PGS Catalog - PGS000532 / Breast cancer (female) (Polygenic Score)

Polygenic Score (PGS) ID: PGS000532

Predicted Trait
Reported Trait	Breast cancer (female)
Mapped Trait(s)	breast carcinoma (EFO_0000305)
Additional Trait Information	PheCode 174.1

Released in PGS Catalog: Dec. 15, 2020

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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	PRSWEB_PHECODE174.1_iCOGS-ER-positive-BRCA_LASSOSUM_UKB_20200608
Development Method
Name	lassosum
Parameters	s=0.5;Lambda=0.01129
Variants
Original Genome Build	GRCh37
Number of Variants	12,277
Effect Weight Type	NR

PGS Source
PGS Catalog Publication (PGP) ID	PGP000118
Citation (link to publication)	Fritsche LG et al. Am J Hum Genet (2020)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 1,063,736 individuals (100%)
Score Development/Training	European: 100% 68,451 individuals (100%)
PGS Evaluation	European: 100% 1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

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Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
Europe PMC: 29059683	175,475 individuals [ 69,501 cases , 105,974 controls ]	European	NR
Europe PMC: 29059683	127,442 individuals [ 21,468 cases , 105,974 controls ]	European	NR
Europe PMC: 29059683	228,951 individuals [ 122,977 cases , 105,974 controls ]	European	NR
Europe PMC: 29059683	175,475 individuals [ 69,501 cases , 105,974 controls ]	European	NR
Europe PMC: 29059683	127,442 individuals [ 21,468 cases , 105,974 controls ]	European	NR
Europe PMC: 29059683	228,951 individuals [ 122,977 cases , 105,974 controls ]	European	NR

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Score Development/Training

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Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)	Phenotype Definitions & Methods	Age of Study Participants	Participant Follow-up Time	Additional Ancestry Description	Additional Sample/Cohort Information
Europe PMC: 32991828	68,451 individuals [ 6,234 cases , 62,217 controls ]	European	UKB	PheCode:174.1; ICD9:233.0; ICD10:C50.0, C50.1, C50.2, C50.3, C50.4, C50.5, C50.6, C50.8, C50.9, D05.... 1, D05.7, D05.9, Z85.3Show more	—	—	—	—

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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
PPM001217	PSS000570\| European Ancestry\| 68,531 individuals	PGP000118 \| Fritsche LG et al. Am J Hum Genet (2020)	Reported Trait: Breast cancer [female]	OR: 1.49 [1.451, 1.529] β: 0.399 (0.0134)	AUROC: 0.608 [0.601, 0.615]	Nagelkerke's Pseudo-R²: 0.0285 Brier score: 0.0816 Odds Ratio (OR, top 1% vs. Rest): 3.0 [2.54, 3.54]	age, sex, batch PCs 1-4	Cancer PRSweb PheWAS Results: PRSWEB_PHECODE174.1_iCOGS-ER-positive-BRCA_LASSOSUM_UKB_20200608

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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
PSS000570	PheCode:174.1; ICD9:233.0; ICD10:C50.0, C50.1, C50.2, C50.3, C50.4, C50.5, C50.6, C50.8, C50.9, D05.... 1, D05.7, D05.9, Z85.3Show more	—	68,531 individuals [ 6,242 cases , 62,289 controls ]	—	European	—	UKB	—

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