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(Variants and weights)

Polygenic Score (PGS) ID: PGS000072

Predicted Trait

Reported Trait: Breast cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): breast carcinoma

Score Details

Name: CC_Breast

Original Genome Build: GRCh37
Number of Variants: 187

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: GCST002346
PubMed: 24493630
6,225 individuals European
GWAS Catalog: GCST001224
PubMed: 21908515
4,128 individuals East Asian
GWAS Catalog: GCST003842
PubMed: 27117709
19,291 individuals European
GWAS Catalog: GCST000952
PubMed: 21263130
6,346 individuals European
GWAS Catalog: GCST000162
PubMed: 18326623
548 individuals European
GWAS Catalog: GCST000811
PubMed: 20872241
8,428 individuals European
GWAS Catalog: GCST001937
PubMed: 23535729
22,627 individuals European
GWAS Catalog: GCST007236
PubMed: 25751625
89,677 individuals European
GWAS Catalog: GCST004988
PubMed: 29059683
139,274 individuals European
GWAS Catalog: GCST005076
PubMed: 29058716
72,261 individuals European
GWAS Catalog: GCST005112
PubMed: 29059430
624 individuals European
GWAS Catalog: GCST001690
PubMed: 23001122
3,618 individuals European
GWAS Catalog: GCST002895
PubMed: 25956309
3,025 individuals European
(Italy)
PubMed: 23717390.0 7,222 individuals
[ 2,750 cases, 4,472 controls]
European
GWAS Catalog: GCST001683
PubMed: 22976474
3,748 individuals African American or Afro-Caribbean
GWAS Catalog: GCST001683
PubMed: 22976474
32,530 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
PPM000192 PSS000111 Graff RE et al. (2020) Reported Trait: Breast cancer OR: 1.26 [1.24 - 1.28] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 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
PSS000111 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): 26000 237,549 individuals
[ 17,901 cases, 219,648 controls]
0.00 % Male samples
European GERA, UKB