PGS Publication: PGP000138

Publication Information (EuropePMC)
Title Disease risk scores for skin cancers.
PubMed ID 33420020(Europe PMC)
doi 10.1038/s41467-020-20246-5
Publication Date Jan. 8, 2021
Journal Nat Commun
Author(s) Fontanillas P, Alipanahi B, Furlotte NA, Johnson M, Wilson CH, 23andMe Research Team, Pitts SJ, Gentleman R, Auton A.
Released in PGS Catalog: Feb. 23, 2021

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:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
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East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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)
PGS000731
(PRS_SCC)
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Squamous cell carcinoma squamous cell carcinoma 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000731/ScoringFiles/PGS000731.txt.gz - Check Terms/Licenses
PGS000730
(PRS_BCC)
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Basal cell carcinoma basal cell carcinoma 47
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000730/ScoringFiles/PGS000730.txt.gz - Check Terms/Licenses
PGS000732
(PRS_Melanoma)
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Melanoma melanoma 18
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000732/ScoringFiles/PGS000732.txt.gz - Check Terms/Licenses

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
PPM001670 PGS000730
(PRS_BCC)
 PSS000871|
European Ancestry|
88,924 individuals
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Reported Trait: Basal cell carcinoma OR: 1.57 [1.55, 1.6] AUROC: 0.624 — — —
PPM001671 PGS000731
(PRS_SCC)
 PSS000873|
European Ancestry|
88,924 individuals
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Reported Trait: Squamous cell carcinoma OR: 1.44 [1.41, 1.48] AUROC: 0.605 — — —
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 — — —

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
PSS000871 Basal cell carcinoma 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) —
[
  • 16,184 cases
  • , 72,740 controls
]
,
38.9 % Male samples
 European — 23andMe —
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 —
PSS000873 Squamous cell carcinoma 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) —
[
  • 7,914 cases
  • , 81,010 controls
]
,
38.9 % Male samples
 European — 23andMe —