Polygenic Score (PGS) ID: PGS001304

Predicted Trait
Reported Trait Melanoma (malignant)
Mapped Trait(s) melanoma (EFO_0000756)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1059
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_cancer1059
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 116
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 3,705 cases
  • , 265,999 controls
]
 European UKB — — — white British ancestry —

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) 		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
PPM009015 PSS007646|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malignant melanoma — AUROC: 0.87614 [0.73822, 1.0] R²: 0.05368
Incremental AUROC (full-covars): -0.02217
PGS R2 (no covariates): 0.03909
PGS AUROC (no covariates): 0.20593 [0.13426, 0.2776]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009016 PSS007647|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malignant melanoma — AUROC: 0.93529 [0.8865, 0.98409] R²: 0.24041
Incremental AUROC (full-covars): 0.005
PGS R2 (no covariates): 0.06103
PGS AUROC (no covariates): 0.75412 [0.53449, 0.97374]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009017 PSS007648|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malignant melanoma — AUROC: 0.63893 [0.6107, 0.66716] R²: 0.02462
Incremental AUROC (full-covars): 0.02384
PGS R2 (no covariates): 0.01149
PGS AUROC (no covariates): 0.5909 [0.56008, 0.62173]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009018 PSS007649|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malignant melanoma — AUROC: 0.81762 [0.60963, 1.0] R²: 0.07256
Incremental AUROC (full-covars): 0.03083
PGS R2 (no covariates): 0.04901
PGS AUROC (no covariates): 0.74493 [0.36901, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009019 PSS007650|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Malignant melanoma — AUROC: 0.60362 [0.58554, 0.6217] R²: 0.01348
Incremental AUROC (full-covars): 0.0279
PGS R2 (no covariates): 0.00707
PGS AUROC (no covariates): 0.57206 [0.55302, 0.5911]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS007646 — —
[
  • 2 cases
  • , 6,495 controls
]
 — African unspecified — UKB —
PSS007647 — —
[
  • 4 cases
  • , 1,700 controls
]
 — East Asian — UKB —
PSS007648 — —
[
  • 347 cases
  • , 24,558 controls
]
 — European non-white British ancestry UKB —
PSS007649 — —
[
  • 3 cases
  • , 7,828 controls
]
 — South Asian — UKB —
PSS007650 — —
[
  • 913 cases
  • , 66,512 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)