Polygenic Score (PGS) ID: PGS002015

Predicted Trait
Reported Trait Breast cancer (female)
Mapped Trait(s) breast carcinoma (EFO_0000305)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_174.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 488,608
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM010994 PSS009274|
European Ancestry|
10,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.1132 [0.094, 0.1324] sex, age, birth date, deprivation index, 16 PCs —
PPM010995 PSS009048|
European Ancestry|
2,440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.0807 [0.041, 0.1201] sex, age, birth date, deprivation index, 16 PCs —
PPM010996 PSS008602|
European Ancestry|
3,484 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.1091 [0.076, 0.1419] sex, age, birth date, deprivation index, 16 PCs —
PPM010997 PSS008380|
Greater Middle Eastern Ancestry|
467 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.0976 [0.005, 0.1885] sex, age, birth date, deprivation index, 16 PCs —
PPM010998 PSS008156|
South Asian Ancestry|
2,782 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.0798 [0.0426, 0.1167] sex, age, birth date, deprivation index, 16 PCs —
PPM010999 PSS007944|
East Asian Ancestry|
1,143 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.1146 [0.0565, 0.1719] sex, age, birth date, deprivation index, 16 PCs —
PPM011000 PSS007726|
African Ancestry|
1,482 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.0482 [-0.0031, 0.0992] sex, age, birth date, deprivation index, 16 PCs —
PPM011001 PSS008828|
African Ancestry|
2,035 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Breast cancer [female] — — Partial Correlation (partial-r): 0.0842 [0.0407, 0.1274] sex, age, birth date, deprivation index, 16 PCs —

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
PSS007944 — — 1,143 individuals — East Asian China (East Asia) UKB —
PSS007726 — — 1,482 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008828 — — 2,035 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009048 — — 2,440 individuals — European Poland (NE Europe) UKB —
PSS008602 — — 3,484 individuals — European Italy (South Europe) UKB —
PSS009274 — — 10,197 individuals — European UK (+ Ireland) UKB —
PSS008380 — — 467 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008156 — — 2,782 individuals — South Asian India (South Asia) UKB —