Polygenic Score (PGS) ID: PGS000072

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_Breast
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 187
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 98.1%
East Asian: 1%
African: 0.9%
419,572 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001937
Europe PMC: 23535729
22,627 individuals European NR
GWAS Catalog: GCST007236
Europe PMC: 25751625
89,677 individuals European NR
GWAS Catalog: GCST004988
Europe PMC: 29059683
139,274 individuals European NR
GWAS Catalog: GCST005076
Europe PMC: 29058716
72,261 individuals European NR
GWAS Catalog: GCST005112
Europe PMC: 2905943
624 individuals European NR
GWAS Catalog: GCST001690
Europe PMC: 23001122
3,618 individuals European NR
GWAS Catalog: GCST002895
Europe PMC: 25956309
3,025 individuals European
(Italy)
NR
Europe PMC: 2371739
[
  • 2,750 cases
  • , 4,472 controls
]
European NR
GWAS Catalog: GCST001224
Europe PMC: 21908515
4,128 individuals East Asian NR
GWAS Catalog: GCST000952
Europe PMC: 2126313
6,346 individuals European NR
GWAS Catalog: GCST000811
Europe PMC: 20872241
8,428 individuals European NR
GWAS Catalog: GCST000162
Europe PMC: 18326623
548 individuals European NR
GWAS Catalog: GCST001683
Europe PMC: 22976474
32,530 individuals European NR
GWAS Catalog: GCST001683
Europe PMC: 22976474
3,748 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST002346
Europe PMC: 2449363
6,225 individuals European NR
GWAS Catalog: GCST003842
Europe PMC: 27117709
19,291 individuals European 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
PPM000192 PSS000111|
European Ancestry|
237,549 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
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
PPM002038 PSS001011|
European Ancestry|
216,273 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.
Reported Trait: Incident breast cancer HR: 1.52 [1.47, 1.56] AUROC: 0.637
C-index: 632.0 (0.005)
Age at assessment, family history of breast cancer, genotyping array, PCs(1-15), parity( ≥1 live birth vs. none), age at menarche, body mass index, menopausal status (pre-menopausal vs. post-menopausal vs. unknown or hysterectomy), ever used hormone replacement therapy, oral contraceptive use, alcool intake, body mass index*menopausal status Only 162 of the original 187 SNPs used based on those that reached p<5e-8 in the BCAC meta-analysis. 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
PSS001011 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases.
[
  • 4,760 cases
  • , 211,513 controls
]
,
0.0 % Male samples
European UKB
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
[
  • 17,901 cases
  • , 219,648 controls
]
,
0.0 % Male samples
European GERA, UKB