Polygenic Score (PGS) ID: PGS000213

Predicted Trait
Reported Trait Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like)
Mapped Trait(s) Her2-receptor negative breast cancer (MONDO_0000618)
Released in PGS: July 14, 2020

Score Details

Score Construction
PGS Name PRS330_LumBHER2neg
Original Genome Build GRCh37
Number of Variants 330
Development Method
Name Fixed-effects two-stage polytomous model
Parameters 313 variants from Mavaddat et al (PGS000004) plus 17 independent variants (P < 5.0 × 10−8, r2 threshold 0.1) from this publication, weights derived from the all-subtype analysis
PGS Source
PGS Catalog Publication (PGP) ID PGP000088
Citation (link to publication) Zhang H et al. Nat Genet (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST010099
EuropePMC: 32424353
197,755 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
PGS Sample Set 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
PPM000652 PSS000361 PGP000088
Zhang H et al. (2020)
Reported Trait: Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like) OR: 1.62[1.54, 1.7] AUROC: 0.633

Evaluated Samples

PGS Sample Set ID
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000361 Defined intrinsic-like breast cancer subtypes based on tumor status of ER, PR, HER2 and grade: (2) luminal B/HER2-negative-like (ER+ and/or PR+, HER2-, grade 3)
  • 1,779 cases
  • , 20,815 controls
0.0 % Male samples
European 6 cohorts
  • BCAC
  • ,MMHS
  • ,PLCO
  • ,UKBGS
  • ,pKARMA
Heldout subset (20%) of the BCAC consortium data