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1. Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes

Author

Mavaddat, N., Michailidou, K., Dennis, J., Lush, M., Fachal, L., Lee, A., Tyrer, J. P., Chen, T. H., Wang, Q., Bolla, M. K., Yang, X., Adank, M. A., Ahearn, T., Aittomaki, K., Allen, J., Andrulis, I. L., Anton-Culver, H., Antonenkova, N. N., Arndt, V., Aronson, K. J., Auer, P. L., Auvinen, P., Barrdahl, M., Beane Freeman, L. E., Beckmann, M. W., Behrens, S., Benitez, J., Bermisheva, M., Bernstein, L., Blomqvist, C., Bogdanova, N. V., Bojesen, S. E., Bonanni, B., Borresen-Dale, A. L., Brauch, H., Bremer, M., Brenner, H., Brentnall, A., Brock, I. W., Brooks-Wilson, A., Brucker, S. Y., Bruning, T., Burwinkel, B., Campa, D., Carter, B. D., Castelao Fernández, José Esteban, Chanock, S. J., Chlebowski, R., Christiansen, H., Clarke, C. L., Collee, J. M., Cordina-Duverger, E., Cornelissen, S., Couch, F. J., Cox, A., Cross, S. S., Czene, K., Daly, M. B., Devilee, P., Dork, T., Dos-Santos-Silva, I., Dumont, M., Durcan, L., Dwek, M., Eccles, D. M., Ekici, A. B., Eliassen, A. H., Ellberg, C., Engel, C., Eriksson, M., Evans, D. G., Fasching, P. A., Figueroa, J., Fletcher, O., Flyger, H., Forsti, A., Fritschi, L., Gabrielson, M., Gago Dominguez, Manuela, Gapstur, S. M., Garcia-Saenz, J. A., Gaudet, M. M., Georgoulias, V., Giles, G. G., Gilyazova, I. R., Glendon, G., Goldberg, M. S., Goldgar, D. E., Gonzalez-Neira, A., Grenaker Alnaes, G. I., Grip, M., Gronwald, J., Grundy, A., Guenel, P., Haeberle, L., Hahnen, E., Haiman, C. A., Hakansson, N., Hamann, U., Hankinson, S. E., Muñoz Garzón, Victor, and others

Subjects
Adult, Aged, 80 and over, Multifactorial Inheritance, anciano, humanos, Age Factors, Reproducibility of Results, Breast Neoplasms, neoplasias de la mama, predisposición genética a la enfermedad, Middle Aged, adulto, Risk Assessment, Polymorphism, Single Nucleotide, herencia multifactorial, reproducibilidad de resultados, Receptors, Estrogen, evaluación de riesgos, Humans, Genetic Predisposition to Disease, anamnesis, Female, Medical History Taking, mediana edad, Aged
Abstract

Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (SNPs) were selected by stepwise regression or lasso penalized regression. The best performing PRSs were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from UK Biobank (3,215 incident breast cancers). For the best PRSs (313 SNPs), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%CI: 1.57-1.65) with area under receiver-operator curve (AUC) = 0.630 (95%CI: 0.628-0.651). The lifetime risk of overall breast cancer in the top centile of the PRSs was 32.6%. Compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing ER-positive and ER-negative disease, respectively. Goodness-of-fit tests indicated that this PRS was well calibrated and predicts disease risk accurately in the tails of the distribution. This PRS is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs.

Published
2019

2. Genetic variation at CYP3A is associated with age at menarche and breast cancer risk: a case-control study

Author

Johnson, N., Dudbridge, F., Orr, N., Gibson, L., Jones, M.E., Schoemaker, M.J., Folkerd, E.J., Haynes, B.P., Hopper, J.L., Southey, M.C., Dite, G.S., Apicella, C., Schmidt, M.K., Broeks, A., Van't Veer, L.J., Atsma, F., Muir, K., Lophatananon, A., Fasching, P.A., Beckmann, M.W., Ekici, A.B., Renner, S.P., Sawyer, E., Tomlinson, I., Kerin, M., Miller, N., Burwinkel, B., Marme, F., Schneeweiss, A., Sohn, C., Guenel, P., Truong, T., Cordina, E., Menegaux, F., Bojesen, S.E., Nordestgaard, B.G., Flyger, H., Milne, R., Zamora, M.P., Arias Perez, J.I., Benitez, J., Bernstein, L., Anton-Culver, H., Ziogas, A., Dur, C.C., Brenner, H., Mueller, H., Arndt, V., Dieffenbach, A.K., Meindl, A., Heil, J., Bartram, C.R., Schmutzler, R.K., Brauch, H., Justenhoven, C., Ko, Y-D., Nevanlinna, H., Muranen, T.A., Aittomaeki, K., Blomqvist, C., Matsuo, K., Doerk, T., Bogdanova, NV., Antonenkova, N.N., Lindblom, A., Mannermaa, A., Kataja, V., Kosma, V-M., Hartikainen, J.M., Chenevix-Trench, G., Beesley, J., Wu, A.H., Van den Berg, D., Tseng, C-C., Lambrechts, D., Smeets, D., Neven, P., Wildiers, H., Chang-Claude, J., Rudolph, A., Nickels, S., Flesch-Janys, D., Radice, P., Peterlongo, P., Bonanni, B., Pensotti, V., Couch, F.J., Olson, J.E., Wang, X., Fredericksen, Z., Pankratz, V.S., Giles, G.G., Severi, G., Baglietto, L., Haiman, C., Simard, J., Goldberg, M.S., Labreche, F., Dumont, M., Soucy, P., Teo, S., Yip, C.H., Phuah, S.Y., Cornes, B.K., Kristensen, V.N., Alnaes, G.G., Borresen-Dale, A-L., Zheng, W., Winqvist, R., Pylkaes, K., Jukkola-Vuorinen, A., Grip, M., Andrulis, I.L, Knight, J.A., Glendon, G., Mulligan, A.M., Devillee, P., Figueroa, J., Chanock, S.J., Lissowska, J., Sherman, M.E., Hall, P., Schoof, N., Hooning, M., Hollestelle, A., Oldenburg, R.A., Tilanus-Linthorst, M., Liu, J., Cox, A., Brock, I.W., Reed, M.W.R., Cross, S.S., Blot, W., Signorello, L.B., Pharoah, P.D.P., Dunning, A.M., Shah, M., Kang, D., Noh, D-Y., Park, S.K., Choi, J-Y., Hartman, M., Miao, H., Lim, W.Y., Tang, A., Hamann, U., Foersti, A., Ruediger, T., Ulmer, H.U., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Sangrajrang, S., Gaborieau, V., Brennan, P., Mckay, J., Slager, S., Toland, A.E., Vachon, C., Yannoukakos, D., Shen, C-Y., Yu, J-C., Huang, C-S., Hou, M-F., Gonzalez-Neira, A., Tessier, D.C., Vincent, D., Bacot, F., Luccarini, C., Dennis, J., Michailidou, K., Bolla, M.K., Wang, J., Easton, D.F., Garcia-Closas, M., Dowsett, M., Ashworth, A., Swerdlow, A.J., Peto, J., Silva, I.D.S., Fletcher, O., Breast, G.E.I., Investigators, K., Grp, AOCS, Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Dennis, Joe [0000-0003-4591-1214], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository

Subjects
Adult, Menarche, Genotype, Age Factors, Breast Neoplasms, Middle Aged, Polymorphism, Single Nucleotide, White People, Premenopause, Risk Factors, Cytochrome P-450 CYP3A, Humans, Female, Genetic Predisposition to Disease, Age of Onset, Reproductive History, Genetic Association Studies, Aged
Abstract

Introduction: We have previously shown that a tag single nucleotide polymorphism (rs10235235), which maps to\ud the CYP3A locus (7q22.1), was associated with a reduction in premenopausal urinary estrone glucuronide levels and\ud a modest reduction in risk of breast cancer in women age ≤50 years.\ud Methods: We further investigated the association of rs10235235 with breast cancer risk in a large case control study of\ud 47,346 cases and 47,570 controls from 52 studies participating in the Breast Cancer Association Consortium. Genotyping\ud of rs10235235 was conducted using a custom Illumina Infinium array. Stratified analyses were conducted to determine\ud whether this association was modified by age at diagnosis, ethnicity, age at menarche or tumor characteristics.\ud Results: We confirmed the association of rs10235235 with breast cancer risk for women of European ancestry but found\ud no evidence that this association differed with age at diagnosis. Heterozygote and homozygote odds ratios (ORs) were\ud OR = 0.98 (95% CI 0.94, 1.01; P = 0.2) and OR = 0.80 (95% CI 0.69, 0.93; P = 0.004), respectively (Ptrend = 0.02). There was\ud no evidence of effect modification by tumor characteristics. rs10235235 was, however, associated with age at menarche\ud in controls (Ptrend = 0.005) but not cases (Ptrend = 0.97). Consequently the association between rs10235235 and breast\ud cancer risk differed according to age at menarche (Phet = 0.02); the rare allele of rs10235235 was associated with a\ud reduction in breast cancer risk for women who had their menarche age ≥15 years (ORhet = 0.84, 95% CI 0.75, 0.94;\ud ORhom = 0.81, 95% CI 0.51, 1.30; Ptrend = 0.002) but not for those who had their menarche age ≤11 years (ORhet = 1.06,\ud 95% CI 0.95, 1.19, ORhom = 1.07, 95% CI 0.67, 1.72; Ptrend = 0.29).\ud Conclusions: To our knowledge rs10235235 is the first single nucleotide polymorphism to be associated with both\ud breast cancer risk and age at menarche consistent with the well-documented association between later age at menarche\ud and a reduction in breast cancer risk. These associations are likely mediated via an effect on circulating hormone levels.

Published
2014

6. Factors associated with oxidative stress and cancer risk in the Breast and Prostate Cancer Cohort Consortium

Author

Blein, S, Berndt, S, Joshi, Ad, Campa, D, Ziegler, Rg, Riboli, E, Cox, Dg, Gaudet, Mm, Stevens, Vl, Diver, Wr, Gapstur, Sm, Chanock, Sj, Hoover, Rn, Yeager, M, Albanes, D, Virtamo, J, Crawford, Ed, Isaacs, C, Berg, C, Trichopoulos, D, Peeters, Ph, Johansson, M, Khaw, Kt, Kraft, P, Hunter, Dj, Lindström, S, Ma, J, Stampfer, M, Gaziano, Jm, Giovannucci, E, Willett, Wh, Hankinson, Se, Lee, Im, Buring, J, Henderson, B, Marchand, Ll, Kolonel, L, Haiman, C.j., PANICO, SALVATORE, Blein, S, Berndt, S, Joshi, Ad, Campa, D, Ziegler, Rg, Riboli, E, Cox, Dg, Gaudet, Mm, Stevens, Vl, Diver, Wr, Gapstur, Sm, Chanock, Sj, Hoover, Rn, Yeager, M, Albanes, D, Virtamo, J, Crawford, Ed, Isaacs, C, Berg, C, Trichopoulos, D, Panico, Salvatore, Peeters, Ph, Johansson, M, Khaw, Kt, Kraft, P, Hunter, Dj, Lindström, S, Ma, J, Stampfer, M, Gaziano, Jm, Giovannucci, E, Willett, Wh, Hankinson, Se, Lee, Im, Buring, J, Henderson, B, Marchand, Ll, Kolonel, L, and Haiman, C. j.

Subjects
MnSOD, Male, Oncology, medicine.medical_specialty, Genotype, Biology, medicine.disease_cause, Polymorphism, Single Nucleotide, Biochemistry, Prostate cancer, Breast cancer, Prostate, Internal medicine, Epidemiology, medicine, Genetic Predisposition to Disease, Breast, Survival analysis, Gynecology, Medicine (all), Oxidative Stre, General Medicine, medicine.disease, Mitochondria, medicine.anatomical_structure, Alcohol, GPX-1, Prostatic Neoplasm, Cohort, Female, Survival Analysi, Reactive Oxygen Specie, Breast Neoplasm, Oxidative stress, Human
Abstract

Both endogenous factors (genomic variations) and exogenous factors (environmental exposures, lifestyle) impact the balance of reactive oxygen species (ROS). Variants of the ND3 (rs2853826; G10398A) gene of the mitochondrial genome, manganese superoxide dismutase (MnSOD; rs4880 Val16Ala) and glutathione peroxidase (GPX-1; rs1050450 Pro198Leu), are purported to have functional effects on regulation of ROS balance. In this study, we examined associations of breast and prostate cancer risks and survival with these variants, and interactions between rs4880-rs1050450, and alcohol consumption-rs2853826. Nested case-control studies were conducted in the Breast and Prostate Cancer Cohort Consortium (BPC3), consisting of nine cohorts. The analyses included over 10726 post-menopausal breast and 7532 prostate cancer cases with matched controls. Logistic regression models were used to evaluate associations with risk, and proportional hazard models were used for survival outcomes. We did not observe significant interactions between polymorphisms in MnSOD and GPX-1, or between mitochondrial polymorphisms and alcohol intake and risk of either breast (p-interaction of 0.34 and 0.98, respectively) or prostate cancer (p-interaction of 0.49 and 0.50, respectively). We observed a weak inverse association between prostate cancer risk and GPX-1 Leu198Leu carriers (OR 0.87, 95% CI 0.79-0.97, p = 0.01). Overall survival among women with breast cancer was inversely associated with G10398 carriers who consumed alcohol (HR 0.66 95% CI 0.49-0.88). Given the high power in our study, it is unlikely that interactions tested have more than moderate effects on breast or prostate cancer risk. Observed associations need both further epidemiological and biological confirmation.

Published
2014

7. Cross Cancer Genomic Investigation of Inflammation Pathway for Five Common Cancers: Lung, Ovary, Prostate, Breast, and Colorectal Cancer

Author

Kenneth Muir, Christopher A. Haiman, S. Lindstrom, Nicholas Wentzensen, Ali A min Al Olama, Rosalind A. Eeles, Heike Bickeböller, Rayjean J. Hung, Loic L e Marchand, Stephen J. Chanock, Brooke L. Fridley, David C. Christiani, Christopher I. Amos, Brian E. Henderson, Peter Kraft, Richard S. Houlston, Zhihua Chen, P Brennan, David N. Rider, Ulrike Peters, Angela Risch, Graham Casey, Joellen M. Schildkraut, Andrew T. Chan, Paolo Boffetta, Catherine M. Phelan, John K. Field, Douglas F. Easton, Stephen B. Gruber, Julia G. Poirier, Cornelia M. Ulrich, Ellen L. Goode, Honglin Song, Sonja I. Berndt, John S. Witte, Fredrik Wiklund, Z Kote-Jarai, M. T. Landi, Henrik Grönberg, Fredrick R. Schumacher, Thomas A. Sellers, Yonathan Brhane, Margaret R. Spitz, David J. Hunter, Martha L. Slattery, Hung, R.J., Ulrich, C.M., Goode, E.L., Brhane, Y., Muir, K., Chan, A.T., Marchand, L.L., Schildkraut, J., Witte, J.S., Eeles, R., Boffetta, P., Spitz, M.R., Poirier, J.G., Rider, D.N., Fridley, B.L., Chen, Z., Haiman, C., Schumacher, F., Easton, D.F., Landi, M.T., Brennan, P., Houlston, R., Christiani, D.C., Field, J.K., Bickeböller, H., Risch, A., Kote-Jarai, Z., Wiklund, F., Grönberg, H., Chanock, S., Berndt, S.I., Kraft, P., Lindström, S., Al Olama, A.A., Song, H., Phelan, C., Wentzensen, N., Peters, U., Slattery, M.L., Sellers, T.A., Casey, G., Gruber, S.B., Hunter, D.J., Amos, C.I., and Henderson, B.

Subjects
Oncology, Male, Cancer Research, medicine.medical_specialty, Lung Neoplasms, Colorectal cancer, Genome-wide association study, Breast Neoplasms, Disease, Mouse model of colorectal and intestinal cancer, Biology, Article, Breast cancer, Prostate, Internal medicine, medicine, Humans, Lung cancer, Adaptor Proteins, Signal Transducing, Inflammation, Ovarian Neoplasms, Lung, ovary, prostate, breast, and colorectal cancer, Intracellular Signaling Peptides and Proteins, Prostatic Neoplasms, Proteins, medicine.disease, 3. Good health, medicine.anatomical_structure, Female, Ovarian cancer, Colorectal Neoplasms, Genome-Wide Association Study, Signal Transduction
Abstract

Background: Inflammation has been hypothesized to increase the risk of cancer development as an initiator or promoter, yet no large-scale study of inherited variation across cancer sites has been conducted. Methods: We conducted a cross-cancer genomic analysis for the inflammation pathway based on 48 genome-wide association studies within the National Cancer Institute GAME-ON Network across five common cancer sites, with a total of 64 591 cancer patients and 74 467 control patients. Subset-based meta-analysis was used to account for possible disease heterogeneity, and hierarchical modeling was employed to estimate the effect of the subcomponents within the inflammation pathway. The network was visualized by enrichment map. All statistical tests were two-sided. Results: We identified three pleiotropic loci within the inflammation pathway, including one novel locus in Ch12q24 encoding SH2B3 (rs3184504), which reached GWAS significance with a P value of 1.78 x 10-8, and it showed an association with lung cancer (P = 2.01 x 10-6), colorectal cancer (GECCO P = 6.72x10-6; CORECT P = 3.32x10-5), and breast cancer (P = .009). We also identified five key subpathway components with genetic variants that are relevant for the risk of these five cancer sites: inflammatory response for colorectal cancer (P = .006), inflammation related cell cycle gene for lung cancer (P = 1.35x10-6), and activation of immune response for ovarian cancer (P = .009). In addition, sequence variations in immune system development played a role in breast cancer etiology (P = .001) and innate immune response was involved in the risk of both colorectal (P = .022) and ovarian cancer (P = .003). Conclusions: Genetic variations in inflammation and its related subpathway components are keys to the development of lung, colorectal, ovary, and breast cancer, including SH2B3, which is associated with lung, colorectal, and breast cancer. © The Author 2015. Published by Oxford University Press. All rights reserved.

Published
2014

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