Polygenic Score (PGS) ID: PGS000120

Predicted Trait
Reported Trait Squamous cell carcinoma
Mapped Trait(s) squamous cell carcinoma (EFO_0000707)
Released in PGS Catalog: March 27, 2020
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Score Details

Score Construction
PGS Name SCC10
Development Method
Name Genome-wide significant variants
Parameters p<5x10-8
Variants
Original Genome Build GRCh37
Number of Variants 10
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000055
Citation (link to publication) Fritsche LG et al. PLoS Genet (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
287,137 individuals (100%)
Score Development/Training
European: 100%
10,234 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003655
Europe PMC: 27424798
 287,137 individuals European NR
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
—
[
  • 273 cases
  • , 9,961 controls
]
,
46.9 % Male samples
 European MGI Squamous cell carcinoma: ICD9-173.02,173.12,173.22,173.32,173.42,173.52,173.62,173.72,173.82,173.92 Mean = 54.2 years
Sd = 15.9 years		 — — —

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
PPM000343 PSS000207|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.34 [1.3, 1.38] AUROC: 0.58 [0.57, 0.6] — age, sex, batch, PC1-4 —
PPM000340 PSS000208|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (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 —
PPM000346 PSS000211|
European Ancestry|
149,857 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.3 [1.3, 1.34] — — age, sex, genotyping array, first 4 genotype PCs —

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
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 —
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 —