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, Dun... ning 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.Show more
Released in PGS Catalog: Dec. 18, 2019

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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Polygenic Score ID & Name
PGS Publication ID (PGP)
Reported Trait
Mapped Trait(s) (Ontology)
Number of Variants
Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS000050
(PRS44)
PGP000035 |
Wen W et al. Breast Cancer Res (2016)
Breast cancerbreast carcinoma44
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000050/ScoringFiles/PGS000050.txt.gz
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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.

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PGS Performance
Metric ID (PPM)
Evaluated Score
PGS Sample Set ID
(PSS)
Performance Source
Trait
PGS Effect Sizes
(per SD change)
Classification Metrics
Other Metrics
Covariates Included in the Model
PGS Performance:
Other Relevant Information
PPM000126PGS000050
(PRS44)
PSS000078|
East Asian Ancestry|
23,567 individuals
PGP000035 |
Wen W et al. Breast Cancer Res (2016)
Reported Trait: Breast cancer—AUROC: 0.606Odds Ratio (OR; per decile of PRS): 1.13 [1.12, 1.14]NRPotentially overfit: samples were used to select the variants included in the PRS (see paper's Discu... ssion section for more information).Show more
PPM000127PGS000050
(PRS44)
PSS000079|
East Asian Ancestry|
5,152 individuals
PGP000035 |
Wen W et al. Breast Cancer Res (2016)
Reported Trait: Breast cancer—C-index: 0.602C-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 be... nign breast diseaseShow morePotentially overfit: samples were used to select the variants included in the PRS (see paper's Discu... ssion section for more information).Show more
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Evaluated Samples

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PGS Sample Set ID
(PSS)
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)		—SGWASSGWAS (Stage 1). Smaller set of the larger test set from this study.
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