PGS Catalog - PGS003448 / Acute lymphoblastic leukemia (Polygenic Score)

Polygenic Score (PGS) ID: PGS003448

Predicted Trait
Reported Trait	Acute lymphoblastic leukemia
Mapped Trait(s)	acute lymphoblastic leukemia (EFO_0000220)

Released in PGS Catalog: March 24, 2023

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Score Details

Score Construction
PGS Name	PRS15_ALL
Development Method
Name	Genome-wide significant SNPs
Parameters	NR
Variants
Original Genome Build	hg19
Number of Variants	15
Effect Weight Type	log(OR)

PGS Source
PGS Catalog Publication (PGP) ID	PGP000448
Citation (link to publication)	Berndt SI et al. Leukemia (2022)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 80.7% Hispanic or Latin American: 14% African: 5.3% 75,027 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: GCST001320 Europe PMC: 22076464	893 individuals	European	NR
GWAS Catalog: GCST002158 Europe PMC: 23996088	6,381 individuals	European	NR
GWAS Catalog: GCST000463 Europe PMC: 19684604	3,305 individuals	European	NR
GWAS Catalog: GCST005832 Europe PMC: 29632299	17,051 individuals	European	NR
GWAS Catalog: GCST000464 Europe PMC: 19684603	19,275 individuals	European	NR
GWAS Catalog: GCST003798 Europe PMC: 27694927	8,882 individuals	European	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: GCST005315 Europe PMC: 29348612	3,972 individuals	African American or Afro-Caribbean	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
PPM017230	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Chronic lymphocytic leukemia	OR: 0.95 [0.9, 1.0]	—	—	—	—
PPM017238	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Diffuse large B-cell lymphoma	OR: 0.99 [0.94, 1.04]	—	—	—	—
PPM017246	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Follicular lymphoma	OR: 1.01 [0.95, 1.06]	—	—	—	—
PPM017254	PSS010176\| European Ancestry\| 20,134 individuals	PGP000448 \| Berndt SI et al. Leukemia (2022)	Reported Trait: Marginal zone lymphoma	OR: 1.02 [0.93, 1.12]	—	—	—	—

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
PSS010176	—	—	20,134 individuals [ 10,629 cases , 9,505 controls ]	—	European	—	NR	Inter- Lymph Consortium