PGS Publication: PGP000234

Publication Information (EuropePMC)
Title Polygenic risk score and risk of monoclonal B-cell lymphocytosis in caucasians and risk of chronic lymphocytic leukemia (CLL) in African Americans.
PubMed ID 34285341(Europe PMC)
doi 10.1038/s41375-021-01344-9
Publication Date July 20, 2021
Journal Leukemia
Author(s) Kleinstern G, Weinberg JB, Parikh SA, Braggio E, Achenbach SJ, Robinson DP, Norman AD, Rabe KG, Boddicker NJ, Vachon CM, Lesnick CE, Call TG, Brander DM, Rassenti LZ, Kipps TJ, Olson JE, Cerhan JR, Kay NE, Furman RR, Hanson CA, Shanafelt TD, Slager SL.
Released in PGS Catalog: Sept. 17, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000874
(PRS41_CLL)
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Chronic lymphocytic leukemia chronic lymphocytic leukemia 41
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000874/ScoringFiles/PGS000874.txt.gz

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) 		Evaluated Score 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
PPM002654 PGS000874
(PRS41_CLL)
 PSS001173|
European Ancestry|
3,191 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Monoclonal B-cell lymphocytosis OR: 1.86 [1.67, 2.07] C-index: 0.72 [0.69, 0.73] Odds Ratio (OR, top 20% vs middle 20%): 2.38 [1.81, 3.13] Age, sex —
PPM002655 PGS000874
(PRS41_CLL)
 PSS001173|
European Ancestry|
3,191 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Monoclonal B-cell lymphocytosis OR: 1.15 [1.13, 1.18] C-index: 0.72 [0.7, 0.74] — Age, sex An unweighted version of PRS41_CLL was used.
PPM002656 PGS000874
(PRS41_CLL)
 PSS001173|
European Ancestry|
3,191 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Low-count monoclonal B-cell lymphocytosis OR: 1.75 [1.55, 1.98] C-index: 0.72 [0.7, 0.75] Odds Ratio (OR, top 20% vs middle 20%): 2.1 [1.53, 2.88] Age, sex —
PPM002657 PGS000874
(PRS41_CLL)
 PSS001173|
European Ancestry|
3,191 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Low-count monoclonal B-cell lymphocytosis OR: 1.14 [1.11, 1.17] C-index: 0.72 [0.7, 0.75] — Age, sex An unweighted version of PRS41_CLL was used.
PPM002658 PGS000874
(PRS41_CLL)
 PSS001173|
European Ancestry|
3,191 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: High-count monoclonal B-cell lymphocytosis OR: 2.14 [1.8, 2.56] C-index: 0.73 [0.69, 0.77] Odds Ratio (OR, top 20% vs middle 20%): 3.13 [1.97, 4.98] Age, sex —
PPM002659 PGS000874
(PRS41_CLL)
 PSS001173|
European Ancestry|
3,191 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: High-count monoclonal B-cell lymphocytosis OR: 1.19 [1.14, 1.23] C-index: 0.725 [0.69, 0.77] — Age, sex An unweighted version of PRS41_CLL was used.
PPM002660 PGS000874
(PRS41_CLL)
 PSS001172|
European Ancestry|
3,327 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Chronic lymphocytic leukemia OR: 2.53 [2.27, 2.81] C-index: 0.77 [0.75, 0.79] Odds Ratio (OR, top 20% vs middle 20%): 3.49 [2.70, 4.51] Age, sex —
PPM002661 PGS000874
(PRS41_CLL)
 PSS001172|
European Ancestry|
3,327 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Chronic lymphocytic leukemia OR: 1.23 [1.2, 1.26] C-index: 0.775 [0.76, 0.79] — Age, sex An unweighted version of PRS41_CLL was used.
PPM002662 PGS000874
(PRS41_CLL)
 PSS001171|
African Ancestry|
408 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Chronic lymphocytic leukemia OR: 1.76 [1.34, 2.31] C-index: 0.62 [0.57, 0.68] — Age, sex —
PPM002663 PGS000874
(PRS41_CLL)
 PSS001171|
African Ancestry|
408 individuals
 PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.		 Reported Trait: Chronic lymphocytic leukemia OR: 1.07 [1.01, 1.13] C-index: 0.57 [0.53, 0.64] — Age, sex An unweighted version of PRS41_CLL was used.

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
PSS001171 Cases were individuals with chronic lymphocytic leukemia (CLL). CLL diagnoses were made based on the 1996 NCI working group criteria and updated to the 2008 International Workshop CLL criteria wherever possible. —
[
  • 173 cases
  • , 235 controls
]
,
66.91 % Male samples
 — African American or Afro-Caribbean — MAYO Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL. Additional cases were obtained from Duke University and Cornell
PSS001172 Cases were individuals with chronic lymphocytic leukemia (CLL). CLL diagnoses were made based on the 1996 NCI working group criteria and updated to the 2008 International Workshop CLL criteria wherever possible. —
[
  • 696 cases
  • , 2,631 controls
]
,
45.36 % Male samples
 — European — MAYO Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL. Additional cases were obtained from Duke University and Cornell
PSS001173 Cases were individuals with monoclonal B-cell lymphocytosis (MBL) from two Mayo Clincs.Within the Mayo Clinic Biobank, MBL was screened for using a highly sensitive, 8-color (CD38, CD45, Kappa, Lambda, CD19, CD23, CD5 and CD20) flow-cytometry assay with the capacity to detect clonal B-cell counts to the 0.005% level (1/20,000 events), and for each individual, 500,000 PBMC events were typically captured. Of the 560 MBL cases, 396 had low-count MBL (LC-MBL) and 164 had high-count MBL (HC-MBL). Wiithin the Mayo Clinic Biobank only a subset of participants had a complete blood count. therefore the percent of clonal B-cells out of total B-cells was used to categorize participants as LC- and HC-MBL. Based on prior evidence, those MBL individuals with a percent clonal B-cell <85% were defined as LC-MBL and those with percent clonal B-cells ≥85% as HC-MBL. Within the Mayo Clinic Chronic lymphocytic leukemia (CLL) Resource, MBL was classified by LC-MBL or HC-MBL according to the B-cell clone size of below or above 0.5 × 109/L threshold, respectively. —
[
  • 560 cases
  • , 2,631 controls
]
,
42.28 % Male samples
 — European — MAYO Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL.