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
Variants
Original Genome Build GRCh37
Number of Variants 187
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST001937
EuropePMC: 23535729		 22,627 individuals European
GWAS Catalog: GCST007236
EuropePMC: 25751625		 89,677 individuals European
GWAS Catalog: GCST004988
EuropePMC: 29059683		 139,274 individuals European
GWAS Catalog: GCST005076
EuropePMC: 29058716		 72,261 individuals European
GWAS Catalog: GCST005112
EuropePMC: 2905943		 624 individuals European
GWAS Catalog: GCST001690
EuropePMC: 23001122		 3,618 individuals European
GWAS Catalog: GCST002895
EuropePMC: 25956309		 3,025 individuals European
(Italy)
EuropePMC: 2371739
[
  • 2,750 cases
  • , 4,472 controls
]
 European
GWAS Catalog: GCST001683
EuropePMC: 22976474		 3,748 individuals African American or Afro-Caribbean
GWAS Catalog: GCST001683
EuropePMC: 22976474		 32,530 individuals European
GWAS Catalog: GCST002346
EuropePMC: 2449363		 6,225 individuals European
GWAS Catalog: GCST001224
EuropePMC: 21908515		 4,128 individuals East Asian
GWAS Catalog: GCST003842
EuropePMC: 27117709		 19,291 individuals European
GWAS Catalog: GCST000952
EuropePMC: 2126313		 6,346 individuals European
GWAS Catalog: GCST000162
EuropePMC: 18326623		 548 individuals European
GWAS Catalog: GCST000811
EuropePMC: 20872241		 8,428 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 ID
(PPM ID) 		PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000192 PSS000111 PGP000050
Graff RE et al. bioRxiv (2020)
Pre		 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 Sample Set ID
(PSS ID) 		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
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 —