Polygenic Score (PGS) ID: PGS000645

Predicted Trait
Reported Trait Lymphoid leukemia
Mapped Trait(s) lymphoid leukemia (EFO_0004289)
Additional Trait Information PheCode 204.1
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE204.1_C-LYMPHOID-LEUKAEMIA_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-06
Variants
Original Genome Build GRCh37
Number of Variants 6
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%
361,194 individuals (100%)
Score Development/Training
European: 100%
1,100 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 518 cases
  • , 360,676 controls
]
 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
[
  • 100 cases
  • , 1,000 controls
]
 European MGI PheCode:204.1; ICD9CM:204.00, 204.01, 204.02, 204.10, 204.11, 204.12, 204.20, 204.21, 204.22, 204.80, 204.81, 204.82, 204.90, 204.91, 204.92, V10.61; ICD10CM:C91, C91.0, C91.00, C91.01, C91.02, C91.1, C91.10, C91.11, C91.12, C91.3, C91.30, C91.31, C91.32, C91.4, C91.40, C91.41, C91.42, C91.5, C91.50, C91.51, C91.52, C91.6, C91.60, C91.61, C91.62, C91.9, C91.90, C91.91, C91.92, C91.A, C91.A0, C91.A1, C91.A2, C91.Z, C91.Z0, C91.Z1, C91.Z2 — — — —

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
PPM001330 PSS000562|
European Ancestry|
957 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Lymphoid leukemia OR: 1.358 [1.113, 1.657]
β: 0.306 (0.102)		 AUROC: 0.578 [0.517, 0.642] Nagelkerke's Pseudo-R²: 0.0193
Brier score: 0.0819
Odds Ratio (OR, top 1% vs. Rest): 3.69 [1.01, 13.4]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.1_C-LYMPHOID-LEUKAEMIA_PT_MGI_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
PSS000562 PheCode:204.1; ICD9CM:204.00, 204.01, 204.02, 204.10, 204.11, 204.12, 204.20, 204.21, 204.22, 204.80, 204.81, 204.82, 204.90, 204.91, 204.92, V10.61; ICD10CM:C91, C91.0, C91.00, C91.01, C91.02, C91.1, C91.10, C91.11, C91.12, C91.3, C91.30, C91.31, C91.32, C91.4, C91.40, C91.41, C91.42, C91.5, C91.50, C91.51, C91.52, C91.6, C91.60, C91.61, C91.62, C91.9, C91.90, C91.91, C91.92, C91.A, C91.A0, C91.A1, C91.A2, C91.Z, C91.Z0, C91.Z1, C91.Z2 —
[
  • 87 cases
  • , 870 controls
]
 — European — MGI —