Publication: Prediction of breast cancer risk based on common genetic variants in women of East Asian ancestry.

Information

PGS Catalog Publication (PGP) ID: PGP000035
PubMed ID: 27931260
doi: 10.1186/s13058-016-0786-1

Publication Date: Dec. 8, 2016

Journal: Breast Cancer Res

Authors: 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.

PGS Associated with PGP000035

PGS Developed By This Study

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 (PPM) ID Evaluated Score 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 PGS000050 (PRS44) 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 PGS000050 (PRS44) 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.