Polygenic Score (PGS) ID: PGS003428

Predicted Trait
Reported Trait Cervical cancer
Mapped Trait(s) cervical carcinoma (EFO_0001061)
Released in PGS Catalog: April 28, 2023
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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 Ldpred_CC_170223
Development Method
Name LDpred
Parameters To decrease the dimension of multicollinearity, SNPs were clumped with maximum LD between them set t... o r2=0.99. Then, 10 versions of PRSs were calculated by varying the fraction of causal SNPs on these values: Inf, 1, 0.3, 0.1, 0.03, 0.01, 0.003, 0.001, 0.0003 and 0.0001.Show more
Variants
Original Genome Build GRCh37
Number of Variants 2,894,555
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000435
Citation (link to publication) Koel M et al. Hum Mol Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
326,610 individuals (100%)
Score Development/Training
European: 100%
4,295 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST90011816
[
  • 6,563 cases
  • , 219,686 controls
]
EuropeanKP, UKB
—
[
  • 1,313 cases
  • , 99,048 controls
]
EuropeanFinnGen
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Score Development/Training
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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
—
[
  • 859 cases
  • , 3,436 controls
]
EuropeanEB—————
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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.

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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
PPM017102PSS010125|
European Ancestry|
128,113 individuals
PGP000435 |
Koel M et al. Hum Mol Genet (2023)
Reported Trait: Incident cervical cancerHR: 1.33 (0.069)C-index: 0.613—age, smoking—
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Evaluated Samples

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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
PSS010125C53, D06—
[
  • 235 cases
  • , 127,878 controls
]
,
0.0 % Male samples
—European—EB—
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