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(Variants and weights)

Polygenic Score (PGS) ID: PGS000050

Predicted Trait

Reported Trait: Breast cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): breast carcinoma

Score Details

Name: PRS44

Original Genome Build: hg19
Number of Variants: 44

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: SNPs confirmed to be associated with breast cancer risk in Asian women (p-value < 0.05)

Citation: Wen W et al. Breast Cancer Res (2016) | PGS Catalog Publication ID: PGP000035

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
PubMed: 23535825.0 49,216 individuals
[ 23,637 cases, 25,579 controls]
0.00 %% Male samples
East Asian
GWAS Catalog: GCST000343
PubMed: 19219042
3,027 individuals East Asian
GWAS Catalog: GCST002537
PubMed: 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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000126 PSS000078 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).
PPM000127 PSS000079 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).

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000078 23,567 individuals
[ 11,905 cases, 11,662 controls]
0.00 %% Male samples
East Asian ACP, BCAC, HERPACC, LAABC, MYBRCA, SBCGS, SGWAS, SGBCC, TWBCS, TBCS, SEBCS
PSS000079 5,152 individuals
[ 2,867 cases, 2,285 controls]
0.00 %% Male samples
East Asian
(Chinese)
SGWAS SGWAS (Stage 1). Smaller set of the larger test set from this study.