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
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
391,124 individuals European UK (+ Ireland) UKB

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