PGS Publication: PGP000035

Publication Information (EuropePMC)
Title Prediction of breast cancer risk based on common genetic variants in women of East Asian ancestry.
PubMed ID 27931260(Europe PMC)
doi 10.1186/s13058-016-0786-1
Publication Date Dec. 8, 2016
Journal Breast Cancer Res
Author(s) Wen W, Shu XO, Guo X, Cai Q, Long J, Bolla MK, Michailidou K, Dennis J, Wang Q, Gao YT, Zheng Y, Dunning AM, García-Closas M, Brennan P, Chen ST, Choi JY, Hartman M, Ito H, Lophatananon A, Matsuo K, Miao H, Muir K, Sangrajrang S, Shen CY, Teo SH, Tseng CC, Wu AH, Yip CH, Simard J, Pharoah PD, Hall P, Kang D, Xiang Y, Easton DF, Zheng W.
Released in PGS: Dec. 18, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000050 PRS44 PGP000035
Wen W et al. Breast Cancer Res (2016)
Breast cancer breast carcinoma 44 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000050/ScoringFiles/PGS000050.txt.gz

PGS 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)
Evaluated Score 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
PPM000126 PGS000050 (PRS44) 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).
PPM000127 PGS000050 (PRS44) 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).

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
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.