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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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 to 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.
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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 1,313 cases
  • , 99,048 controls
]
 European FinnGen
GWAS Catalog: GCST90011816
[
  • 6,563 cases
  • , 219,686 controls
]
 European KP, UKB
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
—
[
  • 859 cases
  • , 3,436 controls
]
 European EB — — — — —

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
PPM017102 PSS010125|
European Ancestry|
128,113 individuals
 PGP000435 |
Koel M et al. Hum Mol Genet (2023)
 Reported Trait: Incident cervical cancer HR: 1.33 (0.069) C-index: 0.613 — age, smoking —

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
PSS010125 C53, D06 —
[
  • 235 cases
  • , 127,878 controls
]
,
0.0 % Male samples
 — European — EB —