Polygenic Score (PGS) ID: PGS000050

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Dec. 18, 2019
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRS44
Development Method
Name Genome-wide significant variants
Parameters SNPs confirmed to be associated with breast cancer risk in Asian women (p-value < 0.05)
Variants
Original Genome Build hg19
Number of Variants 44
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000035
Citation (link to publication) Wen W et al. Breast Cancer Res (2016)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
61,693 individuals (100%)
PGS Evaluation
East Asian: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
Europe PMC: 23535825
[
  • 23,637 cases
  • , 25,579 controls
]
,
0.0 % Male samples
East Asian10 cohorts
  • ACP
  • ,BCAC
  • ,HERPACC
  • ,LAABC
  • ,MYBRCA
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TBCS
  • ,TWBCS
GWAS Catalog: GCST000343
Europe PMC: 19219042
3,027 individualsEast AsianSGWAS
GWAS Catalog: GCST002537
Europe PMC: 25038754
9,450 individualsEast AsianSGWAS
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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)
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
PPM000126PSS000078|
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
PPM000127PSS000079|
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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