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1. Signatures of mutational processes in human cancer.

Author

Van 'T Veer, Laura, Alexandrov, LB, Nik-Zainal, S, Wedge, DC, Aparicio, SAJR, Behjati, S, Biankin, AV, Bignell, GR, Bolli, N, Borg, A, and Børresen-Dale, A-L

Abstract

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been o

Published
2013

2. Risk for contralateral breast cancer among carriers of the CHEK2*1100delC mutation in the WECARE Study.

Author

Mellemkjaer, L, Dahl, C, Olsen, JH, Bertelsen, L, Guldberg, P, Christensen, J, Børresen-Dale, A-L, Stovall, M, Langholz, B, Bernstein, L, Lynch, CF, Malone, KE, Haile, RW, Andersson, M, Thomas, DC, Concannon, P, Capanu, M, Boice, JD, WECARE Study Collaborative Group, and Bernstein, JL

Subjects
WECARE Study Collaborative Group, Humans, Breast Neoplasms, Protein-Serine-Threonine Kinases, SEER Program, Risk Factors, Case-Control Studies, Genotype, Germ-Line Mutation, Middle Aged, Female, Checkpoint Kinase 2, Oncology & Carcinogenesis, Oncology and Carcinogenesis, Public Health and Health Services
Abstract

The protein encoded by the CHEK2 gene is involved in cellular repair of DNA damage. The truncating mutation, CHEK2*1100delC, seems to increase the risk for breast cancer. We investigated whether the CHEK2*1100delC mutation carrier status increases the risk for asynchronous contralateral breast cancer (CBC) and whether it interacts with radiation therapy (RT) or chemotherapy in regard to CBC risk. The germline mutation frequency was assessed in 708 women with CBC and 1395 women with unilateral breast cancer (UBC) in the Women's Environment, Cancer and Radiation Epidemiology (WECARE) Study whose first primary breast cancer was diagnosed before age 55 years and during 1985--1999. Seven women with CBC (1.0%) and 10 women with UBC (0.7%) were CHEK2*1100delC variant carriers (rate ratio (RR)=1.8, 95% confidence interval (CI)=0.6-5.4 for CBC vs UBC). Carriers who received RT for their first breast cancer, compared with non-carriers not treated with RT, had an RR of developing CBC of 2.6 (95% CI=0.8-8.7). We found no significant associations between the CHEK2*1100delC mutation and CBC overall or among those treated with RT. However, the sampling variability was such that modest increases in risk could not be excluded. Nonetheless, because this is a rare mutation, it is unlikely to explain a major fraction of CBC in the population.

Published
2008

3. Risk for contralateral breast cancer among carriers of the CHEK2*1100delC mutation in the WECARE Study

Author

Mellemkjær, L, Dahl, C, Olsen, JH, Bertelsen, L, Guldberg, P, Christensen, J, Børresen-Dale, A-L, Stovall, M, Langholz, B, Bernstein, L, Lynch, CF, Malone, KE, Haile, RW, Andersson, M, Thomas, DC, Concannon, P, Capanu, M, Boice, JD, The WECARE Study Collaborative Group, and Bernstein, JL

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Breast Cancer, Clinical Research, Prevention, Cancer, Genetics, Breast Neoplasms, Case-Control Studies, Checkpoint Kinase 2, Female, Genotype, Germ-Line Mutation, Humans, Middle Aged, Protein Serine-Threonine Kinases, Risk Factors, SEER Program, WECARE Study Collaborative Group, Public Health and Health Services, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

The protein encoded by the CHEK2 gene is involved in cellular repair of DNA damage. The truncating mutation, CHEK2*1100delC, seems to increase the risk for breast cancer. We investigated whether the CHEK2*1100delC mutation carrier status increases the risk for asynchronous contralateral breast cancer (CBC) and whether it interacts with radiation therapy (RT) or chemotherapy in regard to CBC risk. The germline mutation frequency was assessed in 708 women with CBC and 1395 women with unilateral breast cancer (UBC) in the Women's Environment, Cancer and Radiation Epidemiology (WECARE) Study whose first primary breast cancer was diagnosed before age 55 years and during 1985--1999. Seven women with CBC (1.0%) and 10 women with UBC (0.7%) were CHEK2*1100delC variant carriers (rate ratio (RR)=1.8, 95% confidence interval (CI)=0.6-5.4 for CBC vs UBC). Carriers who received RT for their first breast cancer, compared with non-carriers not treated with RT, had an RR of developing CBC of 2.6 (95% CI=0.8-8.7). We found no significant associations between the CHEK2*1100delC mutation and CBC overall or among those treated with RT. However, the sampling variability was such that modest increases in risk could not be excluded. Nonetheless, because this is a rare mutation, it is unlikely to explain a major fraction of CBC in the population.

Published
2008

4. ATM variants 7271T>G and IVS10-6T>G among women with unilateral and bilateral breast cancer

Author

Bernstein, JL, Bernstein, L, Thompson, WD, Lynch, CF, Malone, KE, Teitelbaum, SL, Olsen, JH, Anton-Culver, H, Boice, JD, Rosenstein, BS, Børresen-Dale, A-L, Gatti, RA, Concannon, P, and Haile, RW

Subjects
Prevention, Genetics, Human Genome, Cancer, Breast Cancer, Genetic Testing, Aetiology, 2.1 Biological and endogenous factors, Adult, Aged, Ataxia Telangiectasia, Ataxia Telangiectasia Mutated Proteins, Breast Neoplasms, Case-Control Studies, Cell Cycle Proteins, DNA Mutational Analysis, DNA-Binding Proteins, Female, Genetic Predisposition to Disease, Humans, Leucine Zippers, Mass Screening, Middle Aged, Neoplasms, Second Primary, Pedigree, Phosphatidylinositol 3-Kinases, Protein Serine-Threonine Kinases, Risk Factors, Tumor Suppressor Proteins, ATM gene screening, +G+mutation%22">7271T > G mutation, +G+mutation%22">IVS10-6T > G mutation, breast cancer, bilateral breast cancer, WECARE Study Collaborative Group, Oncology and Carcinogenesis, Public Health and Health Services, Oncology & Carcinogenesis
Abstract

Recent reports suggest that two ATM gene mutations, 7271T>G and IVS10-6T>G, are associated with a high risk of breast cancer among multiple-case families. To assess the importance of these two mutations in another 'high-risk' group, young women (under age 51) with multiple primaries, we screened a large population-based series of young women with bilateral breast cancer and compared the frequency of these mutations among similar women diagnosed with unilateral breast cancer. The 1149 women included were enrolled in an ongoing population-based case-control study of the genetic factors that contribute to bilateral breast cancer; they were not selected on the basis of family history of cancer. Screening for 7271T>G and IVS10-6T>G ATM gene mutations was conducted using DHPLC followed by direct sequencing. The 7271T>G mutation was detected in one out of 638 (0.2%) women with unilateral breast cancer and in none of the bilateral cases, and the IVS10-6T>G mutation in one out of 511 (0.2%) bilateral and in eight out of 638 (1.3%) unilateral breast cancer cases. Carriers of either mutation were not limited to women with a family history. Given the likelihood that young women with bilateral breast cancer have a genetic predisposition, the observed mutation distribution is contrary to that expected if these two mutations were to play an important role in breast carcinogenesis among individuals at high risk.

Published
2003

7. DNA copy number motifs are strong and independent predictors of survival in breast cancer

Author

Pladsen, A.V., Nilsen, G., Rueda, O.M., Aure, M.R., Borgan, Ø., Liestøl, K., Vitelli, V., Frigessi, A., Langerød, A., Mathelier, A., Bathen, T.F., Borgen, E., Børresen-Dale, A.-L., Engebråten, O., Fritzman, B., Garred, Ø., Geisler, J., Geitvik, G.A., Hofvind, S., Kristensen, V., Kåresen, R., Lingjærde, O.C., Mælandsmo, G.M., Naume, B., Russnes, H.G., Sahlberg, K.K., Sauer, T., Skjerven, H.K., Schlichting, E., Sørlie, T., Wedge, D.C., Van Loo, P., Caldas, C., Pladsen, Arne V [0000-0001-7765-6823], Rueda, Oscar M [0000-0003-0008-4884], Mathelier, Anthony [0000-0001-5127-5459], Wedge, David C [0000-0002-7572-3196], Van Loo, Peter [0000-0003-0292-1949], Caldas, Carlos [0000-0003-3547-1489], Russnes, Hege G [0000-0001-8724-1891], Lingjærde, Ole Christian [0000-0003-3565-4912], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Genome instability, Gene Dosage, Medicine (miscellaneous), Tumour biomarkers, chemistry.chemical_compound, Breast cancer, 0302 clinical medicine, Risk Factors, Databases, Genetic, Cancer genomics, Computational models, lcsh:QH301-705.5, Manchester Cancer Research Centre, food and beverages, Middle Aged, Prognosis, 3. Good health, 030220 oncology & carcinogenesis, Female, General Agricultural and Biological Sciences, Algorithms, DNA Copy Number Variations, Clinical Decision-Making, Breast Neoplasms, Computational biology, Biology, Risk Assessment, Article, General Biochemistry, Genetics and Molecular Biology, Genomic Instability, 03 medical and health sciences, Predictive Value of Tests, medicine, Biomarkers, Tumor, Humans, business.industry, ResearchInstitutes_Networks_Beacons/mcrc, Gene Expression Profiling, fungi, Cancer, medicine.disease, 030104 developmental biology, chemistry, lcsh:Biology (General), Spatial behavior, Personalized medicine, business, Outcome prediction, Transcriptome, Genome architecture, DNA
Abstract

Somatic copy number alterations are a frequent sign of genome instability in cancer. A precise characterization of the genome architecture would reveal underlying instability mechanisms and provide an instrument for outcome prediction and treatment guidance. Here we show that the local spatial behavior of copy number profiles conveys important information about this architecture. Six filters were defined to characterize regional traits in copy number profiles, and the resulting Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied to tumors in four breast cancer cohorts (n = 2919). The derived motifs represent a layer of information that complements established molecular classifications of breast cancer. A score reflecting presence or absence of motifs provided a highly significant independent prognostic predictor. Results were consistent between cohorts. The nonsite-specific occurrence of the detected patterns suggests that CARMA captures underlying replication and repair defects and could have a future potential in treatment stratification., Pladsen et al. develop Copy Aberration Regional Mapping Analysis (CARMA), an algorithm that derives motifs for copy number profiles in breast cancers by integrating several features, to predict breast cancer prognosis and stratifications. Their algorithm can detect replication and repair defects and can be used in personalized medicine.

Published
2020
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12. Mendelian randomisation study of smoking exposure in relation to breast cancer risk

Author

Park, HA, Neumeyer, S, Michailidou, K, Bolla, MK, Wang, Q, Dennis, J, Ahearn, TU, Andrulis, IL, Anton-Culver, H, Antonenkova, NN, Arndt, V, Aronson, KJ, Augustinsson, A, Baten, A, Beane Freeman, LE, Becher, H, Beckmann, MW, Behrens, S, Benitez, J, Bermisheva, M, Bogdanova, NV, Bojesen, SE, Brauch, H, Brenner, H, Brucker, SY, Burwinkel, B, Campa, D, Canzian, F, Castelao, JE, Chanock, SJ, Chenevix-Trench, G, Clarke, CL, Børresen-Dale, A-L, Grenaker Alnæs, GI, Sahlberg, KK, Ottestad, L, Kåresen, R, Schlichting, E, Holmen, MM, Sauer, T, Haakensen, V, Engebråten, O, Naume, B, Fosså, A, Kiserud, CE, Reinertsen, KV, Helland, Å, Riis, M, Geisler, J, Conroy, DM, Couch, FJ, Cox, A, Cross, SS, Czene, K, Daly, MB, Devilee, P, Dörk, T, dos-Santos-Silva, I, Dwek, M, Eccles, DM, Eliassen, AH, Engel, C, Eriksson, M, Evans, DG, Fasching, PA, Flyger, H, Fritschi, L, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Giles, GG, Glendon, G, Goldberg, MS, Goldgar, DE, González-Neira, A, Grip, M, Guénel, P, Hahnen, E, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Han, S, Harkness, EF, Hart, SN, He, W, Heemskerk-Gerritsen, BAM, Hopper, JL, Hunter, DJ, Clarke, C, Marsh, D, Scott, R, Baxter, R, Yip, D, Carpenter, J, Davis, A, Pathmanathan, N, Simpson, P, Graham, D, Sachchithananthan, M, Amor, D, Andrews, L, Antill, Y, Balleine, R, Beesley, J, Bennett, I, Bogwitz, M, Botes, L, Brennan, M, Brown, M, Buckley, M, Burke, J, Butow, P, Caldon, L, Campbell, I, Chauhan, D, Chauhan, M, Christian, A, Cohen, P, Colley, A, Crook, A, Cui, J, Cummings, M, Dawson, S-J, DeFazio, A, Delatycki, M, Dickson, R, Dixon, J, Edkins, T, Edwards, S, Farshid, G, Fellows, A, Fenton, G, Field, M, Flanagan, J, Fong, P, Forrest, L, Fox, S, French, J, Friedlander, M, Gaff, C, Gattas, M, George, P, Greening, S, Harris, M, Hart, S, Hayward, N, Hopper, J, Hoskins, C, Hunt, C, James, P, Jenkins, M, Kidd, A, Kirk, J, Koehler, J, Kollias, J, Lakhani, S, Lawrence, M, Lindeman, G, Lipton, L, Lobb, L, Mann, G, McLachlan, SA, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, O’Sullivan, S, Ortega, DG, Pachter, N, Patterson, B, Pearn, A, Phillips, K, Pieper, E, Rickard, E, Robinson, B, Saleh, M, Salisbury, E, Saunders, C, Saunus, J, Scott, C, Sexton, A, Shelling, A, Southey, M, Spurdle, A, Taylor, J, Taylor, R, Thorne, H, Trainer, A, Tucker, K, Visvader, J, Walker, L, Williams, R, Winship, I, Young, MA, Jager, A, Jakubowska, A, John, EM, Jung, A, Kaaks, R, Kapoor, PM, Keeman, R, Khusnutdinova, E, Kitahara, CM, Koppert, LB, Koutros, S, Kristensen, VN, Kurian, AW, Lacey, J, Lambrechts, D, Le Marchand, L, Lo, W-Y, Lubiński, J, Mannermaa, A, Manoochehri, M, Margolin, S, Martinez, ME, Mavroudis, D, Meindl, A, Menon, U, Milne, RL, Muranen, TA, Nevanlinna, H, Newman, WG, Nordestgaard, BG, Offit, K, Olshan, AF, Olsson, H, Park-Simon, T-W, Peterlongo, P, Peto, J, Plaseska-Karanfilska, D, Presneau, N, Radice, P, Rennert, G, Rennert, HS, Romero, A, Saloustros, E, Sawyer, EJ, Schmidt, MK, Schmutzler, RK, Schoemaker, MJ, Schwentner, L, Shah, M, Shu, X-O, Simard, J, Smeets, A, Southey, MC, Spinelli, JJ, Stevens, V, Swerdlow, AJ, Tamimi, RM, Tapper, WJ, Taylor, JA, Terry, MB, Tomlinson, I, Troester, MA, Truong, T, Vachon, CM, van Veen, EM, Vijai, J, Wang, S, Wendt, C, Winqvist, R, Wolk, A, Ziogas, A, Dunning, AM, Pharoah, PDP, Easton, DF, Zheng, W, Kraft, P, Chang-Claude, J, HUS Gynecology and Obstetrics, Department of Obstetrics and Gynecology, Park, Hanla A. [0000-0001-8055-3729], Dennis, Joe [0000-0003-4591-1214], Augustinsson, Annelie [0000-0003-3415-0536], Brenner, Hermann [0000-0002-6129-1572], Canzian, Federico [0000-0002-4261-4583], Cox, Angela [0000-0002-5138-1099], Devilee, Peter [0000-0002-8023-2009], Fasching, Peter A. [0000-0003-4885-8471], Harkness, Elaine F. [0000-0001-6625-7739], Hart, Steven N. [0000-0001-7714-2734], Heemskerk-Gerritsen, Bernadette A. M. [0000-0002-9724-6693], Jakubowska, Anna [0000-0002-5650-0501], Kapoor, Pooja Middha [0000-0001-5503-8215], Kurian, Allison W. [0000-0002-6175-9470], Newman, William G. [0000-0002-6382-4678], Peterlongo, Paolo [0000-0001-6951-6855], Peto, Julian [0000-0002-1685-8912], Sawyer, Elinor J. [0000-0001-8285-4111], Scott, Christopher [0000-0003-1340-0647], Smeets, Ann [0000-0002-5091-6602], Tomlinson, Ian [0000-0003-3037-1470], Truong, Thérèse [0000-0002-2943-6786], Pharoah, Paul D. P. [0000-0001-8494-732X], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Oncology, Medicin och hälsovetenskap, Cancer Research, Genotyping Techniques, Breast Neoplasms, Case-Control Studies, Cigarette Smoking, Female, Genetic Pleiotropy, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Mendelian Randomization Analysis, Polymorphism, Single Nucleotide, ALCOHOL, Medical and Health Sciences, 0302 clinical medicine, Breast cancer, Pleiotropy, Epidemiology, Medicine, TOBACCO, Breast Neoplasms/epidemiology, Cigarette Smoking/adverse effects, WOMEN, ASSOCIATION, Single Nucleotide, 3. Good health, Substance abuse, 692/699/67/1347, 030220 oncology & carcinogenesis, Life Sciences & Biomedicine, 692/499, medicine.medical_specialty, 3122 Cancers, Single-nucleotide polymorphism, Article, 03 medical and health sciences, Internal medicine, ddc:610, Polymorphism, Genetic association, Science & Technology, business.industry, Cancer, medicine.disease, 030104 developmental biology, Clinical research, Risk factors, TISSUE, INFERENCE, CIGARETTE-SMOKING, business
Abstract

Background Despite a modest association between tobacco smoking and breast cancer risk reported by recent epidemiological studies, it is still equivocal whether smoking is causally related to breast cancer risk. Methods We applied Mendelian randomisation (MR) to evaluate a potential causal effect of cigarette smoking on breast cancer risk. Both individual-level data as well as summary statistics for 164 single-nucleotide polymorphisms (SNPs) reported in genome-wide association studies of lifetime smoking index (LSI) or cigarette per day (CPD) were used to obtain MR effect estimates. Data from 108,420 invasive breast cancer cases and 87,681 controls were used for the LSI analysis and for the CPD analysis conducted among ever-smokers from 26,147 cancer cases and 26,072 controls. Sensitivity analyses were conducted to address pleiotropy. Results Genetically predicted LSI was associated with increased breast cancer risk (OR 1.18 per SD, 95% CI: 1.07–1.30, P = 0.11 × 10–2), but there was no evidence of association for genetically predicted CPD (OR 1.02, 95% CI: 0.78–1.19, P = 0.85). The sensitivity analyses yielded similar results and showed no strong evidence of pleiotropic effect. Conclusion Our MR study provides supportive evidence for a potential causal association with breast cancer risk for lifetime smoking exposure but not cigarettes per day among smokers.

Published
2021
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13. Common variants in breast cancer risk loci predispose to distinct tumor subtypes

Author

Ahearn, TU, Zhang, H, Michailidou, K, Milne, RL, Bolla, MK, Dennis, J, Dunning, AM, Lush, M, Wang, Q, Andrulis, IL, Anton-Culver, H, Arndt, V, Aronson, KJ, Auer, PL, Augustinsson, A, Baten, A, Becher, H, Behrens, S, Benitez, J, Bermisheva, M, Blomqvist, C, Bojesen, SE, Bonanni, B, Børresen-Dale, A-L, Brauch, H, Brenner, H, Brooks-Wilson, A, Brüning, T, Burwinkel, B, Buys, SS, Canzian, F, Castelao, JE, Chang-Claude, J, Chanock, SJ, Chenevix-Trench, G, Clarke, CL, Sahlberg, KK, Ottestad, L, Kåresen, R, Schlichting, E, Holmen, MM, Sauer, T, Haakensen, V, Engebråten, O, Naume, B, Fosså, A, Kiserud, CE, Reinertsen, KV, Helland, Å, Riis, M, Geisler, J, Collée, JM, Cox, A, Cross, SS, Czene, K, Daly, MB, Devilee, P, Dörk, T, Dwek, M, Eccles, DM, Evans, DG, Fasching, PA, Figueroa, J, Floris, G, Gago-Dominguez, M, Gapstur, SM, García-Sáenz, JA, Gaudet, MM, Giles, GG, Goldberg, MS, González-Neira, A, Alnæs, GIG, Grip, M, Guénel, P, Haiman, CA, Hall, P, Hamann, U, Harkness, EF, Heemskerk-Gerritsen, BAM, Holleczek, B, Hollestelle, A, Hooning, MJ, Hoover, RN, Hopper, JL, Howell, A, Clarke, C, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, C, Marsh, D, Morey, A, Pathmanathan, N, Scott, R, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Zeps, N, Fox, S, Campbell, I, Bowtell, D, Spurdle, A, Webb, P, de Fazio, A, Tassell, M, Kirk, J, Lindeman, G, Price, M, Southey, M, Milne, R, Deb, S, Jakimovska, M, Jakubowska, A, John, EM, Jones, ME, Jung, A, Kaaks, R, Kauppila, S, Keeman, R, Khusnutdinova, E, Kitahara, CM, Ko, Y-D, Koutros, S, Kristensen, VN, Krüger, U, Kubelka-Sabit, K, Kurian, AW, Kyriacou, K, Lambrechts, D, Lee, DG, Lindblom, A, Linet, M, Lissowska, J, Llaneza, A, Lo, W-Y, MacInnis, RJ, Mannermaa, A, Manoochehri, M, Margolin, S, Martinez, ME, McLean, C, Meindl, A, Menon, U, Nevanlinna, H, Newman, WG, Nodora, J, Offit, K, Olsson, H, Orr, N, Park-Simon, T-W, Patel, AV, Peto, J, Pita, G, Plaseska-Karanfilska, D, Prentice, R, Punie, K, Pylkäs, K, Radice, P, Rennert, G, Romero, A, Rüdiger, T, Saloustros, E, Sampson, S, Sandler, DP, Sawyer, EJ, Schmutzler, RK, Schoemaker, MJ, Schöttker, B, Sherman, ME, Shu, X-O, Smichkoska, S, Southey, MC, Spinelli, JJ, Swerdlow, AJ, Tamimi, RM, Tapper, WJ, Taylor, JA, Teras, LR, Terry, MB, Torres, D, Troester, MA, Vachon, CM, van Deurzen, CHM, van Veen, EM, Wagner, P, Weinberg, CR, Wendt, C, Wesseling, J, Winqvist, R, Wolk, A, Yang, XR, Zheng, W, Couch, FJ, Simard, J, Kraft, P, Easton, DF, Pharoah, PDP, Schmidt, MK, García-Closas, M, Chatterjee, N, Ahearn, Thomas U [0000-0003-0771-7752], Easton, Douglas [0000-0003-2444-3247], Pharoah, Paul [0000-0001-8494-732X], Apollo - University of Cambridge Repository, Medicum, HUS Comprehensive Cancer Center, Department of Oncology, Clinicum, Department of Obstetrics and Gynecology, Biosciences, HUS Gynecology and Obstetrics, Clinical Genetics, Medical Oncology, and Pathology

Subjects
False discovery rate, Oncology, Common breast cancer susceptibility variants, Receptor, ErbB-2, Estrogen receptor, PROGRESSION, Etiologic heterogeneity, Logistic regression, Basic medicine, Breast cancer, 0302 clinical medicine, PRIMARY THERAPY, HETEROGENEITY, RC254-282, HISTOLOGICAL GRADE, 0303 health sciences, Breast Neoplasms/epidemiology, Receptors, Estrogen/genetics, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, INTERNATIONAL EXPERT CONSENSUS, humanities, Receptor, ErbB-2/genetics, 3. Good health, Receptors, Estrogen, Receptors, Progesterone/genetics, 030220 oncology & carcinogenesis, Female, Biomarkers, Tumor/genetics, Receptors, Progesterone, Medical Genetics, Research Article, Risk, medicine.medical_specialty, SUSCEPTIBILITY LOCI, 3122 Cancers, Breast Neoplasms, Single-nucleotide polymorphism, Biology, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Internal medicine, Progesterone receptor, Biomarkers, Tumor, medicine, Genetic predisposition, Humans, ddc:610, GENOME-WIDE ASSOCIATION, Genetic association, Medicinsk genetik, 030304 developmental biology, Cancer och onkologi, medicine.disease, Cancer and Oncology, Clinical medicine, Genome-Wide Association Study
Abstract

Background Genome-wide association studies (GWAS) have identified multiple common breast cancer susceptibility variants. Many of these variants have differential associations by estrogen receptor (ER) status, but how these variants relate with other tumor features and intrinsic molecular subtypes is unclear. Methods Among 106,571 invasive breast cancer cases and 95,762 controls of European ancestry with data on 173 breast cancer variants identified in previous GWAS, we used novel two-stage polytomous logistic regression models to evaluate variants in relation to multiple tumor features (ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and grade) adjusting for each other, and to intrinsic-like subtypes. Results Eighty-five of 173 variants were associated with at least one tumor feature (false discovery rate p Conclusion This report demonstrates a high level of complexity in the etiology heterogeneity of breast cancer susceptibility variants and can inform investigations of subtype-specific risk prediction.

Published
2020
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21. Genome-wide association study of germline variants and breast cancer-specific mortality

Author

Escala-Garcia, M., Guo, Q., Dörk, T., Canisius, S., Keeman, R., Dennis, J., Beesley, J., Lecarpentier, J., Bolla, M.K., Wang, Q., Abraham, J., Andrulis, I.L., Anton-Culver, H., Arndt, V., Auer, P.L., Beckmann, M.W., Behrens, S., Benitez, J., Bermisheva, M., Bernstein, L., Blomqvist, C., Boeckx, B., Bojesen, S.E., Bonanni, B., Børresen-Dale, A.-L., Brauch, H., Brenner, H., Brentnall, A., Brinton, L., Broberg, P., Brock, I.W., Brucker, S.Y., Burwinkel, B., Caldas, C., Caldés, T., Campa, D., Canzian, F., Carracedo, A., Carter, B.D., Castelao, J.E., Chang-Claude, J., Chanock, S.J., Chenevix-Trench, G., Cheng, T.-Y.D., Chin, S.-F., Clarke, C.L., NBCS Collaborators, Cordina-Duverger, E., Couch, F.J., Cox, D.G., Cox, A., Cross, S.S., Czene, K., Daly, M.B., Devilee, P., Dunn, J.A., Dunning, A.M., Durcan, L., Dwek, M., Earl, H.M., Ekici, A.B., Eliassen, A.H., Ellberg, C., Engel, C., Eriksson, M., Evans, D.G., Figueroa, J., Flesch-Janys, D., Flyger, H., Gabrielson, M., Gago-Dominguez, M., Galle, E., Gapstur, S.M., García-Closas, M., García-Sáenz, J.A., Gaudet, M.M., George, A., Georgoulias, V., Giles, G.G., Glendon, G., Goldgar, D.E., González-Neira, A., Alnæs, G.I.G., Grip, M., Guénel, P., Haeberle, L., Hahnen, E., Haiman, C.A., Håkansson, N., Hall, P., Hamann, U., Hankinson, S., Harkness, E.F., Harrington, P.A., Hart, S.N., Hartikainen, J.M., Hein, A., Hillemanns, P., Hiller, L., Holleczek, B., Hollestelle, A., Hooning, M.J., Hoover, R.N., Hopper, J.L., Howell, A., Huang, G., Humphreys, K., Hunter, D.J., Janni, W., John, E.M., Jones, M.E., Jukkola-Vuorinen, A., Jung, A., Kaaks, R., Kabisch, M., Kaczmarek, K., Kerin, M.J., Khan, S., Khusnutdinova, E., Kiiski, J.I., Kitahara, C.M., Knight, J.A., Ko, Y.-D., Koppert, L.B., Kosma, V.-M., Kraft, P., Kristensen, V.N., Krüger, U., Kühl, T., Lambrechts, D., Le Marchand, L., Lee, E., Lejbkowicz, F., Li, L., Lindblom, A., Lindström, S., Linet, M., Lissowska, J., Lo, W.-Y., Loibl, S., Lubiński, J., Lux, M.P., MacInnis, R.J., Maierthaler, M., Maishman, T., Makalic, E., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, M.E., Mavroudis, D., McLean, C., Meindl, A., Middha, P., Miller, N., Milne, R.L., Moreno, F., Mulligan, A.M., Mulot, C., Nassir, R., Neuhausen, S.L., Newman, W.T., Nielsen, S.F., Nordestgaard, B.G., Norman, A., Olsson, H., Orr, N., Pankratz, V.S., Park-Simon, T.-W., Perez, J.I.A., Pérez-Barrios, C., Peterlongo, P., Petridis, C., Pinchev, M., Prajzendanc, K., Prentice, R., Presneau, N., Prokofieva, D., Pylkäs, K., Rack, B., Radice, P., Ramachandran, D., Rennert, G., Rennert, H.S., Rhenius, V., Romero, A., Roylance, R., Saloustros, E., Sawyer, E.J., Schmidt, D.F., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Schumacher, F., Schwentner, L., Scott, R.J., Scott, C., Seynaeve, C., Shah, M., Simard, J., Smeets, A., Sohn, C., Southey, M.C., Swerdlow, A.J., Talhouk, A., Tamimi, R.M., Tapper, W.J., Teixeira, M.R., Tengström, M., Terry, M.B., Thöne, K., Tollenaar, R.A.E.M., Tomlinson, I., Torres, D., Truong, T., Turman, C., Turnbull, C., Ulmer, H.-U., Untch, M., Vachon, C., van Asperen, C.J., van den Ouweland, A.M.W., van Veen, E.M., Wendt, C., Whittemore, A.S., Willett, W., Winqvist, R., Wolk, A., Yang, X.R., Zhang, Y., Easton, D.F., Fasching, P.A., Nevanlinna, H., Eccles, D.M., Pharoah, P.D.P., and Schmidt, M.K.

Abstract

BACKGROUND: We examined the associations between germline variants and breast cancer mortality using a large meta-analysis of women of European ancestry. METHODS: Meta-analyses included summary estimates based on Cox models of twelve datasets using ~10.4 million variants for 96,661 women with breast cancer and 7697 events (breast cancer-specific deaths). Oestrogen receptor (ER)-specific analyses were based on 64,171 ER-positive (4116) and 16,172 ER-negative (2125) patients. We evaluated the probability of a signal to be a true positive using the Bayesian false discovery probability (BFDP). RESULTS: We did not find any variant associated with breast cancer-specific mortality at P

Published
2019

22. Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors

Author

Naume B, Gunderson K, Bruhn L, Sun H, Hicks J, Johansen FE, Aarøe J, Baumbusch LO, Kristensen VN, Liestøl K, Børresen-Dale A-L, and Lingjærde OC

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes. Results We evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from http://www.ifi.uio.no/bioinf/Projects/. Conclusion We conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented.

Published
2008
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24. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

Author

Shi, J., Zhang, Y., Zheng, W., Michailidou, K., Ghoussaini, M., Bolla, M.K., Wang, Q., Dennis, J., Lush, M., Milne, R.L., Shu, X-O., Beesley, J., Kar, S., Andrulis, I.L., Anton-Culver, H., Arndt, V., Beckmann, M.W., Zhao, Z., Guo, X., Benitez, J., Beeghly-Fadiel, A., Blot, W., Bogdanova, N.V., Bojesen, S.E., Brauch, H., Brenner, H., Brinton, L., Broeks, A., Brüning, T., Burwinkel, B., Cai, H., Canisius, S., Chang-Claude, J., Choi, J-Y., Couch, F.J., Cox, A., Cross, S.S., Czene, K., Darabi, H., Devilee, P., Droit, A., Dork, T., Fasching, P.A., Fletcher, O., Flyger, H., Fostira, F., Gaborieau, V., García-Closas, M., Giles, G.G., Grip, M., Guenel, P., Haiman, C.A., Hamann, U., Hartman, M., Miao, H., Hollestelle, A., Hopper, J.L., Hsiung, C-N., Ito, H., Jakubowska, A., Johnson, N., Torres, D., Kabisch, M., Kang, D., Khan, S., Knight, J.A., Kosma, V-M., Lambrechts, D., Li, J., Lindblom, A., Lophatananon, A., Lubinski, J., Mannermaa, A., Manoukian, S., Le Marchand, L., Margolin, S., Marme, F., Matsuo, K., McLean, C., Meindl, A., Muir, K., Neuhausen, S.L., Nevanlinna, H., Nord, S., Børresen-Dale, A-L., Olson, J.E., Orr, N., van den Ouweland, A.M.W, Peterlongo, P., Putti, T.C., Rudolph, A., Sangrajrang, S., Sawyer, E.J., Schmidt, M.K., Schmutzler, R.K., Shen, C-Y., Hou, M-F., Shrubsole, M.J., Southey, M.C., Swerdlow, A., Teo, S.H., Thienpont, B., Toland, A.E., Tollenaar, R.A.E.M., Tomlinson, I., Truong, T., Tseng, C-C., Wen, W., Winqvist, R., Wu, A.H., Yip, C.H., Zamora, P.M., Zheng, Y., Floris, G., Cheng, C-Y., Hooning, M.J., Martens, J.W.M., Seynaeve, C., Kristensen, V.N., Hall, P., Pharoah, P.D.P., Simard, J., Chenevix-Trench, G., Dunning, A.M., Antoniou, A.C., Easton, D.F., Cai, Q., Long, J., Clinical Genetics, Medical Oncology, and Obstetrics & Gynecology

Subjects
SDG 3 - Good Health and Well-being
Abstract

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. We conducted a fine-mapping study across 2.06 Mb (chr8:127,561,724 -129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium. We found three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional P = 5.8 × 10-6), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional P = 1.1 × 10-6), and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional P = 1.1 × 10-4). Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas, and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r2 = 0.77), were putatively functional variants for two of the five independent association signals. Our results highlight multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry

Published
2016

26. Abstract P6-13-01: Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - A randomized phase II study

Author

Haugen, MH, primary, Lindgjærde, OC, additional, Krohn, M, additional, Zhao, W, additional, Lindholm, EM, additional, Silwal-Pandit, L, additional, Borgen, E, additional, Garred, Ø, additional, Fangberget, A, additional, Holmen, MM, additional, Schlichting, E, additional, Skjerven, H, additional, Lundgren, S, additional, Wist, E, additional, Naume, B, additional, Mælandsmo, GM, additional, Lu, Y, additional, Børresen-Dale, A-L, additional, Mills, GB, additional, and Engebråten, O, additional

Published
2017
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28. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Author

Tubio, J. M., Li, Y., Ju, Y. S., Martincorena, I., Cooke, S. L., Tojo Castro, Marta, Gundem, G., Pipinikas, C. P., Zamora, J., Raine, K., Menzies, A., Roman-Garcia, P., Fullam, A., Gerstung, M., Shlien, A., Tarpey, P. S., Papaemmanuil, E., Knappskog, S., Van Loo, P., Ramakrishna, M., Davies, H. R., Marshall, J., Wedge, D. C., Teague, J. W., Butler, A. P., Nik-Zainal, S., Alexandrov, L., Behjati, S., Yates, L. R., Bolli, N., Mudie, L., Hardy, C., Martin, S., McLaren, S., O'Meara, S., Anderson, E., Maddison, M., Gamble, S., Foster, C., Warren, A. Y., Whitaker, H., Brewer, D., Eeles, R., Cooper, C., Neal, D., Lynch, A. G., Visakorpi, T., Isaacs, W. B., van't Veer, L., Caldas, C., Desmedt, C., Sotiriou, C., Aparicio, S., Foekens, J. A., Eyfjörd, J. E., Lakhani, S. R., Thomas, G., Myklebost, O., Span, P. N., Børresen-Dale, A. L., Richardson, A. L., Van de Vijver, M., Vincent-Salomon, A., Van den Eynden, G. G., Flanagan, A. M., Futreal, P. A., Janes, S. M., Bova, G. S., Stratton, M. R., McDermott, U., Campbell, P. J., Group, ICGC Breast Cancer, Group, ICGC Bone Cancer, and Group, ICGC Prostate Cancer

Subjects
Mutagenesis, Insertional, Long Interspersed Nucleotide Elements, Carcinogenesis, Genome, Human, Transduction, Genetic, Neoplasms, DNA Transposable Elements, food and beverages, Humans, Exons, Chromatin, Translocation, Genetic
Abstract

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.

Published
2014

29. Abstract P6-08-10: Mutational signatures impact the breast cancer transcriptome and distinguish mitotic from immune response pathways

Author

Martens, JWM, primary, Smid, M, additional, Rodríguez-González, G, additional, Sieuwerts, AM, additional, Prager-Van der Smissen, WJC, additional, Van Der Vlugt - Daane, M, additional, Van Galen, A, additional, Nik-Zainal, S, additional, Staaf, J, additional, Brinkman, AB, additional, Van de Vijver, MJ, additional, Richardson, AL, additional, Berentsen, K, additional, Caldas, C, additional, Butler, A, additional, Martin, S, additional, Davies, HD, additional, Debets, R, additional, Meijer-Van Gelder, ME, additional, Van Deurzen, CHM, additional, Ramakrishna, MR, additional, Ringnér, M, additional, Viari, A, additional, Birney, E, additional, Børresen-Dale, A-L, additional, Stunnenberg, HG, additional, Stratton, M, additional, and Foekens, JA, additional

Published
2016
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31. Differential expression of miRNAs in pancreatobiliary type of periampullary adenocarcinoma and its associated stroma

Author

Sandhu, V., primary, Bowitz Lothe, I.M., additional, Labori, K.J., additional, Skrede, M.L., additional, Hamfjord, J., additional, Dalsgaard, A.M., additional, Buanes, T., additional, Dube, G., additional, Kale, M.M., additional, Sawant, S., additional, Kulkarni-Kale, U., additional, Børresen-Dale, A.-L., additional, Lingjaerde, O.C., additional, and Kure, E.H., additional

Published
2015
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32. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.

Author

Tubio, Jose M C, Li, Yilong, Ju, Young Seok, Martincorena, Inigo, Cooke, Susanna S.L., Tojo, Marta, Gundem, Gunes, Pipinikas, Christodoulos P, Zamora, Jorge, Raine, Keiran, Menzies, Andrew, Roman-Garcia, Pablo, Fullam, Anthony, Gerstung, Moritz, Shlien, Adam, Tarpey, Patrick S, Papaemmanuil, Elli, Knappskog, Stian, Van Loo, Peter, Ramakrishna, Manasa, Davies, Helen, Marshall, John, Wedge, David C., Teague, Jon W, Butler, Adam P, Nik-Zainal, Serena, Alexandrov, Ludmil, Behjati, Sam, Yates, Lucy R., Bolli, Niccolo, Mudie, Laura, Hardy, Claire, Martin, Sancha, McLaren, Stuart, O'Meara, Sarah, Anderson, Elizabeth, Maddison, Mark, Gamble, Stephen, ICGC Breast Cancer Group, ICGC Bone Cancer Group, ICGC Prostate Cancer Group, Foster, Christopher, Warren, Anne Y, Whitaker, Hayley, Brewer, Daniel, Eeles, Rosalind, Cooper, Colin, Neal, David, Lynch, Andy G, Visakorpi, Tapio, Isaacs, William WB, Van't Veer, Laura, Caldas, Carlos, Desmedt, Christine, Sotiriou, Christos, Aparicio, Samuel, Foekens, John A, Eyfjörd, Jórunn Erla, Lakhani, Sunil R, Thomas, Gilles, Myklebost, Ola, Span, Paul, Børresen-Dale, A L, Richardson, Andrea L, Van de Vijver, Marc J, Vincent-Salomon, Anne, Van den Eynden, Gert, Flanagan, Adrienne M, Futreal, P Andrew, Janes, Sam M, Bova, Steven GS, Stratton, Michael R, McDermott, Ultan, Campbell, Peter J, Tubio, Jose M C, Li, Yilong, Ju, Young Seok, Martincorena, Inigo, Cooke, Susanna S.L., Tojo, Marta, Gundem, Gunes, Pipinikas, Christodoulos P, Zamora, Jorge, Raine, Keiran, Menzies, Andrew, Roman-Garcia, Pablo, Fullam, Anthony, Gerstung, Moritz, Shlien, Adam, Tarpey, Patrick S, Papaemmanuil, Elli, Knappskog, Stian, Van Loo, Peter, Ramakrishna, Manasa, Davies, Helen, Marshall, John, Wedge, David C., Teague, Jon W, Butler, Adam P, Nik-Zainal, Serena, Alexandrov, Ludmil, Behjati, Sam, Yates, Lucy R., Bolli, Niccolo, Mudie, Laura, Hardy, Claire, Martin, Sancha, McLaren, Stuart, O'Meara, Sarah, Anderson, Elizabeth, Maddison, Mark, Gamble, Stephen, ICGC Breast Cancer Group, ICGC Bone Cancer Group, ICGC Prostate Cancer Group, Foster, Christopher, Warren, Anne Y, Whitaker, Hayley, Brewer, Daniel, Eeles, Rosalind, Cooper, Colin, Neal, David, Lynch, Andy G, Visakorpi, Tapio, Isaacs, William WB, Van't Veer, Laura, Caldas, Carlos, Desmedt, Christine, Sotiriou, Christos, Aparicio, Samuel, Foekens, John A, Eyfjörd, Jórunn Erla, Lakhani, Sunil R, Thomas, Gilles, Myklebost, Ola, Span, Paul, Børresen-Dale, A L, Richardson, Andrea L, Van de Vijver, Marc J, Vincent-Salomon, Anne, Van den Eynden, Gert, Flanagan, Adrienne M, Futreal, P Andrew, Janes, Sam M, Bova, Steven GS, Stratton, Michael R, McDermott, Ultan, and Campbell, Peter J

Abstract

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome., SCOPUS: re.j, info:eu-repo/semantics/published

Published
2014

33. Molecular signatures of mRNAs and miRNAs as prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas

Author

Sandhu, V., primary, Bowitz Lothe, I.M., additional, Labori, K.J., additional, Lingjaerde, O.C., additional, Buanes, T., additional, Dalsgaard, A.M., additional, Skrede, M.L., additional, Hamfjord, J., additional, Haaland, T., additional, Eide, T.J., additional, Børresen-Dale, A.-L., additional, Ikdahl, T., additional, and Kure, E.H., additional

Published
2014
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36. Signatures of mutational processes in human cancer

Author

Alexandrov, LB, Nik-Zainal, Serena, Wedge, DC, Aparicio, SA, Behjati, S, Biankin, AV, Bignell, GR, Bolli, N, Borg, A, Børresen-Dale, A L, Boyault, S, Burkhardt, B, Butler, AP, Caldas, Carlos, Davies, HR, Desmedt, Christine, Eils, Roland, Eyfjörd, Jórunn Erla, Foekens, John A, Greaves, M, Hosoda, F, Hutter, B, Ilicic, T, Imbeaud, S, Imielinski, M, Jäger, N, Jones, DT, Jones, Wendell, Knappskog, Stian, Kool, M, Lakhani, Sunil R, López-Otín, C, Martin, S, Munshi, NC, Nakamura, H, Northcott, PA, Pajic, M, Papaemmanuil, Elli, Paradiso, A, Pearson, JV, Puente, XS, Raine, K, Ramakrishna, M, Richardson, Andrea L, Richter, J, Rosenstiel, P, Schlesner, M, Schumacher, TN, Span, Paul, Teague, JW, Totoki, Y, Tutt, AN, Valdés-Mas, R, Van Buuren, MM, Van't Veer, Laura, Vincent-Salomon, Anne, Waddell, N, Yates, LR, Zucman-Rossi, J, Futreal, P Andrew, McDermott, U, Lichter, P, Meyerson, M, Grimmond, SM, Siebert, R, Campo, E, Shibata, T, Pfister, SM, Campbell, Peter J, Stratton, Michael R, Alexandrov, LB, Nik-Zainal, Serena, Wedge, DC, Aparicio, SA, Behjati, S, Biankin, AV, Bignell, GR, Bolli, N, Borg, A, Børresen-Dale, A L, Boyault, S, Burkhardt, B, Butler, AP, Caldas, Carlos, Davies, HR, Desmedt, Christine, Eils, Roland, Eyfjörd, Jórunn Erla, Foekens, John A, Greaves, M, Hosoda, F, Hutter, B, Ilicic, T, Imbeaud, S, Imielinski, M, Jäger, N, Jones, DT, Jones, Wendell, Knappskog, Stian, Kool, M, Lakhani, Sunil R, López-Otín, C, Martin, S, Munshi, NC, Nakamura, H, Northcott, PA, Pajic, M, Papaemmanuil, Elli, Paradiso, A, Pearson, JV, Puente, XS, Raine, K, Ramakrishna, M, Richardson, Andrea L, Richter, J, Rosenstiel, P, Schlesner, M, Schumacher, TN, Span, Paul, Teague, JW, Totoki, Y, Tutt, AN, Valdés-Mas, R, Van Buuren, MM, Van't Veer, Laura, Vincent-Salomon, Anne, Waddell, N, Yates, LR, Zucman-Rossi, J, Futreal, P Andrew, McDermott, U, Lichter, P, Meyerson, M, Grimmond, SM, Siebert, R, Campo, E, Shibata, T, Pfister, SM, Campbell, Peter J, and Stratton, Michael R

Abstract

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2013

37. Signatures of mutational processes in human cancer

Author

Alexandrov, Ludmil B, Nik-Zainal, Serena, Wedge, DC, Aparicio, SA, Behjati, S, Biankin, AV, Bignell, GR, Bolli, N, Borg, A, Børresen-Dale, A L, Boyault, S, Burkhardt, B, Butler, AP, Caldas, Carlos, Davies, HR, Desmedt, Christine, Eils, Roland, Eyfjörd, Jórunn Erla, Foekens, John A, Greaves, M, Hosoda, F, Hutter, B, Ilicic, T, Imbeaud, S, Imielinski, M, Jäger, N, Jones, DT, Jones, Wendell, Knappskog, Stian, Kool, M, Lakhani, Sunil R, López-Otín, C, Martin, S, Munshi, NC, Nakamura, H, Northcott, PA, Pajic, M, Papaemmanuil, Elli, Paradiso, A, Pearson, JV, Puente, XS, Raine, K, Ramakrishna, M, Richardson, Andrea L, Richter, J, Rosenstiel, P, Schlesner, M, Schumacher, TN, Span, Paul, Teague, JW, Totoki, Y, Tutt, AN, Valdés-Mas, R, Van Buuren, MM, Van't Veer, Laura, Vincent-Salomon, Anne, Waddell, N, Yates, LR, Zucman-Rossi, J, Futreal, P Andrew, McDermott, U, Lichter, P, Meyerson, M, Grimmond, SM, Siebert, R, Campo, E, Shibata, T, Pfister, SM, Campbell, Peter J, Stratton, Michael R, Alexandrov, Ludmil B, Nik-Zainal, Serena, Wedge, DC, Aparicio, SA, Behjati, S, Biankin, AV, Bignell, GR, Bolli, N, Borg, A, Børresen-Dale, A L, Boyault, S, Burkhardt, B, Butler, AP, Caldas, Carlos, Davies, HR, Desmedt, Christine, Eils, Roland, Eyfjörd, Jórunn Erla, Foekens, John A, Greaves, M, Hosoda, F, Hutter, B, Ilicic, T, Imbeaud, S, Imielinski, M, Jäger, N, Jones, DT, Jones, Wendell, Knappskog, Stian, Kool, M, Lakhani, Sunil R, López-Otín, C, Martin, S, Munshi, NC, Nakamura, H, Northcott, PA, Pajic, M, Papaemmanuil, Elli, Paradiso, A, Pearson, JV, Puente, XS, Raine, K, Ramakrishna, M, Richardson, Andrea L, Richter, J, Rosenstiel, P, Schlesner, M, Schumacher, TN, Span, Paul, Teague, JW, Totoki, Y, Tutt, AN, Valdés-Mas, R, Van Buuren, MM, Van't Veer, Laura, Vincent-Salomon, Anne, Waddell, N, Yates, LR, Zucman-Rossi, J, Futreal, P Andrew, McDermott, U, Lichter, P, Meyerson, M, Grimmond, SM, Siebert, R, Campo, E, Shibata, T, Pfister, SM, Campbell, Peter J, and Stratton, Michael R

Abstract

All cancers are caused by somatic mutations; however, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single cancer class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, ‘kataegis’, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer, with potential implications for understanding of cancer aetiology, prevention and therapy, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2013

38. SNPs in genes coding for ROS metabolism and signalling in association with docetaxel clearance

Author

Edvardsen, H., Brunsvig, P F., Solvang, H., Tsalenko, A., Andersen, A., Syvänen, Ann-Christine, Yakhini, Z., Børresen-Dale, A-L., Olsen, H., Aamdal, S., Kristensen, V. N., Edvardsen, H., Brunsvig, P F., Solvang, H., Tsalenko, A., Andersen, A., Syvänen, Ann-Christine, Yakhini, Z., Børresen-Dale, A-L., Olsen, H., Aamdal, S., and Kristensen, V. N.

Abstract

The dose of docetaxel is currently calculated based on body surface area and does not reflect the pharmacokinetic, metabolic potential or genetic background of the patients. The influence of genetic variation on the clearance of docetaxel was analysed in a two-stage analysis. In step one, 583 single-nucleotide polymorphisms (SNPs) in 203 genes were genotyped on samples from 24 patients with locally advanced non-small cell lung cancer. We found that many of the genes harbour several SNPs associated with clearance of docetaxel. Most notably these were four SNPs in EGF, three SNPs in PRDX4 and XPC, and two SNPs in GSTA4, TGFBR2, TNFAIP2, BCL2, DPYD and EGFR. The multiple SNPs per gene suggested the existence of common haplotypes associated with clearance. These were confirmed with detailed haplotype analysis. On the basis of analysis of variance (ANOVA), quantitative mutual information score (QMIS) and Kruskal-Wallis (KW) analysis SNPs significantly associated with clearance of docetaxel were confirmed for GSTA4, PRDX4, TGFBR2 and XPC and additional putative markers were found in CYP2C8, EPHX1, IGF2, IL1R2, MAPK7, NDUFB4, TGFBR3, TPMT (2 SNPs), (P<0.05 or borderline significant for all three methods, 14 SNPs in total). In step two, these 14 SNPs were genotyped in additional 9 samples and the results combined with the genotyping results from the first step. For 7 of the 14 SNPs, the results are still significant/borderline significant by all three methods: ANOVA, QMIS and KW analysis strengthening our hypothesis that they are associated with the clearance of docetaxel..

Published
2010
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39. Glomeruloid microvascular proliferation is associated with lack of response to chemotherapy in breast cancer.

Author

Akslen, L. A., Straume, O., Geisler, S., Sørlie, T., Chi, J.-T., Aas, T., Børresen-Dale, A.-L., Lønning, P. E., Sørlie, T, Børresen-Dale, A-L, and Lønning, P E

Subjects
BREAST cancer research, DRUG therapy, MICROCIRCULATION disorders, GENE expression, NEOVASCULARIZATION
Abstract

Background: Glomeruloid microvascular proliferation (GMP), a novel histology-based angiogenesis marker, has been associated with decreased survival in several human cancers.Methods: In this study, we evaluated the ability of GMP to predict clinical response to neoadjuvant chemotherapy in a series of locally advanced breast cancers (n=112).Results: Presence of GMP (21% of the cases) was significantly associated with high-grade tumours and TP53 mutations in addition to the basal-like and HER2 subtypes of breast cancer as defined by gene expression data. GMP was correlated to a gene expression signature for tumour hypoxia response. The GMP pattern was also significantly associated with lack of treatment response and progressive disease (P=0.004).Interpretation: The findings suggest that GMP might be able to predict the lack of response to neoadjuvant chemotherapy in locally advanced breast cancer. Whether GMP may be an independent predictor compared with other factors including TP53 mutation status and tumour grade needs confirmation in larger studies. [ABSTRACT FROM AUTHOR]

Published
2011
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40. Identifying microRNAs regulating B7-H3 in breast cancer: the clinical impact of microRNA-29c

Author

Nygren, M K, primary, Tekle, C, additional, Ingebrigtsen, V A, additional, Mäkelä, R, additional, Krohn, M, additional, Aure, M R, additional, Nunes-Xavier, C E, additional, Perälä, M, additional, Tramm, T, additional, Alsner, J, additional, Overgaard, J, additional, Nesland, J M, additional, Borgen, E, additional, Børresen-Dale, A-L, additional, Fodstad, Ø, additional, Sahlberg, K K, additional, and Leivonen, S-K, additional

Published
2014
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41. Abstract P4-14-02: Molecular response in breast cancer tumors treated with neoadjuvant chemotherapy with and without bevacizumab: Results from NeoAva - A randomized phase II study

Author

Engebraaten, O, primary, Vaske, C, additional, Krohn, M, additional, Silwal-Pandit, L, additional, Moen Vollan, HK, additional, Møller, EK, additional, Nord, S, additional, Fleischer, T, additional, Borgen, E, additional, Edvardsen, H, additional, Garred, Ø, additional, Fangberget, A, additional, Holmen, MM, additional, Schlichting, E, additional, Skjerven, H, additional, Lundgren, S, additional, Wist, E, additional, Naume, B, additional, Børresen-Dale, A-L, additional, and Kristensen, VN, additional

Published
2013
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42. Abstract P4-14-01: A time course study of genomic instability in breast cancer patients receiving neoadjuvant therapy with or without bevacizumab

Author

Møller, EK, primary, Moen Vollan, HK, additional, Nord, S, additional, von der Lippe Gythfeldt, H, additional, Edvardsen, H, additional, Silwal-Pandit, L, additional, Krohn, M, additional, Fleischer, T, additional, Schlitchting, E, additional, Borgen, E, additional, Garred, Ø, additional, Fangberget, A, additional, Holmen, MM, additional, Skjerven, H, additional, Lundgren, S, additional, Wist, E, additional, Naume, B, additional, Børresen-Dale, A-L, additional, Kristensen, VN, additional, and Engebraaten, O, additional

Published
2013
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43. Breast and other cancers in 1445 blood relatives of 75 Nordic patients with ataxia telangiectasia.

Author

Olsen, J. H., Hahnemann, J. M. D., BØrresen-Dale, A-L., Tretli, S., Kleinerman, R., Sankila, R., Hammarstrõm, L., Robsahm, T. E., Kääriäinen, H., Bregard, A, BrØndum-Nielsen, K., Yuen, J., Tucker, M., Børresen-Dale, A-L, Hammarström, L, Kääriäinen, H, Bregård, A, and Brøndum-Nielsen, K

Subjects
BREAST cancer, ATAXIA telangiectasia, CEREBELLUM diseases, GENETIC disorders, IMMUNOLOGICAL deficiency syndromes, VASODILATION, PROTEINS, PROTEIN kinases, RESEARCH, SEQUENCE analysis, AGE distribution, CELL cycle proteins, DISEASE incidence, COMPARATIVE studies, DNA-binding proteins, TRANSFERASES, RESEARCH funding, AMINO acids, GENETIC techniques, BREAST tumors, GENEALOGY, DISEASE complications
Abstract

Epidemiological studies have consistently shown elevated rates of breast cancer among female blood relatives of patients with ataxia telangiectasia (AT), a rare autosomal recessive disease. A large proportion of the members of AT families are carriers of AT-causing gene mutations in ATM (Ataxia Telangiectasia Mutated), and it has been hypothesised that these otherwise healthy carriers are predisposed to breast cancer. This is an extended and enlarged follow-up study of cancer incidence in blood relatives of 75 patients with verified AT in 66 Nordic families. Blood relatives were identified through population registry linkages, and the occurrence of cancer was determined from cancer registry files in each country and compared with national incidence rates. The ATM mutation carrier probabilities of relatives were assigned from the combined information on location in family, consanguinity, if any, and supplementary carrier screening in some families. Among the 1445 blood relatives of AT patients, 225 cancers were observed, with 170.4 expected, yielding a standardised incidence ratio (SIR) of 1.3 (95% confidence interval (CI), 1.1–1.4). Invasive breast cancer occurred in 34 female relatives (SIR, 1.7; 95% CI, 1.2–2.4) and was diagnosed in 21 women before the age of 55 years (SIR, 2.9; 95% CI, 1.8–4.5), including seven mothers of probands (SIR, 8.1; 95% CI, 3.3–17). When the group of mothers was excluded, no clear relationship was observed between the allocated mutation carrier probability of each family member and the extent of breast cancer risk. We concluded that the increased risk for female breast cancer seen in 66 Nordic AT families appeared to be restricted to women under the age of 55 years and was due mainly to a very high risk in the group of mothers. The findings of breast cancer risk in mothers, but not other likely mutation carriers, in this and other studies raises questions about the hypothesis of a simple causal relationship with ATM heterozygosity.British Journal of Cancer (2005) 93, 260–265. doi:10.1038/sj.bjc.6602658 www.bjcancer.com Published online 7 June 2005 [ABSTRACT FROM AUTHOR]

Published
2005
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50. Focal amplification and oncogene dependency of GAB2 in breast cancer

Author

Bocanegra, M, primary, Bergamaschi, A, additional, Kim, Y H, additional, Miller, M A, additional, Rajput, A B, additional, Kao, J, additional, Langerød, A, additional, Han, W, additional, Noh, D -Y, additional, Jeffrey, S S, additional, Huntsman, D G, additional, Børresen-Dale, A -L, additional, and Pollack, J R, additional

Published
2009
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