Polygenic Score (PGS) ID: PGS000383

Predicted Trait
Reported Trait Malignant neoplasm of rectum, rectosigmoid junction, and anus
Mapped Trait(s)
Additional Trait Information PheCode 153.3
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 1,078,799
Development Method
Name PRS-CS
Parameters Parameters = auto; LD reference (eur)
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
EuropePMC: http://www.nealelab.is/uk-biobank/
[
  • 498 cases
  • , 360,696 controls
]
 European
Score Development/Training
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
PheCode:153.3; ICD9CM:154.0, 154.1, 154.2, 154.3, 209.17, 230.4, 230.5, 230.6, 796.70, 796.71, 796.72, 796.73, 796.74, 796.76, V10.06; ICD10CM:C19, C20, C21.0, C21.1, C7A.026, D01.1, D01.2, D01.3, R85.610, R85.611, R85.612, R85.613, R85.614, R85.619 —
[
  • 344 cases
  • , 3,431 controls
]
 — European — MGI —

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) 		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
PPM001068 PSS000539 PGP000118
Fritsche LG et al. (2020) 		Reported Trait: Malignant neoplasm of rectum, rectosigmoid junction, and anus OR: 1.126 [1.005, 1.262]
β: 0.119 (0.0579)		 AUROC: 0.533 [0.5, 0.567] Nagelkerke's Pseudo-R²: 0.00257
Brier score: 0.0829
Odds Ratio (OR, top 1% vs. Rest): 1.34 [0.491, 3.65]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153.3_C19_PRS-CS_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		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
PSS000539 PheCode:153.3; ICD9CM:154.0, 154.1, 154.2, 154.3, 209.17, 230.4, 230.5, 230.6, 796.70, 796.71, 796.72, 796.73, 796.74, 796.76, V10.06; ICD10CM:C19, C20, C21.0, C21.1, C7A.026, D01.1, D01.2, D01.3, R85.610, R85.611, R85.612, R85.613, R85.614, R85.619 —
[
  • 325 cases
  • , 3,232 controls
]
 — European — MGI —