PGS Catalog - PGS000638 / Hodgkin's disease (Polygenic Score)

Polygenic Score (PGS) ID: PGS000638

Predicted Trait
Reported Trait	Hodgkin's disease
Mapped Trait(s)	Hodgkins lymphoma (EFO_0000183)
Additional Trait Information	PheCode 201

Released in PGS Catalog: Dec. 15, 2020

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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	PRSWEB_PHECODE201_GWAS-Catalog-r2019-05-03-X201_P_5e-08_MGI_20200608
Development Method
Name	GWAS Hits
Parameters	LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
Variants
Original Genome Build	GRCh37
Number of Variants	16
Effect Weight Type	NR

PGS Source
PGS Catalog Publication (PGP) ID	PGP000118
Citation (link to publication)	Fritsche LG et al. Am J Hum Genet (2020)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 83,473 individuals (100%)
Score Development/Training	European: 100% 736 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: GCST007062 Europe PMC: 30194254	27,750 individuals	European	NR
GWAS Catalog: GCST002480 Europe PMC: 24920014	9,693 individuals	European	NR
GWAS Catalog: GCST000851 Europe PMC: 21037568	5,788 individuals	European	NR
GWAS Catalog: GCST002237 Europe PMC: 24149102	7,882 individuals	European	NR
GWAS Catalog: GCST005209 Europe PMC: 29196614	16,757 individuals	European	NR
GWAS Catalog: GCST005211 Europe PMC: 29196614	15,603 individuals	European	NR

Score Development/Training

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)	Phenotype Definitions & Methods	Age of Study Participants	Participant Follow-up Time	Additional Ancestry Description	Additional Sample/Cohort Information
Europe PMC: 32991828	736 individuals [ 67 cases , 669 controls ]	European	MGI	PheCode:201; ICD9CM:201.00, 201.01, 201.02, 201.03, 201.04, 201.05, 201.06, 201.07, 201.08, 201.10, 201.11, 201.12, 201.13, 201.14, 201.15, 201.16, 201.17, 201.18, 201.20, 201.21, 201.22, 201.23, 201.24, 201.25, 201.26, 201.27, 201.28, 201.40, 201.41, 201.42, 201.43, 201.44, 201.45, 201.46, 201.47, 201.48, 201.50, 201.51, 201.52, 201.53, 201.54, 201.55, 201.56, 201.57, 201.58, 201.60, 201.61, 201.62, 201.63, 201.64, 201.65, 201.66, 201.67, 201.68, 201.70, 201.71, 201.72, 201.73, 201.74, 201.75, 201.76, 201.77, 201.78, 201.90, 201.91, 201.92, 201.93, 201.94, 201.95, 201.96, 201.97, 201.98, V10.72; ICD10CM:C81, C81.0, C81.00, C81.01, C81.02, C81.03, C81.04, C81.05, C81.06, C81.07, C81.08, C81.09, C81.1, C81.10, C81.11, C81.12, C81.13, C81.14, C81.15, C81.16, C81.17, C81.18, C81.19, C81.2, C81.20, C81.21, C81.22, C81.23, C81.24, C81.25, C81.26, C81.27, C81.28, C81.29, C81.3, C81.30, C81.31, C81.32, C81.33, C81.34, C81.35, C81.36, C81.37, C81.38, C81.39, C81.4, C81.40, C81.41, C81.42, C81.43, C81.44, C81.45, C81.46, C81.47, C81.48, C81.49, C81.7, C81.70, C81.71, C81.72, C81.73, C81.74, C81.75, C81.76, C81.77, C81.78, C81.79, C81.9, C81.90, C81.91, C81.92, C81.93, C81.94, C81.95, C81.96, C81.97, C81.98, C81.99	—	—	—	—

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
PPM001323	PSS000559\| European Ancestry\| 775 individuals	PGP000118 \| Fritsche LG et al. Am J Hum Genet (2020)	Reported Trait: Hodgkin's disease	OR: 1.377 [1.08, 1.755] β: 0.32 (0.124)	AUROC: 0.601 [0.535, 0.671]	Nagelkerke's Pseudo-R²: 0.0193 Brier score: 0.0824 Odds Ratio (OR, top 1% vs. Rest): 1.62 [0.258, 10.1]	age, sex, batch PCs 1-4	Cancer PRSweb PheWAS Results: PRSWEB_PHECODE201_GWAS-Catalog-r2019-05-03-X201_P_5e-08_MGI_20200608

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
PSS000559	PheCode:201; ICD9CM:201.00, 201.01, 201.02, 201.03, 201.04, 201.05, 201.06, 201.07, 201.08, 201.10, 201.11, 201.12, 201.13, 201.14, 201.15, 201.16, 201.17, 201.18, 201.20, 201.21, 201.22, 201.23, 201.24, 201.25, 201.26, 201.27, 201.28, 201.40, 201.41, 201.42, 201.43, 201.44, 201.45, 201.46, 201.47, 201.48, 201.50, 201.51, 201.52, 201.53, 201.54, 201.55, 201.56, 201.57, 201.58, 201.60, 201.61, 201.62, 201.63, 201.64, 201.65, 201.66, 201.67, 201.68, 201.70, 201.71, 201.72, 201.73, 201.74, 201.75, 201.76, 201.77, 201.78, 201.90, 201.91, 201.92, 201.93, 201.94, 201.95, 201.96, 201.97, 201.98, V10.72; ICD10CM:C81, C81.0, C81.00, C81.01, C81.02, C81.03, C81.04, C81.05, C81.06, C81.07, C81.08, C81.09, C81.1, C81.10, C81.11, C81.12, C81.13, C81.14, C81.15, C81.16, C81.17, C81.18, C81.19, C81.2, C81.20, C81.21, C81.22, C81.23, C81.24, C81.25, C81.26, C81.27, C81.28, C81.29, C81.3, C81.30, C81.31, C81.32, C81.33, C81.34, C81.35, C81.36, C81.37, C81.38, C81.39, C81.4, C81.40, C81.41, C81.42, C81.43, C81.44, C81.45, C81.46, C81.47, C81.48, C81.49, C81.7, C81.70, C81.71, C81.72, C81.73, C81.74, C81.75, C81.76, C81.77, C81.78, C81.79, C81.9, C81.90, C81.91, C81.92, C81.93, C81.94, C81.95, C81.96, C81.97, C81.98, C81.99	—	775 individuals [ 71 cases , 704 controls ]	—	European	—	MGI	—