Polygenic Score (PGS) ID: PGS000077

Predicted Trait
Reported Trait Lymphocytic leukemia
Mapped Trait(s) lymphoid leukemia (EFO_0004289)
Released in PGS Catalog: Feb. 12, 2020
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name CC_LL
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 75
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 84.3%
Hispanic or Latin American: 9%
African: 3.7%
Multi-ancestry (excluding European): 3%
  • African
  • Additional Asian Ancestries
145,871 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003468
Europe PMC: 26956414
 10,767 individuals European NR
GWAS Catalog: GCST002073
Europe PMC: 23770605
 8,400 individuals European NR
GWAS Catalog: GCST005965
Europe PMC: 29296818
 3,220 individuals European NR
GWAS Catalog: GCST000224
Europe PMC: 18758461
 1,943 individuals European B58C
GWAS Catalog: GCST001320
Europe PMC: 22076464
 893 individuals European NR
GWAS Catalog: GCST002657
Europe PMC: 25310577
 1,550 individuals European NR
GWAS Catalog: GCST004146
Europe PMC: 28165464
 17,691 individuals European NR
GWAS Catalog: GCST004099
Europe PMC: 28112199
 14,421 individuals European NR
GWAS Catalog: GCST002236
Europe PMC: 24141364
 4,344 individuals African American or Afro-Caribbean, Asian unspecified COG
GWAS Catalog: GCST002236
Europe PMC: 24141364
 1,541 individuals European COG
GWAS Catalog: GCST002236
Europe PMC: 24141364
 1,287 individuals Hispanic or Latin American COG
GWAS Catalog: GCST000463
Europe PMC: 19684604
 3,305 individuals European NR
GWAS Catalog: GCST002299
Europe PMC: 24292274
 6,938 individuals European UK-CLL
GWAS Catalog: GCST000464
Europe PMC: 19684603
 19,275 individuals European COG, GAIN, SJCRH, WTCCC
GWAS Catalog: GCST003798
Europe PMC: 27694927
 8,882 individuals European NR
GWAS Catalog: GCST005832
Europe PMC: 29632299
 17,051 individuals European NR
GWAS Catalog: GCST005315
Europe PMC: 29348612
 3,972 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST005315
Europe PMC: 29348612
 4,735 individuals European NR
GWAS Catalog: GCST005315
Europe PMC: 29348612
 10,533 individuals Hispanic or Latin American NR
GWAS Catalog: GCST001912
Europe PMC: 23512250
 1,452 individuals African American or Afro-Caribbean MESA
GWAS Catalog: GCST001912
Europe PMC: 23512250
 1,313 individuals Hispanic or Latin American MESA
GWAS Catalog: GCST001912
Europe PMC: 23512250
 2,358 individuals European MESA

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
PPM000197 PSS000116|
European Ancestry|
411,207 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Lymphocytic leukemia OR: 1.42 [1.33, 1.51] — — Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002043 PSS001016|
European Ancestry|
391,338 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident Lymphocytic Leukemia HR: 1.45 [1.31, 1.61] AUROC: 0.719
C-index: 0.735 (0.016)		 — Age at assessment, sex, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017175 PSS010147|
European Ancestry|
246 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Lymphocytic leukemia HR: 1.5 [1.33, 1.69] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index —

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
PSS010147 — —
[
  • 24 cases
  • , 222 controls
]
 — European — UKB —
PSS000116 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 35011 - 35013 —
[
  • 853 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
PSS001016 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 340 cases
  • , 390,998 controls
]
 — European — UKB —