Trait: breast carcinoma

Information

Experimental Factor Ontology ID: EFO_0000305

EFO Trait Description: A carcinoma that arises from epithelial cells of the breast [MONDO: DesignPattern]

Associated PGS

PGS 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 (PPM) ID Evaluated Score PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000001 PGS000001 (PRS77_BC) PSS000001 Mavaddat N et al. (2015) Reported Trait: All breast cancer OR: 1.55 [1.52 - 1.58] C-index: 0.622 [0.619 - 0.627]
PPM000011 PGS000001 (PRS77_BC) PSS000004 Mavaddat N et al. (2018) Ext. Reported Trait: Invasive breast cancer OR: 1.46 [1.42 - 1.49] AUROC: 0.603 study, genetic PCs 1-15
PPM000004 PGS000004 (PRS313_BC) PSS000004 Mavaddat N et al. (2018) Reported Trait: Invasive breast cancer OR: 1.61 [1.57 - 1.65] AUROC: 0.63 study, genetic PCs 1-15
PPM000005 PGS000004 (PRS313_BC) PSS000007 Mavaddat N et al. (2018) Reported Trait: Incident breast cancer cases HR: 1.59 [1.54 - 1.64] study, genetic PCs 1-15 Included only 306 of the 313 SNPs
PPM000008 PGS000007 (PRS3820_BC) PSS000004 Mavaddat N et al. (2018) Reported Trait: Invasive breast cancer OR: 1.66 [1.61 - 1.7] AUROC: 0.636 study, genetic PCs 1-15
PPM000024 PGS000015 (GPS_BC) PSS000014 Khera AV et al. (2018) Reported Trait: Breast cancer cases 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
PPM000055 PGS000028 (PRS) PSS000040 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.6 [0.57 - 0.64]
PPM000056 PGS000028 (PRS) PSS000040 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.65 [0.61 - 0.68] BCSC risk model BCSC risk model includes mammographic breast density, age, ethnicity, first-degree relative with breast cancer, and history of breast biopsy
PPM000059 PGS000028 (PRS) PSS000038 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.62 [0.52 - 0.73]
PPM000060 PGS000028 (PRS) PSS000039 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.63 [0.59 - 0.67]
PPM000057 PGS000029 (PRS_AS) PSS000038 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.64 [0.53 - 0.74]
PPM000058 PGS000029 (PRS_AS) PSS000038 Shieh Y et al. (2016) Reported Trait: Breast cancer AUROC: 0.72 [0.62 - 0.82] BCSC risk model BCSC risk model includes mammographic breast density, age, ethnicity, first-degree relative with breast cancer, and history of breast biopsy

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000001 All breast cancer 67,054 individuals
[ 33,673 cases, 33,381 controls]
European ABCS, ABCFS, BBCC, BIGGS, BSUCH, CECILE, CTS, CGPS, ESTHER, GENICA, HMBCS, SZBCS, pKARMA, KBCP, ORIGO, LMBC, MARIE, MCBCS, MCCS, MTLGEBCS, MEC, NBHS, NorBCS, OBCS, PBCS, RPCI, SBCS, SASBAC, SKKDKFZS, SEARCH, OSU, UKBGS, DEMOKRITOS iCOGS
PSS000004 Invasive breast cancer-affected 29,751 individuals
[ 11,428 cases, 18,323 controls]
0.0 % Male samples
European AHS, BGS, PROCAS, EPIC, FHRISK, NHS2, NHS, PLCO, KARMA, SISTER Prospective Test Set
PSS000007 Incident registry-confirmed invasive breast cancers developed 190,040 individuals
[ 3,215 cases, 186,825 controls]
0.0 % Male samples
European UKB Prospective Test Set (UKB)
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. 157,895 individuals
[ 6,586 cases, 164,481 controls]
0.0 % Male samples
European UKB UKB Phase 2
PSS000038 Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. 102 individuals
[ 51 cases, 51 controls]
0.0 % Male samples
East Asian CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.
PSS000039 Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. 774 individuals
[ 387 cases, 387 controls]
0.0 % Male samples
European CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.
PSS000040 Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. 981 individuals
[ 495 cases, 486 controls]
0.0 % Male samples
Other Cohort contains individuals of East Asian, European & Hispanic ancestries CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.