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(Variants and weights)

Polygenic Score (PGS) ID: PGS000080

Predicted Trait

Reported Trait: Non-Hodgkin's lymphoma
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): non-Hodgkins lymphoma

Score Details

Name: CC_NHL

Original Genome Build: GRCh37
Number of Variants: 19

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002636
PubMed: 25261932
11,523 individuals European
GWAS Catalog: GCST002643
PubMed: 25279986
10,486 individuals European
GWAS Catalog: GCST002742
PubMed: 25569183
7,046 individuals European
GWAS Catalog: GCST001826
PubMed: 23349640
4,988 individuals 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000200 PSS000119 Graff RE et al. (2020) 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

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
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 412,765 individuals
[ 2,411 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB