Polygenic Score (PGS) ID: PGS000007

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
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRS3820_BC
Development Method
Name LASSO penalized regression
Parameters p < 0.001
Variants
Original Genome Build GRCh37
Number of Variants 3,820
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000002
Citation (link to publication) Mavaddat N et al. Am J Hum Genet (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
158,648 individuals (100%)
Score Development/Training
European: 100%
10,444 individuals (100%)
PGS Evaluation
European: 60%
African: 20%
Multi-ancestry (including European): 20%
  • African
  • Additional Asian Ancestries
  • Additional Diverse Ancestries
  • European
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 88,916 cases
  • , 69,732 controls
]
,
0.0 % Male samples
 European 68 cohorts
  • 2SISTER
  • ,ABCFS
  • ,ABCS
  • ,ABCTB
  • ,AOCS
  • ,BBCC
  • ,BBCS
  • ,BCEES
  • ,BCFR-NY
  • ,BCFR-PA
  • ,BCFR-UTAH
  • ,BCINIS
  • ,BIGGS
  • ,BREOGAN
  • ,BSUCH
  • ,CBCS
  • ,CCGP
  • ,CECILE
  • ,CGPS
  • ,CNIO-BCS
  • ,CPSII
  • ,CTS
  • ,DIETCOMPLYF
  • ,ESTHER
  • ,GC-HBOC
  • ,GENICA
  • ,GEPARSIXTO
  • ,GESBC
  • ,HCSC
  • ,HEBCS
  • ,HMBCS
  • ,HUOCS
  • ,KARBAC
  • ,KBCP
  • ,LMBC
  • ,MABCS
  • ,MARIE
  • ,MBCSG
  • ,MCBCS
  • ,MCCS
  • ,MEC
  • ,MISS
  • ,MMHS
  • ,MSKCC
  • ,MTLGEBCS
  • ,NBCS
  • ,NBHS
  • ,NC-BCFR
  • ,OBCS
  • ,OFBCR
  • ,ORIGO
  • ,PBCS
  • ,POSH
  • ,PREFACE
  • ,RBCS
  • ,SASBAC
  • ,SBCS
  • ,SEARCH
  • ,SKKDKFZS
  • ,SMC
  • ,SUCCESSB
  • ,SUCCESSC
  • ,SZBCS
  • ,TNBCC
  • ,UCIBCS
  • ,UKOPS
  • ,WHI
  • ,pKARMA
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
—
[
  • 5,159 cases
  • , 5,285 controls
]
,
0.0 % Male samples
 European 25 cohorts
  • ABCTB
  • ,BBCC
  • ,BCEES
  • ,BCINIS
  • ,BREOGAN
  • ,CBCS
  • ,CCGP
  • ,CGPS
  • ,CPSII
  • ,CTS
  • ,GENICA
  • ,HMBCS
  • ,LMBC
  • ,MCBCS
  • ,MCCS
  • ,MISS
  • ,MMHS
  • ,NBHS
  • ,ORIGO
  • ,PBCS
  • ,SEARCH
  • ,SMC
  • ,UCIBCS
  • ,WHI
  • ,pKARMA
 Invasive breast cancer-affected — — — Validation Cohort

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
PPM000008 PSS000004|
European Ancestry|
29,751 individuals
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Reported Trait: Invasive breast cancer OR: 1.66 [1.61, 1.7] AUROC: 0.636 — study, genetic PCs 1-15 —
PPM000386 PSS000218|
European Ancestry|
9,529 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Breast Cancer (personal history) — AUROC: 0.78 — age, sex —
PPM000384 PSS000218|
European Ancestry|
9,529 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Breast Cancer (personal history) OR: 1.56 [1.45, 1.68] — — age at menarche —
PPM000388 PSS000218|
European Ancestry|
9,529 individuals
 PGP000057 |
Homburger JR et al. Genome Med (2019)
|Ext.		 Reported Trait: Breast Cancer (personal history) — AUROC: 0.63 — — —
PPM005169 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.59 [0.58, 0.6] R²: 0.021 — —
PPM005172 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer — AUROC: 0.53 [0.5, 0.57] R²: 0.0002 — —
PPM005160 PSS003599|
European Ancestry|
33,954 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.36 [1.31, 1.41] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM005163 PSS003598|
African Ancestry|
3,801 individuals
 PGP000249 |
Liu C et al. JAMA Netw Open (2021)
|Ext.		 Reported Trait: Breast cancer OR: 1.21 [1.06, 1.39] — — Age, family history, study site, 3 ancestry-specific PCs —
PPM015517 PSS009971|
Multi-ancestry (including European)|
36,422 individuals
 PGP000381 |
Hao L et al. Nat Med (2022)
|Ext.		 Reported Trait: Breast cancer OR: 2.38 [2.07, 2.73] — — 4 genetic 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
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 —
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 —
PSS009971 — — 786 individuals — Asian unspecified — MGBB —
PSS000218 Phenotypic information was self-reported by the individual through an online, interactive health history tool —
[
  • 828 cases
  • , 8,701 controls
]
,
0.0 % Male samples
 — European — CG Samples are individuals whose healthcare provider had ordered a Color Genomics multi-gene panel test
PSS009971 — — 1,807 individuals — African unspecified
(Black)		 — MGBB —
PSS000004 Invasive breast cancer-affected —
[
  • 11,428 cases
  • , 18,323 controls
]
,
0.0 % Male samples
 — European — 10 cohorts
  • AHS
  • ,BGS
  • ,EPIC
  • ,FHRISK
  • ,KARMA
  • ,NHS
  • ,NHS2
  • ,PLCO
  • ,PROCAS
  • ,SISTER
 Prospective Test Set
PSS009971 — — 3,113 individuals — Other — MGBB —
PSS009971 — — 30,716 individuals — European — MGBB —