Polygenic Score (PGS) ID: PGS000648

Predicted Trait
Reported Trait Chronic lymphocytic leukemia
Mapped Trait(s) chronic lymphocytic leukemia (EFO_0000095)
Additional Trait Information PheCode 204.12
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=7e-06
Variants
Original Genome Build GRCh37
Number of Variants 44
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%
51,308 individuals (100%)
Score Development/Training
European: 100%
730 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: GCST000224
Europe PMC: 18758461
 1,943 individuals European NR
GWAS Catalog: GCST002073
Europe PMC: 23770605
 8,400 individuals European NR
GWAS Catalog: GCST002299
Europe PMC: 24292274
 6,938 individuals European NR
GWAS Catalog: GCST003468
Europe PMC: 26956414
 10,767 individuals European NR
GWAS Catalog: GCST004146
Europe PMC: 28165464
 17,691 individuals European NR
GWAS Catalog: GCST000906
Europe PMC: 21131588
 703 individuals European NR
GWAS Catalog: GCST001570
Europe PMC: 22700719
 4,866 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
[
  • 67 cases
  • , 663 controls
]
 European MGI PheCode:204.12; ICD9CM:204.10, 204.11, 204.12; ICD10CM:C91.1, C91.10, C91.11, C91.12 — — — —

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
PPM001333 PSS000561|
European Ancestry|
756 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Lymphoid leukemia, chronic OR: 2.124 [1.648, 2.738]
β: 0.753 (0.13)		 AUROC: 0.696 [0.621, 0.764] Nagelkerke's Pseudo-R²: 0.102
Brier score: 0.0776
Odds Ratio (OR, top 1% vs. Rest): 12.9 [4.45, 37.6]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_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
PSS000561 PheCode:204.12; ICD9CM:204.10, 204.11, 204.12; ICD10CM:C91.1, C91.10, C91.11, C91.12 —
[
  • 69 cases
  • , 687 controls
]
 — European — MGI —