Polygenic Score (PGS) ID: PGS000015

Predicted Trait
Reported Trait Breast cancer
Mapped Trait(s) breast carcinoma (EFO_0000305)
Released in PGS Catalog: Oct. 14, 2019
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Terms and Licenses
Freely available to the academic community for research use. Parties interested in using the scores for commercial purposes should contact the Broad Office of Strategic Alliances and Partnering (partnering@broadinstitute.org).

Score Details

Score Construction
PGS Name GPS_BC
Development Method
Name Pruning and Thresholding (P+T)
Parameters r2 < 0.2; P < 5e−4; LD panel = 503 100G Europeans
Variants
Original Genome Build hg19
Number of Variants 5,218
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000006
Citation (link to publication) Khera AV et al. Nat Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
139,274 individuals (100%)
Score Development/Training
European: 100%
63,347 individuals (100%)
PGS Evaluation
European: 50%
African: 25%
Hispanic or Latin American: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004988
Europe PMC: 29059683
 139,274 individuals European NR
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
—
[
  • 2,576 cases
  • , 60,771 controls
]
,
0.0 % Male samples
 European UKB Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. — — — UKB Phase 1

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
PPM000024 PSS000014|
European Ancestry|
157,895 individuals
 PGP000006 |
Khera AV et al. Nat Genet (2018)
 Reported Trait: Breast cancer — AUROC: 0.69 [0.68, 0.69] Nagelkerke’s R2 (estimate of variance explained by the PGS after covariate adjustment): 0.027 age; sex; Ancestry PC 1-4; genotyping chip —
PPM005170 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.61 [0.6, 0.62] R²: 0.017 — —
PPM005161 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.46 [1.41, 1.51] — Odds Ratio (OR, top 1% vs middle 20%): 2.48 [1.89, 3.25] Age, family history, study site, 3 ancestry-specific PCs —
PPM005164 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.24 [1.08, 1.43] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005166 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.35 [1.11, 1.64] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005173 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.55 [0.52, 0.59] R²: 0.0004 — —
PPM005175 PSS003600|
Hispanic or Latin American Ancestry|
2,196 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.56 [0.51, 0.6] R²: 0.001 — —

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
PSS003598 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 274 cases
  • , 3,527 controls
]
,
0.0 % Male samples
 Mean = 59.6 years
Sd = 16.5 years		 African unspecified — eMERGE —
PSS000014 Breast cancer ascertainment was based on self-report in an interview with a trained nurse, ICD-9 codes (174 or 174.9) or ICD-10 codes (C50.X) in hospitalization records, or a breast cancer diagnosis reported to the national registry before the date of enrollment. —
[
  • 6,586 cases
  • , 151,309 controls
]
,
0.0 % Male samples
 — European — UKB UKB Phase 2
PSS003599 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 3,960 cases
  • , 29,994 controls
]
,
0.0 % Male samples
 Mean = 66.1 years
Sd = 17.7 years		 European — eMERGE —
PSS003600 Cases were individuals with breast cancer. Breast cancer cases were defined by at least one occurrence of the following ICD10CM female breast cancer diagnostic codes: C50.01, C50.011, C50.012, C50.019, C50.1, C50.11, C50.111, C50.112, C50.119, C50.2, C50.21, C50.211, C50.212, C50.219, C50.3, C50.31, C50.311, C50.312, C50.319, C50.4, C50.41, C50.411, C50.412, C50.419, C50.5, C50.51, C50.511, C50.512, C50.519, C50.6, C50.61, C50.611, C50.612, C50.619, C50.81, C50.811, C50.812, C50.819, C50.91, C50.911, C50.912, C50.919, D05, D05.1, D05.10, D05.11, D05.12, D05.8, D05.81, D05.82, D05.9, D05.90, D05.91, D05.92, Z85.3,Z86.000 and ICD9CM female breast cancer diagnostic codes: 174, 174, 174.1, 174.2, 174.3, 174.4, 174.5, 174.6, 174.8, 174.9, 233, V10.3. Alternatively breast cancer cases were defined by at least two occurrences (from distinct calendar days) of breast cancer history from the following ICD10CM codes: Z85.3, Z86.000 and ICD9CM code: V10.3, if she had no breast cancer diagnostic codes. —
[
  • 147 cases
  • , 2,049 controls
]
,
0.0 % Male samples
 Mean = 59.9 years
Sd = 19.4 years		 Hispanic or Latin American — eMERGE —