Publication: Prediction of breast cancer risk based on common genetic variants in women of East Asian ancestry.
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 MetricsDisclaimer: 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).|
|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|
[ 11,905 cases, 11,662 controls]
0.00 %% Male samples
|East Asian||—||ACP, BCAC, HERPACC, LAABC, MYBRCA, SBCGS, SGWAS, SGBCC, TWBCS, TBCS, SEBCS||—|
[ 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.|