Polygenic Score (PGS) ID: PGS000642

Predicted Trait
Reported Trait Non-Hodgkin's lymphoma
Mapped Trait(s) non-Hodgkins lymphoma (EFO_0005952)
Additional Trait Information PheCode 202.2
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_PT_UKB_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-09
Variants
Original Genome Build GRCh37
Number of Variants 10
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
25,391 individuals (100%)
Score Development/Training
European: 100%
9,923 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000448
Europe PMC: 19620980
 781 individuals European NR
GWAS Catalog: GCST000734
Europe PMC: 20639881
 1,431 individuals European NR
GWAS Catalog: GCST001051
Europe PMC: 21533074
 1,170 individuals European NR
GWAS Catalog: GCST002636
Europe PMC: 25261932
 11,523 individuals European NR
GWAS Catalog: GCST002643
Europe PMC: 25279986
 10,486 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
Europe PMC: 32991828
[
  • 901 cases
  • , 9,022 controls
]
 European UKB PheCode:202.2; ICD9:200, 200.2, 200.8, 202.1, 202.2, 202.8, 202.9; ICD10:B21.1, C82.0, C82.1, C82.2, C82.7, C82.9, C83.0, C83.1, C83.2, C83.3, C83.4, C83.5, C83.6, C83.7, C83.8, C83.9, C84.0, C84.1, C84.2, C84.3, C84.4, C84.5, C85.0, C85.1, C85.7, C85.9, C96.7, C96.9, L41.2 — — — —

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
PPM001327 PSS000580|
European Ancestry|
9,952 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Non-Hodgkins lymphoma OR: 1.239 [1.16, 1.324]
β: 0.214 (0.0337)		 AUROC: 0.547 [0.527, 0.566] Nagelkerke's Pseudo-R²: 0.0087
Brier score: 0.082
Odds Ratio (OR, top 1% vs. Rest): 2.05 [1.24, 3.4]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_PT_UKB_20200608

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
PSS000580 PheCode:202.2; ICD9:200, 200.2, 200.8, 202.1, 202.2, 202.8, 202.9; ICD10:B21.1, C82.0, C82.1, C82.2, C82.7, C82.9, C83.0, C83.1, C83.2, C83.3, C83.4, C83.5, C83.6, C83.7, C83.8, C83.9, C84.0, C84.1, C84.2, C84.3, C84.4, C84.5, C85.0, C85.1, C85.7, C85.9, C96.7, C96.9, L41.2 —
[
  • 901 cases
  • , 9,051 controls
]
 — European — UKB —