PGS Catalog - PGS000050 / Breast cancer (Polygenic Score)

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

Download Score FTP directory

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)

Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
Europe PMC: 23535825	49,216 individuals [ 23,637 cases , 25,579 controls ] , 0.0 % Male samples	East Asian	10 cohorts ACP ,BCAC ,HERPACC ,LAABC ,MYBRCA ,SBCGS ,SEBCS ,SGBCC ,TBCS ,TWBCS
GWAS Catalog: GCST000343 Europe PMC: 19219042	3,027 individuals	East Asian	SGWAS
GWAS Catalog: GCST002537 Europe PMC: 25038754	9,450 individuals	East Asian	SGWAS

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)	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
PPM000126	PSS000078\| East Asian Ancestry\| 23,567 individuals	PGP000035 \| Wen W et al. Breast Cancer Res (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	PSS000079\| East Asian Ancestry\| 5,152 individuals	PGP000035 \| Wen W et al. Breast Cancer Res (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)	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	—	—	23,567 individuals [ 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	—	—	5,152 individuals [ 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.