odds Ratio (OR, top 1% vs. Rest): 2.34 [1.55, 3.53]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_LASSOSUM_MGI_20200608
PPM001102 PGS000417
(PRSWEB_PHECODE172.1_C43_PRS-CS_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.228 [1.159, 1.3]
β: 0.205 (0.0294)
AUROC: 0.556 [0.541, 0.571] Nagelkerke's Pseudo-R²: 0.00812
Brier score: 0.0965
Odds Ratio (OR, top 1% vs. Rest): 1.88 [1.2, 2.95]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C43_PRS-CS_MGI_20200608
PPM001104 PGS000419
(PRSWEB_PHECODE172.1_C43_LASSOSUM_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.348 [1.279, 1.421]
β: 0.299 (0.0268)
AUROC: 0.565 [0.549, 0.583] Nagelkerke's Pseudo-R²: 0.0188
Brier score: 0.0959
Odds Ratio (OR, top 1% vs. Rest): 1.93 [1.24, 3.0]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C43_LASSOSUM_MGI_20200608
PPM001105 PGS000420
(PRSWEB_PHECODE172.1_D03_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.066 [1.007, 1.128]
β: 0.0639 (0.029)
AUROC: 0.516 [0.5, 0.533] Nagelkerke's Pseudo-R²: 0.00074
Brier score: 0.0969
Odds Ratio (OR, top 1% vs. Rest): 1.07 [0.603, 1.9]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_D03_PT_MGI_20200608
PPM001107 PGS000422
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_P_5e-08_UKB_20200608)
PSS000567|
European Ancestry|
14,482 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.539 [1.454, 1.629]
β: 0.431 (0.029)
AUROC: 0.615 [0.599, 0.63] Nagelkerke's Pseudo-R²: 0.0332
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 2.57 [1.75, 3.77]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_P_5e-08_UKB_20200608
PPM001108 PGS000423
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx β: 0.394 (0.0301)
OR: 1.484 [1.399, 1.574]
AUROC: 0.608 [0.592, 0.623] Nagelkerke's Pseudo-R²: 0.0289
Brier score: 0.0954
Odds Ratio (OR, top 1% vs. Rest): 2.93 [2.0, 4.3]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_MGI_20200608
PPM001109 PGS000424
(PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_UKB_20200608)
PSS000567|
European Ancestry|
14,482 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.563 [1.475, 1.656]
β: 0.447 (0.0294)
AUROC: 0.619 [0.603, 0.634] Nagelkerke's Pseudo-R²: 0.035
Brier score: 0.0812
Odds Ratio (OR, top 1% vs. Rest): 3.12 [2.18, 4.47]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_GWAS-Catalog-r2019-05-03-X172.1_PT_UKB_20200608
PPM001111 PGS000426
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_P_5e-08_UKB_20200608)
PSS000567|
European Ancestry|
14,482 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.551 [1.463, 1.643]
β: 0.439 (0.0296)
AUROC: 0.62 [0.604, 0.635] Nagelkerke's Pseudo-R²: 0.0335
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 2.81 [1.93, 4.07]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_Melanoma-Ransohoff_P_5e-08_UKB_20200608
PPM001112 PGS000427
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.453 [1.369, 1.542]
β: 0.374 (0.0304)
AUROC: 0.601 [0.585, 0.617] Nagelkerke's Pseudo-R²: 0.0255
Brier score: 0.0955
Odds Ratio (OR, top 1% vs. Rest): 2.54 [1.7, 3.8]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_MGI_20200608
PPM001113 PGS000428
(PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_UKB_20200608)
PSS000567|
European Ancestry|
14,482 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.551 [1.463, 1.643]
β: 0.439 (0.0296)
AUROC: 0.62 [0.604, 0.635] Nagelkerke's Pseudo-R²: 0.0335
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 2.81 [1.93, 4.07]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_Melanoma-Ransohoff_PT_UKB_20200608
PPM001114 PGS000429
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_P_5e-08_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.503 [1.422, 1.589]
β: 0.408 (0.0284)
AUROC: 0.606 [0.591, 0.622] Nagelkerke's Pseudo-R²: 0.0332
Brier score: 0.0951
Odds Ratio (OR, top 1% vs. Rest): 2.62 [1.77, 3.88]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_P_5e-08_MGI_20200608
PPM001116 PGS000431
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PT_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.486 [1.405, 1.571]
β: 0.396 (0.0285)
AUROC: 0.604 [0.587, 0.62] Nagelkerke's Pseudo-R²: 0.0312
Brier score: 0.0952
Odds Ratio (OR, top 1% vs. Rest): 2.97 [2.04, 4.34]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PT_MGI_20200608
PPM001117 PGS000432
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_LASSOSUM_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.391 [1.318, 1.467]
β: 0.33 (0.0273)
AUROC: 0.582 [0.566, 0.599] Nagelkerke's Pseudo-R²: 0.0228
Brier score: 0.0957
Odds Ratio (OR, top 1% vs. Rest): 1.99 [1.29, 3.07]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_LASSOSUM_MGI_20200608
PPM001115 PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.219 [1.151, 1.292]
β: 0.198 (0.0296)
AUROC: 0.555 [0.54, 0.573] Nagelkerke's Pseudo-R²: 0.00721
Brier score: 0.0965
Odds Ratio (OR, top 1% vs. Rest): 1.64 [1.01, 2.66]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608
PPM001094 PGS000409
(PRSWEB_PHECODE172.1_20001-1059_PRS-CS_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.192 [1.126, 1.263]
β: 0.176 (0.0292)
AUROC: 0.547 [0.531, 0.563] Nagelkerke's Pseudo-R²: 0.0061
Brier score: 0.0966
Odds Ratio (OR, top 1% vs. Rest): 1.94 [1.25, 3.02]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_20001-1059_PRS-CS_MGI_20200608
PPM001097 PGS000412
(PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_P_5e-08_MGI_20200608)
PSS000543|
European Ancestry|
11,974 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Melanomas of skin, dx or hx OR: 1.414 [1.338, 1.495]
β: 0.347 (0.0282)
AUROC: 0.585 [0.569, 0.6] Nagelkerke's Pseudo-R²: 0.0236
Brier score: 0.0955
Odds Ratio (OR, top 1% vs. Rest): 3.26 [2.26, 4.7]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.1_C3-MELANOMA-SKIN_P_5e-08_MGI_20200608
PPM001827 PGS000743
(PRS_melanoma)
PSS000928|
European Ancestry|
1,460 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma OR: 1.63 [1.46, 1.83] Odds Ratio (OR, top vs. bottom tertile): 2.84 [2.14, 3.77]
Odds Ratio (OR, top vs. bottom decile): 5.62 [3.41, 9.29]
Age, sex, self reported European ancestry Overlap between testing and score development samples, testing <10% of score development
PPM001829 PGS000743
(PRS_melanoma)
PSS000928|
European Ancestry|
1,460 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma AUROC: 0.68 [0.65, 0.71] Traditional risk factors (hair colour, skin colour, eye colour, freckling as an adult, skin photosensitivity, self reported nevi, sunbed use, keratinocyte cancer personal history, first degree family history of melanoma, vacation sun exposure, blistering sunburns as a child), age, sex, self-reported European ancestry
PPM001830 PGS000744
(PRS_melanoma_pigment.pathway)
PSS000927|
European Ancestry|
1,035 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma OR: 1.71 [1.49, 1.96] Odds Ratio (OR, top vs. bottom tertile): 3.11 [2.21, 4.36]
Odds Ratio (OR, top vs. bottom decile): 5.75 [3.09, 10.72]
Age, sex, recruitment city, self-reported European ancestry
PPM001831 PGS000744
(PRS_melanoma_pigment.pathway)
PSS000928|
European Ancestry|
1,460 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma OR: 1.66 [1.49, 1.86] Odds Ratio (OR, top vs. bottom tertile): 2.94 [2.23, 3.88]
Odds Ratio (OR, top vs. bottom decile): 7.0 [4.12, 11.88]
Age, sex, self reported European ancestry
PPM001832 PGS000745
(PRS_melanoma_telomere.pathway)
PSS000927|
European Ancestry|
1,035 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma OR: 1.15 [1.01, 1.31] Odds Ratio (OR, top vs. bottom tertile): 1.4 [1.01, 1.93] Age, sex, recruitment city, self-reported European ancestry
PPM001833 PGS000745
(PRS_melanoma_telomere.pathway)
PSS000928|
European Ancestry|
1,460 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma OR: 1.18 [1.06, 1.31] Odds Ratio (OR, top vs. bottom decile): 2.0 [1.24, 3.23]
Odds Ratio (OR, top vs. bottom tertile): 1.55 [1.19, 2.02]
Age, sex, self reported European ancestry
PPM001826 PGS000743
(PRS_melanoma)
PSS000927|
European Ancestry|
1,035 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma OR: 1.75 [1.53, 2.01] Odds Ratio (OR, top vs. bottom tertile): 3.22 [2.3, 4.51]
Odds Ratio (OR, top vs. bottom decile): 5.88 [3.14, 11.03]
Age, sex, recruitment city, self-reported European ancestry Overlap between testing and score development samples, testing <10% of score development
PPM001828 PGS000743
(PRS_melanoma)
PSS000927|
European Ancestry|
1,035 individuals
PGP000151 |
Cust AE et al. J Invest Dermatol (2018)
Reported Trait: Melanoma AUROC: 0.74 [0.71, 0.77] Traditional risk factors (hair colour, skin colour, eye colour, freckling as an adult, skin photosensitivity, self reported nevi, sunbed use, keratinocyte cancer personal history, first degree family history of melanoma, vacation sun exposure, blistering sunburns as a child), age, sex, recruitment city, self-reported European ancestry

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
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
PSS000872 Melanoma cases were determined by a baseline survey containing 34 questions regarding personal history of skin cancer(including skin cancer type, age at diagnosis, body location, prescribed treatments and information regarding cancer recurrence)
[
  • 4,179 cases
  • , 84,745 controls
]
,
38.9 % Male samples
European 23andMe
PSS000567 PheCode:172.1; ICD9:-; ICD10:C43.0, C43.1, C43.2, C43.3, C43.4, C43.5, C43.6, C43.7, C43.8, C43.9, D03.0, D03.1, D03.2, D03.3, D03.4, D03.5, D03.6, D03.7, D03.8, D03.9
[
  • 1,317 cases
  • , 13,165 controls
]
European UKB
PSS000928 Cases include histopathologically confirmed invasive melanoma cases in patients between 18 and 82 years.
[
  • 964 cases
  • , 496 controls
]
,
40.0 % Male samples
European LMC
PSS000543 PheCode:172.1; ICD9CM:172.0, 172.1, 172.2, 172.3, 172.4, 172.5, 172.6, 172.7, 172.8, 172.9, V10.82; ICD10CM:C43, C43.0, C43.1, C43.10, C43.11, C43.12, C43.2, C43.20, C43.21, C43.22, C43.3, C43.30, C43.31, C43.39, C43.4, C43.5, C43.51, C43.52, C43.59, C43.6, C43.60, C43.61, C43.62, C43.7, C43.70, C43.71, C43.72, C43.8, C43.9, D03, D03.0, D03.1, D03.10, D03.11, D03.12, D03.2, D03.20, D03.21, D03.22, D03.3, D03.30, D03.39, D03.4, D03.5, D03.51, D03.52, D03.59, D03.6, D03.60, D03.61, D03.62, D03.7, D03.70, D03.71, D03.72, D03.8, D03.9
[
  • 1,325 cases
  • , 10,649 controls
]
European MGI
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
PSS000927 Cases include invasive cutaneous melanoma diagnoses between ages 18 and 39 years
[
  • 578 cases
  • , 457 controls
]
,
40.0 % Male samples
European AMFS
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