Polygenic Score (PGS) ID: PGS000080

Predicted Trait
Reported Trait Non-Hodgkin's lymphoma
Mapped Trait(s) non-Hodgkins lymphoma (EFO_0005952)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_NHL
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 19
Effect Weight Type log(OR)
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: 85.3%
Not Reported: 14.7%
34,043 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: GCST002636
Europe PMC: 25261932
 11,523 individuals European NR
GWAS Catalog: GCST002643
Europe PMC: 25279986
 10,486 individuals European NR
GWAS Catalog: GCST002742
Europe PMC: 25569183
 7,046 individuals European NR
GWAS Catalog: GCST001826
Europe PMC: 2334964
 4,988 individuals NR NR

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
PPM000200 PSS000119|
European Ancestry|
412,765 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Non-Hodgkin's lymphoma OR: 1.25 [1.2, 1.3] — — Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002046 PSS001019|
European Ancestry|
391,968 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident non-hodgkin's lymphoma HR: 1.16 [1.09, 1.24] AUROC: 0.677
C-index: 0.676 (0.01)		 — 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.
PPM017168 PSS010148|
European Ancestry|
721 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Non-Hodgkin's lymphoma HR: 1.19 [1.11, 1.28] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —

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
PSS001019 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 970 cases
  • , 390,998 controls
]
 — European — UKB —
PSS010148 — —
[
  • 61 cases
  • , 660 controls
]
 — European — UKB —
PSS000119 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): 33041, and 33042 —
[
  • 2,411 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —