Polygenic Score (PGS) ID: PGS000791

Predicted Trait
Reported Trait Non-Hodgkin's lymphoma
Mapped Trait(s) non-Hodgkins lymphoma (EFO_0005952)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name CC_NHL_IV
Development Method
Name 19 variants from Graff et al (PGS000080) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 19
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 85.3%
Not Reported: 14.7%
34,043 individuals (100%)
PGS Evaluation
European: 100%
1 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 23 cohorts
  • ATBC
  • ,BCCA
  • ,CPSII
  • ,ELCCS
  • ,ENGELA
  • ,EPIC
  • ,EpiLymph
  • ,GELA
  • ,HPFS
  • ,Iowa-Mayo
  • ,Italian_GxE
  • ,MAYO
  • ,MCCS
  • ,MSKCC
  • ,NCI-SEER
  • ,NHS
  • ,NSW
  • ,NYU-WHS
  • ,PLCO
  • ,SCALE
  • ,UCSF2
  • ,WHI
  • ,Yale
GWAS Catalog: GCST002643
Europe PMC: 25279986
 10,486 individuals European 20 cohorts
  • ATBC
  • ,BCCA
  • ,CPSII
  • ,ELCCS
  • ,EPIC
  • ,EpiLymph
  • ,HPFS
  • ,Iowa-Mayo
  • ,Italian_GxE
  • ,MAYO
  • ,MCCS
  • ,MSKCC
  • ,NCI-SEER
  • ,NHS
  • ,NYU-WHS
  • ,PLCO
  • ,SCALE
  • ,UCSF2
  • ,WHI
  • ,Yale
GWAS Catalog: GCST001826
Europe PMC: 23349640
 4,988 individuals Not reported DFHCC, HPFS, MSKCC, NHS
GWAS Catalog: GCST002742
Europe PMC: 25569183
 7,046 individuals European 22 cohorts
  • ATBC
  • ,BCCA
  • ,CPSII
  • ,ELCCS
  • ,ENGELA
  • ,EPIC
  • ,EpiLymph
  • ,HPFS
  • ,Iowa-Mayo
  • ,Italian_GxE
  • ,MAYO
  • ,MCCS
  • ,MSKCC
  • ,NCI-SEER
  • ,NHS
  • ,NSW
  • ,NYU-WHS
  • ,PLCO
  • ,SCALE
  • ,UCSF2
  • ,WHI
  • ,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
PPM002062 PSS001019|
European Ancestry|
391,968 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident non-hodgkin's lymphoma HR: 1.15 [1.08, 1.22] AUROC: 0.677
C-index: 0.674 (0.01)		 R²: 0.227 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.

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 —