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

Polygenic Score (PGS) ID PGS Name Publication ID Reported Trait Mapped Trait(s) (EFO) Number of Variants PGS Download Links
PGS000001 PRS77_BC Mavaddat N et al. J Natl Cancer Inst (2015) Breast Cancer breast carcinoma 77 FTP Link
PGS000004 PRS313_BC Mavaddat N et al. Am J Hum Genet (2018) Breast Cancer breast carcinoma 313 FTP Link
PGS000007 PRS3820_BC Mavaddat N et al. Am J Hum Genet (2018) Breast Cancer breast carcinoma 3,820 FTP Link
PGS000015 GPS_BC Khera AV et al. Nat Genet (2018) Breast cancer breast carcinoma 5,218 FTP Link
PGS000028 PRS Shieh Y et al. Breast Cancer Res Treat (2016) Breast cancer breast carcinoma 83 FTP Link
PGS000029 PRS_AS Shieh Y et al. Breast Cancer Res Treat (2016) Breast cancer breast carcinoma 76 FTP Link
PGS000045 BCPRS_Overall Kuchenbaecker KB et al. J Natl Cancer Inst (2017) Breast cancer breast carcinoma 88 FTP Link
PGS000050 PRS44 Wen W et al. Breast Cancer Res (2016) Breast cancer breast carcinoma 44 FTP Link
PGS000051 PRS67 Zhang X et al. PLoS Med (2018) Breast Cancer breast carcinoma 67 FTP Link
PGS000052 sPRS161 Lakeman IMM et al. J Med Genet (2019) Breast cancer breast carcinoma 161 FTP Link

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 —
PPM000114 PGS000001 (PRS77_BC) PSS000070 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.13 [1.1 - 1.16] — — Country, birth year —
PPM000117 PGS000001 (PRS77_BC) PSS000071 Kuchenbaecker KB et al. (2017) Ext. Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.17 - 1.28] — — Country, birth year —
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 — 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
PPM000106 PGS000045 (BCPRS_Overall) PSS000070 Kuchenbaecker KB et al. (2017) Reported Trait: Breast cancer in BRCA1 mutation carriers HR: 1.14 [1.11 - 1.17] C-index: 0.541 [0.53 - 0.551] — Country, birth year —
PPM000107 PGS000045 (BCPRS_Overall) PSS000071 Kuchenbaecker KB et al. (2017) Reported Trait: Breast cancer in BRCA2 mutation carriers HR: 1.22 [1.17 - 1.28] C-index: 0.566 [0.551 - 0.581] — Country, birth year —
PPM000120 PGS000045 (BCPRS_Overall) PSS000074 Lecarpentier J et al. (2017) Ext. Reported Trait: Breast cancer in male carriers of BRCA1/2 mutations OR: 1.36 [1.19 - 1.56] AUROC: 0.59 [0.55 - 0.63] — 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2 PGS predicting Male Breast Cancer are based on association statistics from a Female Breast Cancer GWAS
PPM000126 PGS000050 (PRS44) PSS000078 Wen W et al. (2016) Reported Trait: Breast cancer — AUROC: 0.606 Odds Ratio (OR; per decile of PRS): 1.13 [1.12 - 1.14] NR Potentially overfit: samples were used to select the variants included in the PRS (see paper's Discussion section for more information).
PPM000127 PGS000050 (PRS44) PSS000079 Wen W et al. (2016) Reported Trait: Breast cancer — C-index: 0.602 C-index improvement (with PRS): 0.0386 [0.0259 - 0.0513] age at menarche, age at first live birth, waist-to-hip ratio, breast cancer family history, prior benign breast disease Potentially overfit: samples were used to select the variants included in the PRS (see paper's Discussion section for more information).
PPM000128 PGS000051 (PRS67) PSS000080 Zhang X et al. (2018) Reported Trait: Invasive breast cancer — AUROC: 0.65 [0.64 - 0.66] — Gail BC risk model, Mammographic density (MD), Testoterone (T), estrone sulfate (E1S), prolactin (PRL) Age-adjusted AUC
PPM000129 PGS000051 (PRS67) PSS000081 Zhang X et al. (2018) Reported Trait: Invasive breast cancer — AUROC: 0.678 [0.666 - 0.69] — Rosner–Colditz BC risk model, Mammographic density (MD), Testoterone (T), estrone sulfate (E1S), prolactin (PRL) Age-adjusted AUC
PPM000130 PGS000051 (PRS67) PSS000080 Zhang X et al. (2018) Reported Trait: Invasive breast cancer — — Relative Risk (RR; higest vs. lowest quartile PRS): 2.5 [2.2 - 2.8] Demographics and parameters of baseline blood draw (age, BMI, fasting status, time of day, season), history of benign breast disease, family history of breast cancer, age at menopause, age at menarche, physical activity, age at first birth and parity —
PPM000131 PGS000052 (sPRS161) PSS000082 Lakeman IMM et al. (2019) Reported Trait: breast cancer HR: 1.16 [1.03 - 1.28] — — family history (estimated using the BOADICEA risk model) —

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]
0.00 %% 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]
0.00 %% 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]
0.00 %% 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]
0.00 %% 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]
0.00 %% 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]
0.00 %% Male samples		 Other Cohort contains individuals of East Asian, European & Hispanic ancestries CPMCBHC Nested case-control study from the CPMC Breast Health Cohort.
PSS000070 BRCA1 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. 15,252 individuals
[ 7,797 cases, 7,455 controls]
0.00 %% Male samples		 European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 40
PSS000071 BRCA2 mutation carriers were followed until breast or ovarian cancer diagnosis, bilateral prophylactic mastectomy, or age at last observation whichever occurred first. 8,211 individuals
[ 4,330 cases, 3,881 controls]
0.00 %% Male samples		 European Some analyses accounted for samples part of the larger cohort with Ashkenazi Jewish ancestry CIMBA Median censoring age (cases) = 43
PSS000074 Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. 1,590 individuals
[ 277 cases, 1,313 controls]
1.00 %% Male samples		 European Self-reported European ancestry BFBOCC, BRICOH, BCFR, CONSIT, CBCS, Chicago, CIMBA, DKFZ, HEBON, EMBRACE, FCCC, G-FaST, GEMO, GC-HBOC, HCSC, HUNBOCS, HVH, HEBCS, ICO, IOVHBOCS, IPOBCS, MUV, MSKCC, NCI, OCGN, OUH, PBCS, CNIO, MAYO, OSU, DEMOKRITOS, ILUH, KCONFAB, SWE-BRCA, UPENN, UPITT, VFCTG —
PSS000078 — 23,567 individuals
[ 11,905 cases, 11,662 controls]
0.00 %% Male samples		 East Asian — ACP, BCAC, HERPACC, LAABC, MYBRCA, SBCGS, SGWAS, SGBCC, TWBCS, TBCS, SEBCS —
PSS000079 — 5,152 individuals
[ 2,867 cases, 2,285 controls]
0.00 %% Male samples		 East Asian
(Chinese)		 — SGWAS SGWAS (Stage 1). Smaller set of the larger test set from this study.
PSS000080 Questionnaires were mailed to women biennially to collect information on breast cancer risk factors, including age at menarche, age at first birth, parity, family history of breast cancer, height, weight, physical activity, menopausal status, age at menopause, and HT use. Incident breast cancer cases up to 1 June 2010 were also identified through biennial questionnaires. Diagnoses were confirmed with the participants (or next of kin), and permission was obtained to collect relevant medical or pathology reports. Analysis was restricted to invasive breast cancer. 11,880 individuals
[ 4,006 cases, 7,874 controls]
0.00 %% Male samples		 Other The study population was described as “predominantly white” [PGS Catalog Broad Ancestral Category: European] NHS2, NHS Performance metrics are reported for the "All women" results of Table 2
PSS000081 Questionnaires were mailed to women biennially to collect information on breast cancer risk factors, including age at menarche, age at first birth, parity, family history of breast cancer, height, weight, physical activity, menopausal status, age at menopause, and HT use. Incident breast cancer cases up to 1 June 2010 were also identified through biennial questionnaires. Diagnoses were confirmed with the participants (or next of kin), and permission was obtained to collect relevant medical or pathology reports. Analysis was restricted to invasive breast cancer. 8,160 individuals
[ 2,676 cases, 5,484 controls]
0.00 %% Male samples		 Other The study population was described as “predominantly white” [PGS Catalog Broad Ancestral Category: European] NHS2, NHS Performance metrics are reported for the "All women" results of Table 3
PSS000082 A family-based cohort including 323 breast cancer cases and 262 unaffected relatives from 101 families. Unaffected relatives derived from 49 out of 101 families. 585 individuals
[ 323 cases, 262 controls]
0.00 %% Male samples		 European — —