PGS Catalog - PGS000029 / Breast cancer (Polygenic Score)

Polygenic Score (PGS) ID: PGS000029

Predicted Trait
Reported Trait	Breast cancer
Mapped Trait(s)	breast carcinoma (EFO_0000305)

Released in PGS Catalog: Oct. 14, 2019

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Score Details

Score Construction
PGS Name	PRS_AS
Development Method
Name	composite likelihood ratio
Parameters	SNPs with p<5x10-8 in studies of invasive breast cancer in Asian populations, or proxy SNP on Illumina Oncoarray in strong LD (r2>0.9)
Variants
Original Genome Build	hg38
Number of Variants	76
Effect Weight Type	log(OR)

PGS Source
PGS Catalog Publication (PGP) ID	PGP000018
Citation (link to publication)	Shieh Y et al. Breast Cancer Res Treat (2016)

Ancestry Distribution
Source of Variant Associations (GWAS)	East Asian: 100% 59,199 individuals (100%)
PGS Evaluation	East Asian: 100% 1 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	NR
GWAS Catalog: GCST001420 Europe PMC: 22383897	5,242 individuals	East Asian	NR
GWAS Catalog: GCST002234 Europe PMC: 2414319	4,741 individuals	East Asian	NR

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
PPM000058	PSS000038\| East Asian Ancestry\| 102 individuals	PGP000018 \| Shieh Y et al. Breast Cancer Res Treat (2016)	Reported Trait: Breast cancer	—	AUROC: 0.72 [0.62, 0.82]	—	BCSC risk model	BCSC risk model includes mammographic breast density, age, ethnicity, first-degree relative with breast cancer, and history of breast biopsy
PPM000057	PSS000038\| East Asian Ancestry\| 102 individuals	PGP000018 \| Shieh Y et al. Breast Cancer Res Treat (2016)	Reported Trait: Breast cancer	—	AUROC: 0.64 [0.53, 0.74]	—	—	—

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
PSS000038	Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded.	—	102 individuals [ 51 cases , 51 controls ] , 0.0 % Male samples	—	East Asian	—	CPMCBHC	Nested case-control study from the CPMC Breast Health Cohort.