Polygenic Score (PGS) ID: PGS000874

Predicted Trait
Reported Trait Chronic lymphocytic leukemia
Mapped Trait(s) chronic lymphocytic leukemia (EFO_0000095)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name PRS41_CLL
Development Method
Name Representative SNPs from chronic lymphocytic leukemia susceptibility loci
Parameters Representative SNPs were those with the most significant p value in each locus, p > e-6
Variants
Original Genome Build hg19
Number of Variants 41
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000220
Citation (link to publication) Kleinstern G et al. Blood (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
17,691 individuals (100%)
PGS Evaluation
Not Reported: 50%
European: 25%
African: 12.5%
Multi-ancestry (including European): 12.5%
  • European
  • Not Reported
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004146
Europe PMC: 28165464
 17,691 individuals European 22 cohorts
  • ATBC
  • ,BCCA
  • ,CPSII
  • ,ENGELA
  • ,EPIC
  • ,EpiLymph
  • ,HPFS
  • ,Italian_GxE
  • ,MAYO
  • ,MCCS
  • ,MSKCC
  • ,NCI-SEER
  • ,NHS
  • ,NSW
  • ,NYU-WHS
  • ,PLCO
  • ,SCALE
  • ,UCSF
  • ,UCSF2
  • ,UK-CLL
  • ,UTAH
  • ,Yale

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
PPM002493 PSS001123|
Multi-ancestry (including European)|
3,958 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Chronic lymphocytic leukemia OR: 2.49 [2.28, 2.8] C-index: 0.79 [0.78, 0.8] — Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 3.64 [2.94 - 4.51]
PPM002494 PSS001123|
Multi-ancestry (including European)|
3,958 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Chronic lymphocytic leukemia in individuals with no family history of hematological cancers OR: 2.46 [2.19, 2.76] C-index: 0.791 [0.77, 0.81] — Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 3.29 [2.49 - 4.35]
PPM002495 PSS001123|
Multi-ancestry (including European)|
3,958 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Chronic lymphocytic leukemia in individuals with a family history of hematological cancers OR: 3.79 [2.44, 5.87] C-index: 0.861 [0.82, 0.9] — Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 7.58 [2.74 - 21.0]
PPM002496 PSS001121|
Ancestry Not Reported|
218 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Chronic lymphocytic leukemia OR: 2.44 [1.65, 3.62] C-index: 0.798 [0.74, 0.85] — Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 3.51 [1.39 - 8.86]
PPM002497 PSS001122|
Ancestry Not Reported|
153 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Monoclonal B-cell lymphocytosis OR: 2.3 [1.44, 3.67] C-index: 0.773 [0.7, 0.85] — Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 4.36 [1.45 - 13.1]
PPM002498 PSS001119|
Ancestry Not Reported|
1,468 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Chronic lymphocytic leukemia OR: 3.02 [2.49, 3.65] C-index: 0.779 [0.74, 0.81] — Age, sex Odds Ratio (OR, top 20% vs middle 20%) = 4.47 [2.76 - 7.24]
PPM002499 PSS001120|
Ancestry Not Reported|
1,362 individuals
 PGP000220 |
Kleinstern G et al. Blood (2018)
 Reported Trait: Monoclonal B-cell lymphocytosis OR: 2.81 [2.18, 3.61] C-index: 0.774 [0.73, 0.82] — Age, sex Odds Ratio (OR, top 20% vs middle 20%) = 4.34 [2.21 - 8.50]
PPM002654 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 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 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 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 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 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 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 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 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 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
PSS001119 Cases were individuals with chronic lymphocytic leukemia. —
[
  • 201 cases
  • , 1,267 controls
]
 — Not reported — MAYO Cases were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001120 Cases were individuals with monoclonal B-cell lymphocytosis. —
[
  • 95 cases
  • , 1,267 controls
]
 — Not reported — MAYO Cases were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001121 Cases were individuals with chronic lymphocytic leukemia. —
[
  • 135 cases
  • , 83 controls
]
 — Not reported — NR Cases and controls were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001122 Cases were individuals with monoclonal B-cell lymphocytosis. —
[
  • 95 cases
  • , 58 controls
]
 — Not reported — NR Cases and controls were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001123 Cases were individuals with chronic lymphocytic leukemia (CLL). Of the 3,958 individuals, 242 had a family history (FH) of hematological cancers, whereas 2,409 had no FH of hematological cancers. Of the 242 individuals with a FH, 112 had CLL. Of the 2,409 without a FH, 783 had CLL. FH was defined as a person self-reporting any hematological maligcancy among first-degree relatives. Hematological malignancies were defined as any non-Hodgkin lymphoma, Hodgkin lymphoma, multiple myeloma, or leukemia. —
[
  • 1,499 cases
  • , 2,459 controls
]
,
60.81 % Male samples
 — European, NR — 8 cohorts
  • BC
  • ,ENGELA
  • ,EpiLymph
  • ,MAYO
  • ,NCI-SEER
  • ,NSW
  • ,SCALE
  • ,UCSF2
 Possible significant sample overlap between this dataset and the dataset used to source PRS41_CLL.
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.