Polygenic Score (PGS) ID: PGS001804

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-PLR_174.1
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 2,984
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
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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
391,124 individualsEuropeanUKBUK (+ Ireland)
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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
PPM009338PSS009274|
European Ancestry|
10,197 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Breast cancer [female]Partial Correlation (partial-r): 0.1101 [0.0908, 0.1292]sex, age, birth date, deprivation index, 16 PCs
PPM009339PSS009048|
European Ancestry|
2,440 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Breast cancer [female]Partial Correlation (partial-r): 0.0843 [0.0446, 0.1237]sex, age, birth date, deprivation index, 16 PCs
PPM009340PSS008602|
European Ancestry|
3,484 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Breast cancer [female]Partial Correlation (partial-r): 0.1125 [0.0795, 0.1453]sex, age, birth date, deprivation index, 16 PCs
PPM009341PSS008380|
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): 0.0772 [-0.0155, 0.1687]sex, age, birth date, deprivation index, 16 PCs
PPM009342PSS008156|
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): 0.0673 [0.0301, 0.1044]sex, age, birth date, deprivation index, 16 PCs
PPM009343PSS007944|
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): 0.0983 [0.0401, 0.1559]sex, age, birth date, deprivation index, 16 PCs
PPM009344PSS007726|
African Ancestry|
1,482 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Breast cancer [female]Partial Correlation (partial-r): 0.0416 [-0.0097, 0.0927]sex, age, birth date, deprivation index, 16 PCs
PPM009345PSS008828|
African Ancestry|
2,035 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Breast cancer [female]Partial Correlation (partial-r): 0.0889 [0.0454, 0.132]sex, age, birth date, deprivation index, 16 PCs
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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
PSS0077261,482 individualsAfrican American or Afro-CaribbeanCarribeanUKB
PSS0079441,143 individualsEast AsianChina (East Asia)UKB
PSS0081562,782 individualsSouth AsianIndia (South Asia)UKB
PSS008380467 individualsGreater Middle Eastern (Middle Eastern, North African or Persian)Iran (Middle East)UKB
PSS0086023,484 individualsEuropeanItaly (South Europe)UKB
PSS0088282,035 individualsAfrican unspecifiedNigeria (West Africa)UKB
PSS0090482,440 individualsEuropeanPoland (NE Europe)UKB
PSS00927410,197 individualsEuropeanUK (+ Ireland)UKB
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