PGS Publication: PGP000055

Publication Information (EuropePMC)
Title Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb.
PubMed ID 31194742(Europe PMC)
doi 10.1371/journal.pgen.1008202
Publication Date June 13, 2019
Journal PLoS Genet
Author(s) Fritsche LG, Beesley LJ, VandeHaar P, Peng RB, Salvatore M, Zawistowski M, Gagliano Taliun SA, Das S, LeFaive J, Kaleba EO, Klumpner TT, Moser SE, Blanc VM, Brummett CM, Kheterpal S, Abecasis GR, Gruber SB, Mukherjee B.
Released in PGS: March 27, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000120 SCC10 PGP000055
Fritsche LG et al. PLoS Genet (2019)
Squamous cell carcinoma squamous cell carcinoma 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000120/ScoringFiles/PGS000120.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
PGS000119 BCC32 PGP000055
Fritsche LG et al. PLoS Genet (2019)
Basal cell carcinoma basal cell carcinoma 32 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000119/ScoringFiles/PGS000119.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
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
PPM000347 PGS000119 (BCC32) PSS000211 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.4[1.42, 1.48] age, sex, genotyping array, first 4 genotype PCs
PPM000346 PGS000120 (SCC10) PSS000211 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.3[1.3, 1.34] age, sex, genotyping array, first 4 genotype PCs
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
PPM000344 PGS000119 (BCC32) PSS000207 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.32[1.27, 1.36] AUROC: 0.58[0.56, 0.58] age, sex, batch, PC1-4
PPM000343 PGS000120 (SCC10) PSS000207 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Skin cancer OR: 1.34[1.3, 1.38] AUROC: 0.58[0.57, 0.6] 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
PPM000341 PGS000119 (BCC32) PSS000209 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Basal cell carcinoma OR: 1.65[1.56, 1.75] AUROC: 0.64[0.62, 0.66] age, sex, batch, PC1-4
PPM000340 PGS000120 (SCC10) PSS000208 PGP000055
Fritsche LG et al. (2019)
Reported Trait: Squamous cell carcinoma OR: 1.4[1.31, 1.5] AUROC: 0.59[0.56, 0.61] age, sex, batch, PC1-4
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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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
PSS000208 Squamous cell carcinoma: ICD9-173.02,173.12,173.22,173.32,173.42,173.52,173.62,173.72,173.82,173.92
[
  • 563 cases
  • , 19,905 controls
]
,
46.9 % Male samples
Mean = 54.2 years
Sd = 15.9 years
European MGI
PSS000209 Basal cell carcinoma: ICD9-173.01,173.11,173.21,173.31,173.41,173.51,173.61,173.71,173.81,173.91
[
  • 884 cases
  • , 19,584 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