Trait: family history of breast cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005606
Description A reported family history of breast cancer in one or more family members.
Trait category
Other trait
Synonyms 2 synonyms
  • breast cancer family history
  • family history of breast carcinoma

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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Polygenic Score ID & Name
PGS Publication ID (PGP)
Reported Trait
Mapped Trait(s) (Ontology)
Number of Variants
Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS001337
(GBE_FH1002)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Family history of breast cancerfamily history of breast cancer195
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001337/ScoringFiles/PGS001337.txt.gz
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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)
Evaluated Score
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
PPM009171PGS001337
(GBE_FH1002)
PSS004034|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Breast cancer (FH)—AUROC: 0.57882 [0.5595, 0.59814]R²: 0.01774
Incremental AUROC (full-covars): 0.00262
PGS R2 (no covariates): 0.00016
PGS AUROC (no covariates): 0.50866 [0.48823, 0.52909]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009172PGS001337
(GBE_FH1002)
PSS004035|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Breast cancer (FH)—AUROC: 0.60865 [0.56929, 0.64801]R²: 0.03344
Incremental AUROC (full-covars): 0.01456
PGS R2 (no covariates): 0.0091
PGS AUROC (no covariates): 0.56734 [0.52563, 0.60905]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009173PGS001337
(GBE_FH1002)
PSS004036|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Breast cancer (FH)—AUROC: 0.57917 [0.56994, 0.5884]R²: 0.01887
Incremental AUROC (full-covars): 0.00313
PGS R2 (no covariates): 0.002
PGS AUROC (no covariates): 0.52353 [0.51419, 0.53286]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009174PGS001337
(GBE_FH1002)
PSS004037|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Breast cancer (FH)—AUROC: 0.60464 [0.58531, 0.62397]R²: 0.02766
Incremental AUROC (full-covars): 0.00261
PGS R2 (no covariates): 0.00157
PGS AUROC (no covariates): 0.52221 [0.5025, 0.54191]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM009175PGS001337
(GBE_FH1002)
PSS004038|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Breast cancer (FH)—AUROC: 0.57389 [0.56837, 0.57941]R²: 0.01618
Incremental AUROC (full-covars): 0.00514
PGS R2 (no covariates): 0.0022
PGS AUROC (no covariates): 0.527 [0.52143, 0.53258]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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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
PSS004034——
[
  • 886 cases
  • , 5,611 controls
]
—African unspecified—UKB—
PSS004035——
[
  • 205 cases
  • , 1,499 controls
]
—East Asian—UKB—
PSS004036——
[
  • 4,521 cases
  • , 20,384 controls
]
—Europeannon-white British ancestryUKB—
PSS004037——
[
  • 966 cases
  • , 6,865 controls
]
—South Asian—UKB—
PSS004038——
[
  • 12,512 cases
  • , 54,913 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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