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(Variants and weights)

Polygenic Score (PGS) ID: PGS000077

Predicted Trait

Reported Trait: Lymphocytic leukemia
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): lymphoid leukemia

Score Details

Name: CC_LL

Original Genome Build: GRCh37
Number of Variants: 75

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: GCST003468
PubMed: 26956414
10,767 individuals European
GWAS Catalog: GCST002073
PubMed: 23770605
8,400 individuals European
GWAS Catalog: GCST005965
PubMed: 29296818
3,220 individuals European
GWAS Catalog: GCST000224
PubMed: 18758461
1,943 individuals European
GWAS Catalog: GCST001320
PubMed: 22076464
893 individuals European
GWAS Catalog: GCST002657
PubMed: 25310577
1,550 individuals European
GWAS Catalog: GCST004146
PubMed: 28165464
17,691 individuals European
GWAS Catalog: GCST004099
PubMed: 28112199
14,421 individuals European
GWAS Catalog: GCST002236
PubMed: 24141364
4,344 individuals African American or Afro-Caribbean, Asian unspecified
GWAS Catalog: GCST002236
PubMed: 24141364
1,541 individuals European
GWAS Catalog: GCST002236
PubMed: 24141364
1,287 individuals Hispanic or Latin American
GWAS Catalog: GCST000463
PubMed: 19684604
3,305 individuals European
GWAS Catalog: GCST002299
PubMed: 24292274
6,938 individuals European
GWAS Catalog: GCST000464
PubMed: 19684603
19,275 individuals European
GWAS Catalog: GCST003798
PubMed: 27694927
8,882 individuals European
GWAS Catalog: GCST005832
PubMed: 29632299
17,051 individuals European
GWAS Catalog: GCST005315
PubMed: 29348612
3,972 individuals African American or Afro-Caribbean
GWAS Catalog: GCST005315
PubMed: 29348612
4,735 individuals European
GWAS Catalog: GCST005315
PubMed: 29348612
10,533 individuals Hispanic or Latin American
GWAS Catalog: GCST001912
PubMed: 23512250
1,452 individuals African American or Afro-Caribbean
GWAS Catalog: GCST001912
PubMed: 23512250
1,313 individuals Hispanic or Latin American
GWAS Catalog: GCST001912
PubMed: 23512250
2,358 individuals European

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
PPM000197 PSS000116 Graff RE et al. (2020) Reported Trait: Lymphocytic leukemia OR: 1.42 [1.33 - 1.51] 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
PSS000116 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): 35011 - 35013 411,207 individuals
[ 853 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB