Polygenic Score (PGS) ID: PGS000050

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS: Dec. 18, 2019

Score Details

Score Construction
PGS Name PRS44
Variants
Original Genome Build hg19
Number of Variants 44
Development Method
Name Genome-wide significant SNPs
Parameters SNPs confirmed to be associated with breast cancer risk in Asian women (p-value < 0.05)
PGS Source
PGS Catalog Publication (PGP) ID PGP000035
Citation (link to publication) Wen W et al. Breast Cancer Res (2016)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
EuropePMC: 23535825.0
[
  • 23,637 cases
  • , 25,579 controls
]
,
0.0 % Male samples
East Asian
GWAS Catalog: GCST000343
EuropePMC: 19219042
3,027 individuals East Asian
GWAS Catalog: GCST002537
EuropePMC: 25038754
9,450 individuals East Asian

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
PPM000127 PSS000079 PGP000035
Wen W et al. (2016)
Reported Trait: Breast cancer C-index: 0.602 C-index improvement (with PRS): 0.0386[0.0259, 0.0513] age at menarche, age at first live birth, waist-to-hip ratio, breast cancer family history, prior benign breast disease Potentially overfit: samples were used to select the variants included in the PRS (see paper's Discussion section for more information).
PPM000126 PSS000078 PGP000035
Wen W et al. (2016)
Reported Trait: Breast cancer AUROC: 0.606 Odds Ratio (OR; per decile of PRS): 1.13[1.12, 1.14] NR Potentially overfit: samples were used to select the variants included in the PRS (see paper's Discussion section for more information).

Evaluated Samples

PGS Sample Set ID
(PSS 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
PSS000078
[
  • 11,905 cases
  • , 11,662 controls
]
,
0.0 % Male samples
East Asian 11 cohorts
  • ACP
  • ,BCAC
  • ,HERPACC
  • ,LAABC
  • ,MYBRCA
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,SGWAS
  • ,TBCS
  • ,TWBCS
PSS000079
[
  • 2,867 cases
  • , 2,285 controls
]
,
0.0 % Male samples
East Asian
(Chinese)
SGWAS SGWAS (Stage 1). Smaller set of the larger test set from this study.