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
Download Score FTP directory
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 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)
JSONXMLCSVTXTMS-Excel
Loading, please wait
Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST003655
Europe PMC: 27424798
287,137 individualsEuropeanNR
Showing 1 to 1 of 1 rows
Score Development/Training
JSONXMLCSVTXTMS-Excel
Loading, please wait
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
EuropeanMGISquamous cell carcinoma: ICD9-173.02,173.12,173.22,173.32,173.42,173.52,173.62,173.72,173.82,173.92Mean = 54.2 years
Sd = 15.9 years		———
Showing 1 to 1 of 1 rows

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.

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PPM000340PSS000208|
European Ancestry|
20,468 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Squamous cell carcinomaOR: 1.4 [1.31, 1.5]AUROC: 0.59 [0.56, 0.61]—age, sex, batch, PC1-4—
PPM000343PSS000207|
European Ancestry|
20,468 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Skin cancerOR: 1.34 [1.3, 1.38]AUROC: 0.58 [0.57, 0.6]—age, sex, batch, PC1-4—
PPM000346PSS000211|
European Ancestry|
149,857 individuals
PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
Reported Trait: Skin cancerOR: 1.3 [1.3, 1.34]——age, sex, genotyping array, first 4 genotype PCs—
Showing 1 to 3 of 3 rows

Evaluated Samples

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PSS000207PheCode 172—
[
  • 3,002 cases
  • , 17,466 controls
]
,
46.9 % Male samples
Mean = 54.2 years
Sd = 15.9 years		European—MGI—
PSS000208Squamous 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—
PSS000211PheCode 172—
[
  • 13,624 cases
  • , 136,233 controls
]
,
45.9 % Male samples
Mean = 57.7 years
Sd = 8.1 years		EuropeanWhite British SubsetUKB—
Showing 1 to 3 of 3 rows