Polygenic Score (PGS) ID: PGS000213

Predicted Trait
Reported Trait Breast cancer intrinsic-like subtype (luminal B/HER2-negative-like)
Mapped Trait(s) HER2 negative breast carcinoma (EFO_0009780)
Released in PGS Catalog: July 14, 2020
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRS330_LumBHER2neg
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
Variants
Original Genome Build GRCh37
Number of Variants 330
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000088
Citation (link to publication) Zhang H et al. Nat Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
197,755 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010099
Europe PMC: 32424353
 197,755 individuals European 82 cohorts
  • 2SISTER
  • ,ABCFS
  • ,ABCS
  • ,ABCS-F
  • ,ABCTB
  • ,AHS
  • ,BBCC
  • ,BBCS
  • ,BCAC
  • ,BCEES
  • ,BCFR-NY
  • ,BCFR-PA
  • ,BCFR-UTAH
  • ,BCINIS
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CBCS
  • ,CCGP
  • ,CECILE
  • ,CGPS
  • ,CNIO-BCS
  • ,CPSII
  • ,CTS
  • ,DIETCOMPLYF
  • ,EPIC
  • ,ESTHER
  • ,FHRISK
  • ,GC-HBOC
  • ,GENICA
  • ,GEPARSIXTO
  • ,GESBC
  • ,HABCS
  • ,HCSC
  • ,HEBCS
  • ,HUBCS
  • ,KARBAC
  • ,KARMA
  • ,KBCP
  • ,KCONFAB/AOCS
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MISS
  • ,MMHS
  • ,MSKCC
  • ,MTLGEBCS
  • ,NBCS
  • ,NBHS
  • ,NC-BCFR
  • ,NCBCS
  • ,NHS
  • ,NHS2
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,PLCO
  • ,POSH
  • ,PREFACE
  • ,PROCAS
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SISTER
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
  • ,UKBGS
  • ,UKOPS
  • ,USRT
  • ,WHI
  • ,pKARMA

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
PPM000652 PSS000361|
European Ancestry|
22,594 individuals
 PGP000088 |
Zhang H et al. Nat Genet (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
(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
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
  • ,SISTER
  • ,UKBGS
  • ,pKARMA
 Heldout subset (20%) of the BCAC consortium data