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1. CLASSIFICATION AND PREDICTION OF BENTHIC HABITAT FROM SCIENTIFIC ECHOSOUNDER DATA: APPLICATION OF MACHINE LEARNING ALGORITHMS

Author: Baigo HAMUNA, Sri PUJIYATI, Jonson Lumban GAOL, and Totok HESTIRIANOTO
Subjects: Acoustic parameters, Single-beam echosounder, Mapping Accuracy, Random Forest, Support Vector Machine, Information technology, T58.5-58.64, Electronic computers. Computer science, QA75.5-76.95
Abstract: This study aims to map three main benthic habitats (coral, seagrass, and sand) in Kapota Atoll (Wakatobi, Indonesia) using single-beam echosounder (SBES) Simrad EK15. Eight acoustic parameters are used as classification aThis study aims to map three main benthic habitats (coral, seagrass, and sand) in Kapota Atoll (Wakatobi, Indonesia) using a single-beam echosounder (SBES) Simrad EK15. The acoustic data were processed using Sonar5-Pro software. Eight acoustic parameters were used as input for the classification and prediction of benthic habitats, including depth (D), five acoustic parameters of the first echo (BD, BP, AttSv1, DecSv1, and AttDecSv1), and cumulative energy of the second and third echoes (AttDecSv2 and AttDecSv3). The classification and prediction process of benthic habitats uses two machine learning algorithms, Random Forest (RF) and Support Vector Machine (SVM), in XLSTAT Basic+ software. The study results show that 49 combinations of acoustic parameters produce benthic habitat maps that meet the minimum accuracy standards for benthic habitat mapping (≥60%). Using eight acoustic parameters produces a more accurate benthic habitat map than using only two main SBES parameters (DecSv1 and AttDecSv2 parameters or E1 and E2 in the RoxAnn system indicating the roughness and hardness indices). The RF and SVM algorithms produce benthic habitat maps with the highest accuracy of 79.33% and 78.67%, respectively. Each acoustic parameter has a different importance for the classification of benthic habitats, where the order of importance of each acoustic parameter in the overall classification follows the following order: AttDecSv2 > D > DecSv1 > BD > AttDecSv3 > AttSv1 > AttDecSv1 > BP. Overall, using more acoustic parameters can significantly improve the accuracy of benthic habitat mapsinput, including depth (D), five acoustic parameters of the first echo (BD, BP, AttSv1, DecSv1, and AttDecSv1) and cumulative energy of the second and third echoes (AttDecSv2 and AttDecSv3). The classification and prediction process of benthic habitats uses two machine learning algorithms, namely Random Forest (RF) and Support Vector Machine (SVM). The study results show that using eight acoustic parameters produces a more accurate benthic habitat map than using only two main SBES parameters (as in the RoxAnn system: roughness and hardness indices). The RF and SVM algorithms produce benthic habitat maps with the highest accuracy of 79.33% and 78.67%, respectively. Each acoustic parameter has a different importance for the classification of benthic habitats, where five acoustic parameters have the highest importance for the overall classification, namely AttDecSv2, D, DecSv1, BD, and AttDecSv3.
Published: 2024
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2. ESTIMASI RADIUS DEFORMASI UPWELLING DARI DATA SATELIT DAN ARGO FLOAT

Author: Hariansyah Noor, Jonson Lumban Gaol, and I Wayan Nurjaya
Subjects: argo float, radius deformasi, satelit, spl, upwelling, Aquaculture. Fisheries. Angling, SH1-691
Abstract: Upwelling adalah proses naiknya massa air laut dari lapisan bawah ke permukaan akibat perbedaan tekanan permukaan. Terjadi proses upwelling akan meningkatkan kesuburan perairan karena massa air di lapisan dalam naik ke permukaan yang kaya nutrisi yang dibutuhkan fitoplankton untuk berkembang. Luas sebaran daerah upwelling (radius deformasi) akan menentukan dampak proses upwelling di perairan. Penelitian ini bertujuan untuk menganalisis proses upwelling dan radius deformasi dari data satelit sensor termal. Data yang digunakan adalah data satelit termal harian dan rata-rata bulanan selama tahun 2014-2018. Data dari buoy Argo digunakan untuk memvalidasi data satelit dan menghitung radius deformasi upwelling. Analisis statistik seperti korelasi, Root Mean Square Error (RMSE), bias, dan standar deviasi digunakan untuk menguji keakuratan perkiraan data Suhu Permukaan Laut (SPL) dari satelit. Data perhitungan radius deformasi dari Argo menunjukkan bahwa pada musim timur terjadi upwelling, SPL berkisaran antara 24-26ºC, normalnya berkisaran antara 27-29ºC. Korelasi antara SPL dari data satelit dan data SPL dari Argo adalah 0,92, nilai RMSE 0,0236, bias 0,017, dan standar deviasi 0,287. Koefisien korelasi antara radius deformasi dari data in situ dan data satelit yang dihitung tinggi (r=0,9) menunjukkan bahwa citra satelit dapat digunakan untuk menentukan radius deformasi.
Published: 2024
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3. Estimation of Attenuation Coefficient Values Using Remote Sensing and Its Relationship With Shallow Water Depth

Author: Anggi Tiarasani, Vincentius Paulus Siregar, and Jonson Lumban Gaol
Subjects: diffuse attenuation coefficient, remote sensing, sentinel-2 imagery, algorithm, Geography. Anthropology. Recreation, Geology, QE1-996.5
Abstract: In ocean remote sensing, the intensity of light entering the water column decreases exponentially with increasing depth due to scattering and particle absorption in the water column. This process of decreasing light intensity is called attenuation. Attenuation is a limiting factor in detecting objects in the water column and seafloor using remote sensing, which relies on light intensity. The attenuation coefficient (Kd) is an important optical property of seawater as it provides information about water clarity and the level of light attenuation. This study aims to analyze the estimation of the attenuation coefficient values and their variability using in-situ measurements and Sentinel-2 level 2A data in Karang Lebar, Pulau Panggang, and Pulau Air, in the Seribu Islands Regency, North Jakarta. We tested several algorithms to estimate the attenuation coefficient values. The research results show that the in-situ Kd and the estimated model values have a good correlation (r = 0.75-0.86). The distribution of attenuation coefficient values in the shallow waters of the study area ranges from 0.06 to 0.18m-1. The accuracy of estimating shallow water depth at the study sites was best represented by R2 and RMSE values in the range of 0-5m with an attenuation coefficient of 0.06-0.11m-1. Keywords: Diffuse Attenuation Coefficient, Remote Sensing, Sentinel-2 Imagery, Algorithm.
Published: 2023
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4. Assessing associations between the AURKAHMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers

Author: Blanco, I, Kuchenbaecker, K, Cuadras, D, Wang, X, Barrowdale, D, De Garibay, GR, Librado, P, Sánchez-Gracia, A, Rozas, J, Bonifaci, N, McGuffog, L, Pankratz, VS, Islam, A, Mateo, F, Berenguer, A, Petit, A, Català, I, Brunet, J, Feliubadaló, L, Tornero, E, Benítez, J, Osorio, A, Teresa, R, Teresa, C, Nevanlinna, H, Aittomäki, K, Arun, BK, Toland, AE, Karlan, BY, Walsh, C, Lester, J, Greene, MH, Mai, PL, Nussbaum, RL, Andrulis, IL, Domchek, SM, Nathanson, KL, Rebbeck, TR, Barkardottir, RB, Jakubowska, A, Lubinski, J, Durda, K, Jaworska-Bieniek, K, Claes, K, Van Maerken, T, Díez, O, Hansen, TV, Jønson, L, Gerdes, AM, Ejlertsen, B, De La Hoya, M, Caldés, T, Dunning, AM, Oliver, C, Fineberg, E, Cook, M, Peock, S, McCann, E, Murray, A, Jacobs, C, Pichert, G, Lalloo, F, Chu, C, Dorkins, H, Paterson, J, Ong, KR, Teixeira, MR, Teixeira, T, Hogervorst, FBL, Van Der Hout, AH, Seynaeve, C, Van Der Luijt, RB, Ligtenberg, MJL, Devilee, P, Wijnen, JT, Rookus, MA, Meijers-Heijboer, HEJ, Blok, MJ, Van Den Ouweland, AMW, Aalfs, CM, Rodriguez, GC, Phillips, KAA, Piedmonte, M, Nerenstone, SR, Bae-Jump, VL, O'Malley, DM, Ratner, ES, Schmutzler, RK, Wappenschmidt, B, Rhiem, K, Engel, C, Meindl, A, Ditsch, N, Arnold, N, Plendl, HJ, Niederacher, D, Sutter, C, and Wang-Gohrke, S
Subjects: skin and connective tissue diseases
Abstract: While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04 - 1.15, p = 1.9 × 10-4(false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03 - 1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteractionvalues > 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers.
Published: 2015
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5. Sea Level Rise, Land Subsidence, and Flood Disaster Vulnerability Assessment: A Case Study in Medan City, Indonesia

Author: Jonson Lumban-Gaol, Josaphat Tetuko Sri Sumantyo, Efendy Tambunan, David Situmorang, I Made Oka Guna Antara, Maya Eria Sinurat, Ni Putu Asri Ratna Suhita, Takahiro Osawa, and Risti Endriani Arhatin
Subjects: AHP, DInSAR, disaster, flood, GIS, land subsidence, Science
Abstract: Global sea level rise (SLR) has emerged as a pressing concern because of its impacts, especially increased vulnerability of coastal urban areas flooding. This study addresses the pressing concern of SLR and flood vulnerability in the East Coast of North Sumatra (ECNS) and Medan City. We employ a data-driven approach integrating multicriteria analysis, analytical hierarchy process (AHP)-based weighting, and spatial modeling within a geographic information system framework. The analysis considers crucial factors such as slope, land use, soil type, SLR, and land deformation. The study expands the existing framework by incorporating SLR and land subsidence, acknowledging their significant roles in exacerbating flood vulnerability. Future flood-intensity scenarios are simulated based on SLR projections. Data for spatial analysis primarily originated from multisensor satellite imagery, secondary sources from published literature, and field surveys. We validated the consistency of the variable weightings assigned for vulnerability analysis using a consistency ratio threshold (
Published: 2024
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6. Candidate genetic modifiers for breast and ovarian cancer risk inBRCA1andBRCA2 mutation carriers

Author: Peterlongo, P, Chang-Claude, J, Moysich, KB, Rudolph, A, Schmutzler, RK, Simard, J, Soucy, P, Eeles, RA, Easton, DF, Hamann, U, Wilkening, S, Chen, B, Rookus, MA, Schmidt, MK, Van Der Baan, FH, Spurdle, AB, Walker, LC, Lose, F, Maia, AT, Montagna, M, Matricardi, L, Lubinski, J, Jakubowska, A, Garcia, EBG, Olopade, OI, Nussbaum, RL, Nathanson, KL, Domchek, SM, Rebbeck, TR, Arun, BK, Karlan, BY, Orsulic, S, Lester, J, Chung, WK, Miron, A, Southey, MC, Goldgar, DE, Buys, SS, Janavicius, R, Dorfling, CM, Van Rensburg, EJ, Ding, YC, Neuhausen, SL, Hansen, TVO, Gerdes, AM, Ejlertsen, B, Jønson, L, Osorio, A, Martínez-Bouzas, C, Benitez, J, Conway, EE, Blazer, KR, Weitzel, JN, Manoukian, S, Peissel, B, Zaffaroni, D, Scuvera, G, Barile, M, Ficarazzi, F, Mariette, F, Fortuzzi, S, Viel, A, Giannini, G, Papi, L, Martayan, A, Tibiletti, MG, Radice, P, Vratimos, A, Fostira, F, Garber, JE, Donaldson, A, Brewer, C, Foo, C, Evans, DGR, Frost, D, Eccles, D, Brady, A, Cook, J, Tischkowitz, M, Adlard, J, Barwell, J, Walker, L, Izatt, L, Side, LE, Kennedy, MJ, Rogers, MT, Porteous, ME, Morrison, PJ, Platte, R, Davidson, R, and Hodgson, SV
Subjects: endocrine system diseases, skin and connective tissue diseases
Abstract: © 2014 American Association for Cancer Research. Background: BRCA1 and BRCA2 mutation carriers are at substantially increased risk for developing breast and ovarian cancer. The incomplete penetrance coupled with the variable age at diagnosis in carriers of the same mutation suggests the existence of genetic and nongenetic modifying factors. In this study, we evaluated the putative role of variants inmany candidate modifier genes. Methods: Genotyping data from 15,252 BRCA1 and 8,211 BRCA2 mutation carriers, for known variants (n = 3,248) located within or around 445 candidate genes, were available through the iCOGS custom-designed array. Breast and ovarian cancer association analysiswas performed within a retrospective cohort approach. Results: The observed P values of association ranged between 0.005 and 1.000. None of the variants was significantly associated with breast or ovarian cancer risk in either BRCA1 or BRCA2 mutation carriers, after multiple testing adjustments. Conclusion: There is little evidence that any of the evaluated candidate variants act as modifiers of breast and/or ovarian cancer risk in BRCA1 or BRCA2 mutation carriers. Impact: Genome-wide association studies have been more successful at identifying genetic modifiers of BRCA1/2 penetrance than candidate gene studies.
Published: 2015
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7. DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Author: Osorio, A, Milne, RL, Kuchenbaecker, K, Vaclová, T, Pita, G, Alonso, R, Peterlongo, P, Blanco, I, de la Hoya, M, Duran, M, Díez, O, Ramón y Cajal, T, Konstantopoulou, I, Martínez-Bouzas, C, Andrés Conejero, R, Soucy, P, McGuffog, L, Barrowdale, D, Lee, A, Arver, B, Rantala, J, Loman, N, Ehrencrona, H, Olopade, OI, Beattie, MS, Domchek, SM, Nathanson, K, Rebbeck, TR, Arun, BK, Karlan, BY, Walsh, C, Lester, J, John, EM, Whittemore, AS, Daly, MB, Southey, M, Hopper, J, Terry, MB, Buys, SS, Janavicius, R, Dorfling, CM, van Rensburg, EJ, Steele, L, Neuhausen, SL, Ding, YC, Hansen, TVO, Jønson, L, Ejlertsen, B, Gerdes, AM, Infante, M, Herráez, B, Moreno, LT, Weitzel, JN, Herzog, J, Weeman, K, Manoukian, S, Peissel, B, Zaffaroni, D, Scuvera, G, Bonanni, B, Mariette, F, Volorio, S, Viel, A, Varesco, L, Papi, L, Ottini, L, Tibiletti, MG, Radice, P, Yannoukakos, D, Garber, J, Ellis, S, Frost, D, Platte, R, Fineberg, E, Evans, G, Lalloo, F, Izatt, L, Eeles, R, Adlard, J, Davidson, R, Cole, T, Eccles, D, Cook, J, Hodgson, S, Brewer, C, Tischkowitz, M, Douglas, F, Porteous, M, Side, L, Walker, L, Morrison, P, Donaldson, A, Kennedy, J, Foo, C, Godwin, AK, Schmutzler, RK, Wappenschmidt, B, Rhiem, K, and Engel, C
Subjects: endocrine system diseases, skin and connective tissue diseases
Abstract: Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the components of the BER pathway, PARP1 (poly ADP ribose polymerase), and both BRCA1 and BRCA2. In the present study, we have performed a comprehensive analysis of 18 genes involved in BER using a tagging SNP approach in a large series of BRCA1 and BRCA2 mutation carriers. 144 SNPs were analyzed in a two stage study involving 23,463 carriers from the CIMBA consortium (the Consortium of Investigators of Modifiers of BRCA1 and BRCA2). Eleven SNPs showed evidence of association with breast and/or ovarian cancer at p
Published: 2014
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8. Assessing associations between the AURKAHMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers

Author: Blanco, I. (Ignacio), Kuchenbaecker, K.B. (Karoline), Cuadras, D. (Daniel), Wang, X. (Xing), Barrowdale, D. (Daniel), De Garibay, G.R. (Gorka Ruiz), Librado, P. (Pablo), Sánchez-Gracia, A. (Alejandro), Rozas, J. (Julio), Bonifaci, N. (Núria), McGuffog, L. (Lesley), Pankratz, V.S. (Shane), Islam, A.B.M.M.K. (Abul), Mateo, F. (Francesca), Berenguer, A. (Antonio), Petit, A. (Anna), Català, I. (Isabel), Brunet, J. (Joan), Feliubadaló, L. (L.), Tornero, E. (Eva), Benítez, J. (Javier), Osorio, A. (Ana), Teresa, R. (Ramón), Teresa, C. (Cajal), Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Arun, B.K. (Banu), Toland, A.E. (Amanda), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Lester, K.J. (Kathryn), Greene, M.H. (Mark), Mai, P.L. (Phuong), Nussbaum, R.L. (Robert L.), Andrulis, I.L. (Irene), Domchek, S.M. (Susan), Nathanson, K.L. (Katherine), Rebbeck, R. (Timothy), Barkardottir, R.B. (Rosa), Jakubowska, A. (Anna), Lubinski, J. (Jan), Durda, K. (Katarzyna), Jaworska-Bieniek, K. (Katarzyna), Claes, K. (Kathleen), Van Maerken, T. (Tom), Díez, O. (Orland), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Gerdes, A.-M. (Anne-Marie), Ejlertsen, B. (Bent), Hoya, M. (Miguel) de La, Caldes, T. (Trinidad), Dunning, A.M. (Alison), Oliver, C.T. (Clare), Fineberg, E. (Elena), Cook, M. (Margaret), Peock, S. (Susan), McCann, E. (Emma), Murray, A. (Alexandra), Jacobs, C. (Chris), Pichert, G. (Gabriella), Lalloo, F. (Fiona), Chu, C. (Carol), Dorkins, H. (Huw), Paterson, J. (Joan), Ong, K.-R. (Kai-Ren), Teixeira, M.R. (Manuel R.), Teixeira, T. (T.), Hogervorst, F.B.L. (Frans), Hout, A.H. (Annemarie) van der, Seynaeve, C.M. (Caroline), Van Der Luijt, R.B. (Rob B.), Ligtenberg, M.J. (Marjolijn), Devilee, P. (Peter), Wijnen, J.T. (Juul), Rookus, M.A. (Matti), Meijers-Heijboer, E.J. (Hanne), Blok, M.J. (Marinus), Ouweland, A.M.W. (Ans) van den, Aalfs, C.M. (Cora), Rodriguez, G.C. (Gustavo C.), Phillips, K.-A. (Kelly-Anne), Piedmonte, M. (Marion), Nerenstone, S. (Stacy), Bae-Jump, V.L. (Victoria L.), O'Malley, D.M. (David M.), Ratner, E.S. (Elena S.), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Rhiem, K. (Kerstin), Engel, C. (Christoph), Meindl, A. (Alfons), Ditsch, N. (Nina), Arnold, N. (Norbert), Plendl, H. (Hansjoerg), Niederacher, D. (Dieter), Sutter, C. (Christian), Wang-Gohrke, S. (Shan), Steinemann, D. (Doris), Preisler-Adams, S. (Sabine), Kast, K. (Karin), Varon-Mateeva, R. (Raymonda), Gehrig, P.A. (Paola A.), Bojesen, A. (Anders), Pedersen, I.S. (Inge Sokilde), Sunde, L. (Lone), Jensen, U.B., Thomassen, M. (Mads), Kruse, T.A. (Torben), Foretova, L. (Lenka), Peterlongo, P. (Paolo), Bernard, L. (Loris), Peissel, B. (Bernard), Scuvera, G. (Giulietta), Manoukian, S. (Siranoush), Radice, P. (Paolo), Ottini, L. (Laura), Montagna, M. (Marco), Agata, S. (Simona), Maugard, C., Simard, J. (Jacques), Soucy, P. (Penny), Berger, A. (Annemarie), Fink-Retter, A. (Anneliese), Singer, C.F. (Christian), Rappaport, C. (Christine), Geschwantler Kaulich, D. (Daphne), Tea, M.-K., Pfeiler, G. (Georg), John, E.M. (Esther), Miron, A. (Alexander), Neuhausen, S.L. (Susan), Terry, M.B. (Mary Beth), Chung, W.K. (Wendy K.), Daly, M.B. (Mary), Goldgar, D. (David), Janavicius, R. (Ramunas), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Fostira, F. (Florentia), Konstantopoulou, I. (I.), Garber, J., Godwin, A.K. (Andrew), Olah, E., Narod, S.A. (Steven A.), Rennert, G. (Gad), Paluch, S.S. (Shani), Laitman, Y. (Yael), Friedman, E. (Eitan), Liljegren, A. (Annelie), Rantala, J. (Johanna), Stenmark-Askmalm, M. (Marie), Loman, N. (Niklas), Imyanitov, E.N. (Evgeny), Hamann, U. (Ute), Spurdle, A.B. (Amanda), Healey, S. (Sue), Weitzel, J.N. (Jeffrey), Herzog, J. (Josef), Margileth, D. (David), Gorrini, C. (Chiara), Esteller, M. (Manel), Gómez, A. (Antonio), Sayols, S. (Sergi), Vidal, E. (Enrique), Heyn, H. (Holger), Stoppa-Lyonnet, D. (Dominique), Léone, M. (Mélanie), Barjhoux, L. (Laure), Fassy-Colcombet, M. (Marion), Pauw, A. (Antoine) de, Lasset, C. (Christine), Ferrer, S.F., Castera, L. (Laurent), Berthet, P. (Pascaline), Cornelis, F. (Franco̧is), Bignon, Y.-J. (Yves-Jean), Damiola, F. (Francesca), Mazoyer, S. (Sylvie), Sinilnikova, O. (Olga), Maxwell, C.A. (Christopher), Vijai, J. (Joseph), Robson, M. (Mark), Kauff, N. (Noah), Corines, M.J. (Marina J.), Villano, D. (Danylko), Cunningham, J.M. (Julie), Lee, A. (Adam), Lindor, N.M. (Noralane), Lázaro, C. (Conxi), Easton, D.F. (Douglas), Offit, K. (Kenneth), Chenevix-Trench, G. (Georgia), Couch, F.J. (Fergus), Antoniou, A.C. (Antonis C.), Pujana, M.A. (Miguel), Blanco, I. (Ignacio), Kuchenbaecker, K.B. (Karoline), Cuadras, D. (Daniel), Wang, X. (Xing), Barrowdale, D. (Daniel), De Garibay, G.R. (Gorka Ruiz), Librado, P. (Pablo), Sánchez-Gracia, A. (Alejandro), Rozas, J. (Julio), Bonifaci, N. (Núria), McGuffog, L. (Lesley), Pankratz, V.S. (Shane), Islam, A.B.M.M.K. (Abul), Mateo, F. (Francesca), Berenguer, A. (Antonio), Petit, A. (Anna), Català, I. (Isabel), Brunet, J. (Joan), Feliubadaló, L. (L.), Tornero, E. (Eva), Benítez, J. (Javier), Osorio, A. (Ana), Teresa, R. (Ramón), Teresa, C. (Cajal), Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Arun, B.K. (Banu), Toland, A.E. (Amanda), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Lester, K.J. (Kathryn), Greene, M.H. (Mark), Mai, P.L. (Phuong), Nussbaum, R.L. (Robert L.), Andrulis, I.L. (Irene), Domchek, S.M. (Susan), Nathanson, K.L. (Katherine), Rebbeck, R. (Timothy), Barkardottir, R.B. (Rosa), Jakubowska, A. (Anna), Lubinski, J. (Jan), Durda, K. (Katarzyna), Jaworska-Bieniek, K. (Katarzyna), Claes, K. (Kathleen), Van Maerken, T. (Tom), Díez, O. (Orland), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Gerdes, A.-M. (Anne-Marie), Ejlertsen, B. (Bent), Hoya, M. (Miguel) de La, Caldes, T. (Trinidad), Dunning, A.M. (Alison), Oliver, C.T. (Clare), Fineberg, E. (Elena), Cook, M. (Margaret), Peock, S. (Susan), McCann, E. (Emma), Murray, A. (Alexandra), Jacobs, C. (Chris), Pichert, G. (Gabriella), Lalloo, F. (Fiona), Chu, C. (Carol), Dorkins, H. (Huw), Paterson, J. (Joan), Ong, K.-R. (Kai-Ren), Teixeira, M.R. (Manuel R.), Teixeira, T. (T.), Hogervorst, F.B.L. (Frans), Hout, A.H. (Annemarie) van der, Seynaeve, C.M. (Caroline), Van Der Luijt, R.B. (Rob B.), Ligtenberg, M.J. (Marjolijn), Devilee, P. (Peter), Wijnen, J.T. (Juul), Rookus, M.A. (Matti), Meijers-Heijboer, E.J. (Hanne), Blok, M.J. (Marinus), Ouweland, A.M.W. (Ans) van den, Aalfs, C.M. (Cora), Rodriguez, G.C. (Gustavo C.), Phillips, K.-A. (Kelly-Anne), Piedmonte, M. (Marion), Nerenstone, S. (Stacy), Bae-Jump, V.L. (Victoria L.), O'Malley, D.M. (David M.), Ratner, E.S. (Elena S.), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Rhiem, K. (Kerstin), Engel, C. (Christoph), Meindl, A. (Alfons), Ditsch, N. (Nina), Arnold, N. (Norbert), Plendl, H. (Hansjoerg), Niederacher, D. (Dieter), Sutter, C. (Christian), Wang-Gohrke, S. (Shan), Steinemann, D. (Doris), Preisler-Adams, S. (Sabine), Kast, K. (Karin), Varon-Mateeva, R. (Raymonda), Gehrig, P.A. (Paola A.), Bojesen, A. (Anders), Pedersen, I.S. (Inge Sokilde), Sunde, L. (Lone), Jensen, U.B., Thomassen, M. (Mads), Kruse, T.A. (Torben), Foretova, L. (Lenka), Peterlongo, P. (Paolo), Bernard, L. (Loris), Peissel, B. (Bernard), Scuvera, G. (Giulietta), Manoukian, S. (Siranoush), Radice, P. (Paolo), Ottini, L. (Laura), Montagna, M. (Marco), Agata, S. (Simona), Maugard, C., Simard, J. (Jacques), Soucy, P. (Penny), Berger, A. (Annemarie), Fink-Retter, A. (Anneliese), Singer, C.F. (Christian), Rappaport, C. (Christine), Geschwantler Kaulich, D. (Daphne), Tea, M.-K., Pfeiler, G. (Georg), John, E.M. (Esther), Miron, A. (Alexander), Neuhausen, S.L. (Susan), Terry, M.B. (Mary Beth), Chung, W.K. (Wendy K.), Daly, M.B. (Mary), Goldgar, D. (David), Janavicius, R. (Ramunas), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Fostira, F. (Florentia), Konstantopoulou, I. (I.), Garber, J., Godwin, A.K. (Andrew), Olah, E., Narod, S.A. (Steven A.), Rennert, G. (Gad), Paluch, S.S. (Shani), Laitman, Y. (Yael), Friedman, E. (Eitan), Liljegren, A. (Annelie), Rantala, J. (Johanna), Stenmark-Askmalm, M. (Marie), Loman, N. (Niklas), Imyanitov, E.N. (Evgeny), Hamann, U. (Ute), Spurdle, A.B. (Amanda), Healey, S. (Sue), Weitzel, J.N. (Jeffrey), Herzog, J. (Josef), Margileth, D. (David), Gorrini, C. (Chiara), Esteller, M. (Manel), Gómez, A. (Antonio), Sayols, S. (Sergi), Vidal, E. (Enrique), Heyn, H. (Holger), Stoppa-Lyonnet, D. (Dominique), Léone, M. (Mélanie), Barjhoux, L. (Laure), Fassy-Colcombet, M. (Marion), Pauw, A. (Antoine) de, Lasset, C. (Christine), Ferrer, S.F., Castera, L. (Laurent), Berthet, P. (Pascaline), Cornelis, F. (Franco̧is), Bignon, Y.-J. (Yves-Jean), Damiola, F. (Francesca), Mazoyer, S. (Sylvie), Sinilnikova, O. (Olga), Maxwell, C.A. (Christopher), Vijai, J. (Joseph), Robson, M. (Mark), Kauff, N. (Noah), Corines, M.J. (Marina J.), Villano, D. (Danylko), Cunningham, J.M. (Julie), Lee, A. (Adam), Lindor, N.M. (Noralane), Lázaro, C. (Conxi), Easton, D.F. (Douglas), Offit, K. (Kenneth), Chenevix-Trench, G. (Georgia), Couch, F.J. (Fergus), Antoniou, A.C. (Antonis C.), and Pujana, M.A. (Miguel)
Abstract: While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood appro
Published: 2015
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9. Candidate genetic modifiers for breast and ovarian cancer risk inBRCA1andBRCA2 mutation carriers

Author: Peterlongo, P. (Paolo), Chang-Claude, J. (Jenny), Moysich, K.B. (Kirsten), Rudolph, A. (Anja), Schmutzler, R.K. (Rita), Simard, J. (Jacques), Soucy, P. (Penny), Eeles, R. (Rosalind), Easton, D.F. (Douglas), Hamann, U. (Ute), Wilkening, S. (Stefan), Chen, B. (Bowang), Rookus, M.A. (Matti), Schmidt, M.K. (Marjanka), Baan, F.H. (Frederieke) van der, Spurdle, A.B. (Amanda), Walker, L.C. (Logan), Lose, F. (Felicity), Maia, A.-T. (Ana-Teresa), Montagna, M. (Marco), Matricardi, L. (Laura), Lubinski, J. (Jan), Jakubowska, A. (Anna), Garcia, E.B.G., Olopade, O.I. (Olofunmilayo), Nussbaum, R.L. (Robert L.), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Rebbeck, R. (Timothy), Arun, B.K. (Banu), Karlan, B.Y. (Beth), Orsulic, S. (Sandra), Lester, K.J. (Kathryn), Chung, W.K. (Wendy K.), Miron, A. (Alexander), Southey, M.C. (Melissa), Goldgar, D. (David), Buys, S.S. (Saundra), Janavicius, R. (Ramunas), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Ding, Y.C. (Yuan Chun), Neuhausen, S.L. (Susan), Hansen, T.V.O. (Thomas), Gerdes, A.-M. (Anne-Marie), Ejlertsen, B. (Bent), Jønson, L. (Lars), Osorio, A. (Ana), Martínez-Bouzas, C. (Cristina), Benítez, J. (Javier), Conway, E.E. (Edye E.), Blazer, K.R. (Kathleen R.), Weitzel, J.N. (Jeffrey), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (Daniela), Scuvera, G. (Giulietta), Barile, M. (Monica), Ficarazzi, F. (Filomena), Mariette, F. (F.), Fortuzzi, S. (S.), Viel, A. (Alessandra), Giannini, G. (Giuseppe), Papi, L. (Laura), Martayan, A. (Aline), Tibiletti, M.G. (Maria Grazia), Radice, P. (Paolo), Vratimos, A. (Athanassios), Fostira, F. (Florentia), Garber, J. (Judy), Donaldson, A. (Alan), Brewer, C. (Carole), Foo, C. (Claire), Evans, D.G. (Gareth), Frost, D. (Debra), Eccles, D. (Diana), Brady, A. (A.), Cook, J. (Jackie), Tischkowitz, M. (Marc), Adlard, L., Barwell, J. (Julian), Walker, L.J. (Lisa), Izatt, L. (Louise), Side, L. (Lucy), Kennedy, M.J. (John), Rogers, M.T. (Mark), Porteous, M.E. (Mary), Morrison, P.J. (Patrick), Platte, R. (Radka), Davidson, R. (Rosemarie), Hodgson, S. (Shirley), Ellis, S.D. (Steve), Cole, T. (Trevor), Godwin, A.K. (Andrew), Claes, K.B.M. (Kathleen B.M.), Van Maerken, T. (Tom), Meindl, A. (Alfons), Gehrig, P.A. (Paola A.), Sutter, C. (Christian), Engel, C. (Christoph), Niederacher, D. (Dieter), Steinemann, D. (Doris), Plendl, H. (Hansjoerg), Kast, K. (Karin), Rhiem, K. (Kerstin), Ditsch, N. (Nina), Arnold, N. (Norbert), Varon-Mateeva, R. (Raymonda), Wapenschmidt, B. (Barbara), Wang-Gohrke, S. (Shan), Bressac-de Paillerets, B. (Brigitte), Buecher, B. (Bruno), Delnatte, C.D. (Capucine), Houdayer, C. (Claude), Stoppa-Lyonnet, D. (Dominique), Damiola, F. (Francesca), Coupier, I. (Isabelle), Barjhoux, L. (Laure), Vénat-Bouvet, L. (Laurence), Golmard, L. (Lisa), Boutry-Kryza, N. (N.), Sinilnikova, O. (Olga), Caron, O. (Olivier), Pujol, P. (Pascal), Mazoyer, S. (Sylvie), Belotti, M. (Muriel), Piedmonte, M. (Marion), Friedlander, M.L. (Michael L.), Rodriguez, G. (Gustavo), Copeland, L.J. (Larry J.), Hoya, M. (Miguel) de La, Perez-Segura, P. (Pedro), Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Os, T.A.M. (Theo) van, Meijers-Heijboer, E.J. (Hanne), Hout, A.H. (Annemarie) van der, Vreeswijk, M.P. (Maaike), Hoogerbrugge, N. (Nicoline), Ausems, M.G.E.M. (Margreet), Doorn, H.C. (Lena) van, Collée, J.M. (Margriet), Olah, E., Díez, O. (Orland), Blanco, I. (Ignacio), Lázaro, C. (Conxi), Brunet, J. (Joan), Feliubadaló, L. (L.), Cybulski, C. (Cezary), Gronwald, J. (Jacek), Durda, K. (Katarzyna), Jaworska-Bieniek, K. (Katarzyna), Sukiennicki, G. (Grzegorz), Arason, A. (Adalgeir), Chiquette, J. (Jocelyne), Teixeira, P.J., Olswold, C. (Curtis), Couch, F.J. (Fergus), Lindor, N.M. (Noralane), Wang, X. (X.), Szabo, C. (Csilla), Offit, K. (Kenneth), Corines, M. (Marina), Jacobs, L. (Lauren), Robson, M.E. (Mark E.), Zhang, L. (Lingling), Joseph, V. (Vijai), Berger, A. (Andreas), Singer, C.F. (Christian), Rappaport, C. (Christine), Kaulich, D.G. (Daphne Gschwantler), Pfeiler, G. (Georg), Tea, M.-K., Phelan, C. (Catherine), Greene, M.H. (Mark), Mai, P.L. (Phuong), Rennert, G. (Gad), Mulligan, A.-M. (Anna-Marie), Glendon, G. (Gord), Tchatchou, S. (Sandrine), Andrulis, I.L. (Irene), Toland, A.E. (Amanda), Bojesen, A. (Anders), Pedersen, I.S. (Inge Sokilde), Thomassen, M. (Mads), Jensen, U.B., Laitman, Y. (Yael), Rantala, J. (Johanna), Wachenfeldt, A. (Anna) von, Ehrencrona, H. (Hans), Askmalm, M.S. (Marie), Borg, Å. (Åke), Kuchenbaecker, K.B. (Karoline), McGuffog, L. (Lesley), Barrowdale, D. (Daniel), Healey, S. (Sue), Lee, A. (Andrew), Pharoah, P.D.P. (Paul D.P.), Chenevix-Trench, G. (Georgia), Antoniou, A.C. (Antonis), Friedman, E. (Eitan), Peterlongo, P. (Paolo), Chang-Claude, J. (Jenny), Moysich, K.B. (Kirsten), Rudolph, A. (Anja), Schmutzler, R.K. (Rita), Simard, J. (Jacques), Soucy, P. (Penny), Eeles, R. (Rosalind), Easton, D.F. (Douglas), Hamann, U. (Ute), Wilkening, S. (Stefan), Chen, B. (Bowang), Rookus, M.A. (Matti), Schmidt, M.K. (Marjanka), Baan, F.H. (Frederieke) van der, Spurdle, A.B. (Amanda), Walker, L.C. (Logan), Lose, F. (Felicity), Maia, A.-T. (Ana-Teresa), Montagna, M. (Marco), Matricardi, L. (Laura), Lubinski, J. (Jan), Jakubowska, A. (Anna), Garcia, E.B.G., Olopade, O.I. (Olofunmilayo), Nussbaum, R.L. (Robert L.), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Rebbeck, R. (Timothy), Arun, B.K. (Banu), Karlan, B.Y. (Beth), Orsulic, S. (Sandra), Lester, K.J. (Kathryn), Chung, W.K. (Wendy K.), Miron, A. (Alexander), Southey, M.C. (Melissa), Goldgar, D. (David), Buys, S.S. (Saundra), Janavicius, R. (Ramunas), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Ding, Y.C. (Yuan Chun), Neuhausen, S.L. (Susan), Hansen, T.V.O. (Thomas), Gerdes, A.-M. (Anne-Marie), Ejlertsen, B. (Bent), Jønson, L. (Lars), Osorio, A. (Ana), Martínez-Bouzas, C. (Cristina), Benítez, J. (Javier), Conway, E.E. (Edye E.), Blazer, K.R. (Kathleen R.), Weitzel, J.N. (Jeffrey), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (Daniela), Scuvera, G. (Giulietta), Barile, M. (Monica), Ficarazzi, F. (Filomena), Mariette, F. (F.), Fortuzzi, S. (S.), Viel, A. (Alessandra), Giannini, G. (Giuseppe), Papi, L. (Laura), Martayan, A. (Aline), Tibiletti, M.G. (Maria Grazia), Radice, P. (Paolo), Vratimos, A. (Athanassios), Fostira, F. (Florentia), Garber, J. (Judy), Donaldson, A. (Alan), Brewer, C. (Carole), Foo, C. (Claire), Evans, D.G. (Gareth), Frost, D. (Debra), Eccles, D. (Diana), Brady, A. (A.), Cook, J. (Jackie), Tischkowitz, M. (Marc), Adlard, L., Barwell, J. (Julian), Walker, L.J. (Lisa), Izatt, L. (Louise), Side, L. (Lucy), Kennedy, M.J. (John), Rogers, M.T. (Mark), Porteous, M.E. (Mary), Morrison, P.J. (Patrick), Platte, R. (Radka), Davidson, R. (Rosemarie), Hodgson, S. (Shirley), Ellis, S.D. (Steve), Cole, T. (Trevor), Godwin, A.K. (Andrew), Claes, K.B.M. (Kathleen B.M.), Van Maerken, T. (Tom), Meindl, A. (Alfons), Gehrig, P.A. (Paola A.), Sutter, C. (Christian), Engel, C. (Christoph), Niederacher, D. (Dieter), Steinemann, D. (Doris), Plendl, H. (Hansjoerg), Kast, K. (Karin), Rhiem, K. (Kerstin), Ditsch, N. (Nina), Arnold, N. (Norbert), Varon-Mateeva, R. (Raymonda), Wapenschmidt, B. (Barbara), Wang-Gohrke, S. (Shan), Bressac-de Paillerets, B. (Brigitte), Buecher, B. (Bruno), Delnatte, C.D. (Capucine), Houdayer, C. (Claude), Stoppa-Lyonnet, D. (Dominique), Damiola, F. (Francesca), Coupier, I. (Isabelle), Barjhoux, L. (Laure), Vénat-Bouvet, L. (Laurence), Golmard, L. (Lisa), Boutry-Kryza, N. (N.), Sinilnikova, O. (Olga), Caron, O. (Olivier), Pujol, P. (Pascal), Mazoyer, S. (Sylvie), Belotti, M. (Muriel), Piedmonte, M. (Marion), Friedlander, M.L. (Michael L.), Rodriguez, G. (Gustavo), Copeland, L.J. (Larry J.), Hoya, M. (Miguel) de La, Perez-Segura, P. (Pedro), Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Os, T.A.M. (Theo) van, Meijers-Heijboer, E.J. (Hanne), Hout, A.H. (Annemarie) van der, Vreeswijk, M.P. (Maaike), Hoogerbrugge, N. (Nicoline), Ausems, M.G.E.M. (Margreet), Doorn, H.C. (Lena) van, Collée, J.M. (Margriet), Olah, E., Díez, O. (Orland), Blanco, I. (Ignacio), Lázaro, C. (Conxi), Brunet, J. (Joan), Feliubadaló, L. (L.), Cybulski, C. (Cezary), Gronwald, J. (Jacek), Durda, K. (Katarzyna), Jaworska-Bieniek, K. (Katarzyna), Sukiennicki, G. (Grzegorz), Arason, A. (Adalgeir), Chiquette, J. (Jocelyne), Teixeira, P.J., Olswold, C. (Curtis), Couch, F.J. (Fergus), Lindor, N.M. (Noralane), Wang, X. (X.), Szabo, C. (Csilla), Offit, K. (Kenneth), Corines, M. (Marina), Jacobs, L. (Lauren), Robson, M.E. (Mark E.), Zhang, L. (Lingling), Joseph, V. (Vijai), Berger, A. (Andreas), Singer, C.F. (Christian), Rappaport, C. (Christine), Kaulich, D.G. (Daphne Gschwantler), Pfeiler, G. (Georg), Tea, M.-K., Phelan, C. (Catherine), Greene, M.H. (Mark), Mai, P.L. (Phuong), Rennert, G. (Gad), Mulligan, A.-M. (Anna-Marie), Glendon, G. (Gord), Tchatchou, S. (Sandrine), Andrulis, I.L. (Irene), Toland, A.E. (Amanda), Bojesen, A. (Anders), Pedersen, I.S. (Inge Sokilde), Thomassen, M. (Mads), Jensen, U.B., Laitman, Y. (Yael), Rantala, J. (Johanna), Wachenfeldt, A. (Anna) von, Ehrencrona, H. (Hans), Askmalm, M.S. (Marie), Borg, Å. (Åke), Kuchenbaecker, K.B. (Karoline), McGuffog, L. (Lesley), Barrowdale, D. (Daniel), Healey, S. (Sue), Lee, A. (Andrew), Pharoah, P.D.P. (Paul D.P.), Chenevix-Trench, G. (Georgia), Antoniou, A.C. (Antonis), and Friedman, E. (Eitan)
Abstract: Background: BRCA1 and BRCA2 mutation carriers are at substantially increased risk for developing breast and ovarian cancer. The incomplete penetrance coupled with the variable age at diagnosis in carriers of the same mutation suggests the existence of genetic and nongenetic modifying factors. In this study, we evaluated the putative role of variants inmany candidate modifier genes. Methods: Genotyping data from 15,252 BRCA1 and 8,211 BRCA2 mutation carriers, for known variants (n = 3,248) located within or around 445 candidate genes, were available through the iCOGS custom-designed array. Breast and ovarian cancer association analysiswas performed within a retrospective cohort approach. Results: The observed P values of association ranged between 0.005 and 1.000. None of the variants was significantly associated with breast or ovarian cancer risk in either BRCA1 or BRCA2 mutation carriers, after multiple testing adjustments. Conclusion: There is little evidence that any of the evaluated candidate variants act as modifiers of breast and/or ovarian cancer risk in BRCA1 or BRCA2 mutation carriers. Impact: Genome-wide association studies have been more successful at identifying genetic modifiers of BRCA1/2 penetrance than candidate gene studies.
Published: 2015
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10. Molecular profiling of tumour budding implicates TGFβ-mediated epithelial-mesenchymal transition as a therapeutic target in oral squamous cell carcinoma

Author: Jensen, DH, primary, Dabelsteen, E, additional, Specht, L, additional, Fiehn, AMK, additional, Therkildsen, MH, additional, Jønson, L, additional, Vikesaa, J, additional, Nielsen, FC, additional, and von Buchwald, C, additional
Published: 2015
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11. DNA Glycosylases Involved in Base Excision Repair May Be Associated with Cancer Risk in BRCA1 and BRCA2 Mutation Carriers

Author: Osorio, A. (Ana), Milne, R.L. (Roger), Kuchenbaecker, K.B. (Karoline), Vaclová, T. (Tereza), Pita, G. (Guillermo), Alonso, M.R. (Rosario), Peterlongo, P. (Paolo), Blanco, I. (Ignacio), Hoya, M. (Miguel) de La, Durán, M. (Mercedes), Díez, O. (Orland), Ramon Y Cajal, T., Konstantopoulou, I. (I.), Martínez-Bouzas, C. (Cristina), Andrés Conejero, R. (Raquel), Soucy, P. (Penny), McGuffog, L. (Lesley), Barrowdale, D. (Daniel), Lee, A. (Andrew), Arver, B. (Brita Wasteson), Rantala, J. (Johanna), Loman, N. (Niklas), Ehrencrona, H. (Hans), Olopade, O.I. (Olofunmilayo), Beattie, M.S. (Mary), Domchek, S.M. (Susan), Nathanson, K.L. (Katherine), Rebbeck, R. (Timothy), Arun, B.K. (Banu), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Lester, K.J. (Kathryn), John, E.M. (Esther), Whittemore, A.S. (Alice), Daly, M.B. (Mary), Southey, M.C. (Melissa), Hopper, J.L. (John), Terry, M.-B. (Mary-Beth), Buys, S.S. (Saundra), Janavicius, R. (Ramunas), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Steele, L. (Linda), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Ejlertsen, B. (Bent), Gerdes, A-M. (Anne-Marie), Infante, J. (Jon), Herráez, B. (Belén), Moreno, L.T. (Leticia Thais), Weitzel, J.N. (Jeffrey), Herzog, J. (Josef), Weeman, K. (Kisa), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Scuvera, G. (Giulietta), Bonnani, B. (Bernardo), Mariette, F. (F.), Volorio, S. (Sara), Viel, A. (Alessandra), Varesco, L. (Liliana), Papi, L. (Laura), Ottini, L. (Laura), Tibiletti, M.G. (Maria Grazia), Radice, P. (Paolo), Yannoukakos, D. (Drakoulis), Garber, J., Ellis, S.D. (Steve), Frost, D. (Debra), Platte, R. (Radka), Fineberg, E. (Elena), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Izatt, L. (Louise), Eeles, R. (Rosalind), Adlard, J.W. (Julian), Davidson, R. (Rosemarie), Cole, T.J. (Trevor), Eccles, D. (Diana), Cook, J. (Jackie), Hodgson, S.V. (Shirley), Brewer, C. (Carole), Tischkowitz, M. (Marc), Douglas, F. (Fiona), Porteous, M.E. (Mary), Side, L. (Lucy), Walker, L.J. (Lisa), Morrison, P.J. (Patrick), Donaldson, A. (Alan), Kennedy, J. (John), Foo, C. (Claire), Godwin, A.K. (Andrew), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Rhiem, K. (Kerstin), Engel, C. (Christoph), Meindl, A. (Alfons), Ditsch, N. (Nina), Arnold, N. (Norbert), Plendl, H. (Hansjoerg), Niederacher, D. (Dieter), Sutter, C. (Christian), Wang-Gohrke, S. (Shan), Steinemann, D. (Doris), Preisler-Adams, S. (Sabine), Kast, K. (Karin), Varon-Mateeva, R. (Raymonda), Gehrig, P.A. (Paola A.), Stoppa-Lyonnet, D. (Dominique), Sinilnikova, O. (Olga), Mazoyer, S. (Sylvie), Damiola, F. (Francesca), Poppe, B. (Bruce), Claes, K. (Kathleen), Piedmonte, M. (Marion), Tucker, K. (Kathryn), Backes, F.J. (Floor), Rodríguez, P.M., Brewster, W. (Wendy), Wakeley, K. (Katie), Rutherford, T. (Thomas), Caldes, T. (Trinidad), Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Rookus, M.A. (Matti), Os, T.A.M. (Theo) van, Kolk, L.E. (Lizet) van der, Lange, J.L. (J.) de, Meijers-Heijboer, E.J. (Hanne), Hout, A.H. (Annemarie) van der, Asperen, C.J. (Christi) van, Gómez García, E.B. (Encarna), Hoogerbrugge, N. (Nicoline), Collée, J.M. (Margriet), Deurzen, C.H.M. (Carolien) van, Luijt, R.B. (Rob) van der, Devilee, P. (Peter), Olah, E. (Edith), Lázaro, C. (Conxi), Teulé, A. (A.), Menéndez, M. (Mireia), Jakubowska, A. (Anna), Cybulski, C. (Cezary), Gronwald, J. (Jacek), Lubinski, J. (Jan), Durda, K. (Katarzyna), Jaworska-Bieniek, K. (Katarzyna), Johannson, O.T. (Oskar), Maugard, C., Montagna, M. (Marco), Tognazzo, S. (Silvia), Teixeira, P.J., Healey, S. (Sue), Olswold, C. (Curtis), Guidugli, L. (Lucia), Lindor, N.M. (Noralane), Slager, S. (Susan), Szabo, C. (Csilla), Vijai, J. (Joseph), Robson, M. (Mark), Kauff, N. (Noah), Zhang, L. (Lingling), Rau-Murthy, R. (Rohini), Fink-Retter, A. (Anneliese), Singer, C.F. (Christian), Rappaport, C. (Christine), Geschwantler Kaulich, D. (Daphne), Pfeiler, G. (Georg), Tea, M.-K., Berger, A. (Annemarie), Phelan, C. (Catherine), Greene, M.H. (Mark), Mai, P.L. (Phuong), Lejbkowicz, F. (Flavio), Andrulis, I.L. (Irene), Mulligan, A.M. (Anna Marie), Glendon, G. (Gord), Toland, A.E. (Amanda), Bojesen, S.E. (Stig), Pedersen, I.S. (Inge Sokilde), Sunde, L. (Lone), Thomassen, M. (Mads), Kruse, T.A. (Torben), Jensen, U.B., Friedman, E. (Eitan), Laitman, Y. (Yael), Shimon, S.P. (Shani Paluch), Simard, J. (Jacques), Easton, D.F. (Douglas), Offit, K. (Kenneth), Couch, F.J. (Fergus), Chenevix-Trench, G. (Georgia), Antoniou, A.C. (Antonis), Benítez, J. (Javier), Osorio, A. (Ana), Milne, R.L. (Roger), Kuchenbaecker, K.B. (Karoline), Vaclová, T. (Tereza), Pita, G. (Guillermo), Alonso, M.R. (Rosario), Peterlongo, P. (Paolo), Blanco, I. (Ignacio), Hoya, M. (Miguel) de La, Durán, M. (Mercedes), Díez, O. (Orland), Ramon Y Cajal, T., Konstantopoulou, I. (I.), Martínez-Bouzas, C. (Cristina), Andrés Conejero, R. (Raquel), Soucy, P. (Penny), McGuffog, L. (Lesley), Barrowdale, D. (Daniel), Lee, A. (Andrew), Arver, B. (Brita Wasteson), Rantala, J. (Johanna), Loman, N. (Niklas), Ehrencrona, H. (Hans), Olopade, O.I. (Olofunmilayo), Beattie, M.S. (Mary), Domchek, S.M. (Susan), Nathanson, K.L. (Katherine), Rebbeck, R. (Timothy), Arun, B.K. (Banu), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Lester, K.J. (Kathryn), John, E.M. (Esther), Whittemore, A.S. (Alice), Daly, M.B. (Mary), Southey, M.C. (Melissa), Hopper, J.L. (John), Terry, M.-B. (Mary-Beth), Buys, S.S. (Saundra), Janavicius, R. (Ramunas), Dorfling, C.M. (Cecilia), Rensburg, E.J. (Elizabeth) van, Steele, L. (Linda), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Ejlertsen, B. (Bent), Gerdes, A-M. (Anne-Marie), Infante, J. (Jon), Herráez, B. (Belén), Moreno, L.T. (Leticia Thais), Weitzel, J.N. (Jeffrey), Herzog, J. (Josef), Weeman, K. (Kisa), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Scuvera, G. (Giulietta), Bonnani, B. (Bernardo), Mariette, F. (F.), Volorio, S. (Sara), Viel, A. (Alessandra), Varesco, L. (Liliana), Papi, L. (Laura), Ottini, L. (Laura), Tibiletti, M.G. (Maria Grazia), Radice, P. (Paolo), Yannoukakos, D. (Drakoulis), Garber, J., Ellis, S.D. (Steve), Frost, D. (Debra), Platte, R. (Radka), Fineberg, E. (Elena), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Izatt, L. (Louise), Eeles, R. (Rosalind), Adlard, J.W. (Julian), Davidson, R. (Rosemarie), Cole, T.J. (Trevor), Eccles, D. (Diana), Cook, J. (Jackie), Hodgson, S.V. (Shirley), Brewer, C. (Carole), Tischkowitz, M. (Marc), Douglas, F. (Fiona), Porteous, M.E. (Mary), Side, L. (Lucy), Walker, L.J. (Lisa), Morrison, P.J. (Patrick), Donaldson, A. (Alan), Kennedy, J. (John), Foo, C. (Claire), Godwin, A.K. (Andrew), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Rhiem, K. (Kerstin), Engel, C. (Christoph), Meindl, A. (Alfons), Ditsch, N. (Nina), Arnold, N. (Norbert), Plendl, H. (Hansjoerg), Niederacher, D. (Dieter), Sutter, C. (Christian), Wang-Gohrke, S. (Shan), Steinemann, D. (Doris), Preisler-Adams, S. (Sabine), Kast, K. (Karin), Varon-Mateeva, R. (Raymonda), Gehrig, P.A. (Paola A.), Stoppa-Lyonnet, D. (Dominique), Sinilnikova, O. (Olga), Mazoyer, S. (Sylvie), Damiola, F. (Francesca), Poppe, B. (Bruce), Claes, K. (Kathleen), Piedmonte, M. (Marion), Tucker, K. (Kathryn), Backes, F.J. (Floor), Rodríguez, P.M., Brewster, W. (Wendy), Wakeley, K. (Katie), Rutherford, T. (Thomas), Caldes, T. (Trinidad), Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Rookus, M.A. (Matti), Os, T.A.M. (Theo) van, Kolk, L.E. (Lizet) van der, Lange, J.L. (J.) de, Meijers-Heijboer, E.J. (Hanne), Hout, A.H. (Annemarie) van der, Asperen, C.J. (Christi) van, Gómez García, E.B. (Encarna), Hoogerbrugge, N. (Nicoline), Collée, J.M. (Margriet), Deurzen, C.H.M. (Carolien) van, Luijt, R.B. (Rob) van der, Devilee, P. (Peter), Olah, E. (Edith), Lázaro, C. (Conxi), Teulé, A. (A.), Menéndez, M. (Mireia), Jakubowska, A. (Anna), Cybulski, C. (Cezary), Gronwald, J. (Jacek), Lubinski, J. (Jan), Durda, K. (Katarzyna), Jaworska-Bieniek, K. (Katarzyna), Johannson, O.T. (Oskar), Maugard, C., Montagna, M. (Marco), Tognazzo, S. (Silvia), Teixeira, P.J., Healey, S. (Sue), Olswold, C. (Curtis), Guidugli, L. (Lucia), Lindor, N.M. (Noralane), Slager, S. (Susan), Szabo, C. (Csilla), Vijai, J. (Joseph), Robson, M. (Mark), Kauff, N. (Noah), Zhang, L. (Lingling), Rau-Murthy, R. (Rohini), Fink-Retter, A. (Anneliese), Singer, C.F. (Christian), Rappaport, C. (Christine), Geschwantler Kaulich, D. (Daphne), Pfeiler, G. (Georg), Tea, M.-K., Berger, A. (Annemarie), Phelan, C. (Catherine), Greene, M.H. (Mark), Mai, P.L. (Phuong), Lejbkowicz, F. (Flavio), Andrulis, I.L. (Irene), Mulligan, A.M. (Anna Marie), Glendon, G. (Gord), Toland, A.E. (Amanda), Bojesen, S.E. (Stig), Pedersen, I.S. (Inge Sokilde), Sunde, L. (Lone), Thomassen, M. (Mads), Kruse, T.A. (Torben), Jensen, U.B., Friedman, E. (Eitan), Laitman, Y. (Yael), Shimon, S.P. (Shani Paluch), Simard, J. (Jacques), Easton, D.F. (Douglas), Offit, K. (Kenneth), Couch, F.J. (Fergus), Chenevix-Trench, G. (Georgia), Antoniou, A.C. (Antonis), and Benítez, J. (Javier)
Abstract: Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the components of the BER pathway, PARP1 (poly ADP ribose polymerase), and both BRCA1 and BRCA2. In the present study, we have performed a comprehensive analysis of 18 genes involved in BER using a tagging SNP approach in a large series of BRCA1 and BRCA2 mutation carriers. 144 SNPs were analyzed in a two stage study involving 23,463 carriers from the CIMBA consortium (the Consortium of Investigators of Modifiers of BRCA1 and BRCA2). Eleven SNPs showed evidence of association with breast and/or ovarian cancer at p<0.05 in the combined analysis. Four of the five genes for which strongest evidence of association was observed were DNA glycosylases. The strongest evidence was for rs1466785 in the NEIL2 (endonuclease VIII-like 2) gene (HR: 1.09, 95% CI (1.03-1.1
Published: 2014
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12. SY2-1: Insulin-like growth factor 2 mRNA binding proteins (IMP/IGF2BP) as mRNA safe houses in cancer and development

Author: Christiansen, J., primary, Jønson, L., additional, Vikesaa, J., additional, Hansen, T.v.O., additional, and Nielsen, F.C., additional
Published: 2014
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13. Detection of Potential Fishing Zones of Bigeye Tuna (Thunnus Obesus) at Profundity of 155 m in the Eastern Indian Ocean

Author: Achmad Fachruddin-Syah, Jonson Lumban Gaol, Mukti Zainuddin, Nadela Rista Apriliya, Dessy Berlianty, and Dendy Mahabror
Subjects: bigeye tuna, profundity of 155 m, eastern indian ocean, maximum entropy model, potential fishing zone, Geography. Anthropology. Recreation, Geography (General), G1-922
Abstract: Remotely sensed data and habitat model approach were employed to evaluate the present of oceanographic aspect in the Bigeye tuna's potential fishing zone (PFZ) at a profundity of 155 m. Vessel monitoring system was employed to acquire the angling vessels for Bigeye tuna from January through December, 2015-2016. Daily data of sub-surface temperature (Sub_ST), sub-surface chlorophyll-a (Sub_SC), and sub-surface salinity (Sub_SS) were downloaded from INDESO Project website. Vessel monitoring system and environmental data were employed for maximum entropy (maxent) model development. The model predictive achievement was then estimated applying the area under the curve (AUC) value. Maxent model results (AUC>0.745) exhibited its probable to understand the Bigeye tuna's spatial dispersion on the specific sub-surface. In addition, the results also showed Sub_ST (43,1%) was the most affective aspect in the Bigeye tuna dispersion, pursued by Sub_SC (35,2%) and Sub_SS (21,6%).
Published: 2020
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14. Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

Author: Couch, F.J. (Fergus), McGuffog, L. (Lesley), Lee, A. (Andrew), Olswold, C. (Curtis), Kuchenbaecker, K.B. (Karoline), Soucy, P. (Penny), Fredericksen, Z. (Zachary), Barrowdale, D. (Daniel), Dennis, J. (Joe), Gaudet, M.M. (Mia), Dicks, E. (Ed), Kosel, M. (Matthew), Healey, S. (Sue), Sinilnikova, O. (Olga), Bacot, F. (Francois), Vincent, D. (Daniel), Hogervorst, F.B.L. (Frans), Peock, S. (Susan), Stoppa-Lyonnet, D. (Dominique), Jakubowska, A. (Anna), Radice, P. (Paolo), Schmutzler, R.K. (Rita), Domchek, S.M. (Susan), Piedmonte, M. (Marion), Singer, C.F. (Christian), Friedman, E. (Eitan), Thomassen, M. (Mads), Hansen, T.V.O. (Thomas), Neuhausen, S.L. (Susan), Szabo, C. (Csilla), Blanco, I. (Ignacio), Greene, M.H. (Mark), Karlan, B.Y. (Beth), Garber, J., Phelan, C. (Catherine), Weitzel, J.N. (Jeffrey), Montagna, M. (Marco), Olah, E., Andrulis, I.L. (Irene), Godwin, A.K. (Andrew), Yannoukakos, D. (Drakoulis), Goldgar, D. (David), Caldes, T. (Trinidad), Nevanlinna, H. (Heli), Osorio, A. (Ana), Terry, M.-B. (Mary-Beth), Daly, M.B. (Mary), Rensburg, E.J. (Elizabeth) van, Hamann, U. (Ute), Ramus, S.J. (Susan), Ewart-Toland, A. (Amanda), Caligo, M.A. (Maria), Olopade, O.I. (Olofunmilayo), Tung, N. (Nadine), Claes, K. (Kathleen), Beattie, M.S. (Mary), Southey, M.C. (Melissa), Imyanitov, E.N. (Evgeny), Tischkowitz, M. (Marc), Janavicius, R. (Ramunas), John, E.M. (Esther), Kwong, A. (Ava), Diez, O. (Orland), Balmana, J. (Judith), Barkardottir, R.B. (Rosa), Arun, B.K. (Banu), Rennert, G. (Gad), Teo, S.-H. (Soo-Hwang), Ganz, P.A. (Patricia), Campbell, I. (Ian), Hout, A.H. (Annemarie) van der, Deurzen, C.H.M. (Carolien) van, Seynaeve, C.M. (Caroline), Gómez García, E.B. (Encarna), Leeuwen, F.E. (Flora) van, Meijers-Heijboer, H. (Hanne), Gille, J.J. (Johan), Ausems, M.G.E.M. (Margreet), Blok, M.J. (Marinus), Ligtenberg, M.J. (Marjolijn), Rookus, M.A. (Matti), Devilee, P. (Peter), Verhoef, S., Os, T.A.M. (Theo) van, Wijnen, J.T. (Juul), Frost, D. (Debra), Ellis, S. (Steve), Fineberg, E. (Elena), Platte, R. (Radka), Evans, D.G. (Gareth), Izatt, L. (Louise), Eeles, R. (Rosalind), Adlard, J.W. (Julian), Eccles, D. (Diana), Cook, J. (Jackie), Brewer, C. (C.), Douglas, F. (Fiona), Hodgson, S.V. (Shirley), Morrison, P.J. (Patrick), Side, L. (Lucy), Donaldson, A. (Alan), Houghton, C. (Catherine), Rogers, M.T. (Mark), Dorkins, H. (Huw), Eason, J. (Jacqueline), Gregory, H. (Helen), McCann, E. (Emma), Murray, A. (Alexandra), Calender, A. (Alain), Hardouin, A. (Agnès), Berthet, P. (Pascaline), Delnatte, C.D. (Capucine), Nogues, C. (Catherine), Lasset, C. (Christine), Houdayer, C. (Claude), Leroux, D. (Dominique), Rouleau, E. (Etienne), Prieur, F. (Fabienne), Damiola, F. (Francesca), Sobol, H. (Hagay), Coupier, I. (Isabelle), Vénat-Bouvet, L. (Laurence), Castera, L. (Laurent), Gauthier-Villars, M. (Marion), Léone, M. (Mélanie), Pujol, P. (Pascal), Mazoyer, S. (Sylvie), Bignon, Y.-J. (Yves-Jean), Złowocka-Perłowska, E. (Elzbieta), Gronwald, J. (Jacek), Lubinski, J. (Jan), Durda, K. (Katarzyna), Jaworska, K. (Katarzyna), Huzarski, T. (Tomasz), Spurdle, A.B. (Amanda), Viel, A. (Alessandra), Peissel, B. (Bernard), Bonnani, B. (Bernardo), Melloni, G. (Giulia), Ottini, L. (Laura), Papi, L. (Laura), Varesco, L. (Liliana), Tibiletti, M.G. (Maria Grazia), Peterlongo, P. (Paolo), Volorio, S. (Sara), Manoukian, S. (Siranoush), Pensotti, V. (Valeria), Arnold, N. (Norbert), Engel, C. (Christoph), Deissler, H. (Helmut), Gadzicki, D. (Dorothea), Gehrig, P.A. (Paola A.), Kast, K. (Karin), Rhiem, K. (Kerstin), Meindl, A. (Alfons), Niederacher, D. (Dieter), Ditsch, N. (Nina), Plendl, H. (Hansjoerg), Preisler-Adams, S. (Sabine), Engert, S. (Stefanie), Sutter, C. (Christian), Varon-Mateeva, R. (Raymonda), Wapenschmidt, B. (Barbara), Weber, B.H.F. (Bernhard), Arver, B. (Brita Wasteson), Stenmark-Askmalm, M. (M.), Loman, N. (Niklas), Rosenquist, R. (R.), Einbeigi, Z. (Zakaria), Nathanson, K.L. (Katherine), Rebbeck, R. (Timothy), Blank, S.V. (Stephanie), Cohn, D.E. (David), Rodriguez, G.C. (Gustavo), Small, L. (Laurie), Friedlander, M. (Michael), Bae-Jump, V.L. (Victoria L.), Fink-Retter, A. (Anneliese), Rappaport, C. (Christine), Gschwantler-Kaulich, D. (Daphne), Pfeiler, G. (Georg), Tea, M.-K., Lindor, N.M. (Noralane), Kaufman, B. (Bella), Shimon Paluch, S. (Shani), Laitman, Y. (Yael), Skytte, A.-B. (Anne-Bine), Gerdes, A-M. (Anne-Marie), Pedersen, I.S. (Inge Sokilde), Moeller, S.T. (Sanne Traasdahl), Kruse, T.A. (Torben), Jensen, U.B., Vijai, J. (Joseph), Sarrel, K. (Kara), Robson, M. (Mark), Kauff, N. (Noah), Mulligan, A.M. (Anna Marie), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Ejlertsen, B. (Bent), Nielsen, F.C. (Finn), Jønson, L. (Lars), Andersen, M.K. (Mette), Ding, Y.C. (Yuan), Steele, L. (Linda), Foretova, L. (Lenka), Teulé, A. (A.), Lázaro, C. (Conxi), Brunet, J. (Joan), Pujana, M.A. (Miguel), Mai, P.L. (Phuong), Loud, J.T. (Jennifer), Walsh, C.S. (Christine), Lester, K.J. (Kathryn), Orsulic, S. (Sandra), Narod, S. (Steven), Herzog, J. (Josef), Sand, S.R. (Sharon), Tognazzo, S. (Silvia), Agata, S. (Simona), Vaszko, T. (Tibor), Weaver, J. (JoEllen), Stavropoulou, A. (Alexandra), Buys, S.S. (Saundra), Romero, A. (Alfonso), Hoya, M. (Miguel) de La, Aittomäki, K. (Kristiina), Muranen, T.A. (Taru), Durán, M. (Mercedes), Chung, W.K. (Wendy), Lasa, A. (Adriana), Dorfling, C.M. (Cecelia), Miron, A. (Alexander), Benítez, J. (Javier), Senter, L. (Leigha), Huo, D. (Dezheng), Chan, S. (Salina), Sokolenko, A. (Anna), Chiquette, J. (Jocelyne), Tihomirova, L. (Laima), Friebel, M.O.W. (Mark ), Agnarsson, B.A. (Bjarni), Lu, K.H. (Karen), Lejbkowicz, F. (Flavio), James, P.A. (Paul ), Hall, A.S. (Alistair), Dunning, A.M. (Alison), Tessier, Y. (Yann), Cunningham, J. (Jane), Slager, S. (Susan), Wang, C. (Chen), Hart, S. (Stewart), Stevens, K. (Kristen), Simard, J. (Jacques), Pastinen, T. (Tomi), Pankratz, V.S. (Shane), Offit, K. (Kenneth), Easton, D.F. (Douglas), Chenevix-Trench, G. (Georgia), Antoniou, A.C. (Antonis), Thorne, H. (Heather), Niedermayr, E. (Eveline), Borg, Å. (Åke), Olsson, H., Jernström, H. (H.), Henriksson, K. (Karin), Harbst, K. (Katja), Soller, M. (Maria), Kristoffersson, U. (Ulf), Wang, X. (Xianshu), Öfverholm, A. (Anna), Nordling, M. (Margareta), Karlsson, P. (Per), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Lindblom, A. (Annika), Bustinza, G.B., Rantala, J. (Johanna), Melin, B. (Beatrice), Ardnor, C.E. (Christina Edwinsdotter), Emanuelsson, M. (Monica), Ehrencrona, H. (Hans), Pigg, M.H. (Maritta ), Liedgren, S. (Sigrun), Rookus, M.A. (M.), Verhoef, S. (S.), Schmidt, M.K. (Marjanka), Lange, J.L. (J.) de, Collée, J.M. (Margriet), Ouweland, A.M.W. (Ans) van den, Hooning, M.J. (Maartje), Asperen, C.J. (Christi) van, Tollenaar, R.A.E.M. (Rob), Cronenburg, T.C.T.E.F. van, Kets, C.M. (Marleen), Mensenkamp, A.R. (Arjen), Luijt, R.B. (Rob) van der, Aalfs, C.M. (Cora), Waisfisz, Q. (Quinten), Meijers-Heijboer, E.J. (Hanne), Gomez Garcia, E.B. (Encarna), Oosterwijk, J.C. (Jan), Mourits, M.J. (Marjan), Bock, G.H. (Geertruida) de, Ellis, S.D. (Steve), Miedzybrodzka, Z. (Zosia), Jeffers, L. (Lisa), Cole, T.J. (Trevor), Ong, K.-R. (Kai-Ren), Hoffman, J. (Jonathan), James, M. (Margaret), Paterson, J. (Joan), Taylor, A. (Amy), Murray, A. (Anna), Kennedy, M.J. (John), Barton, D.E. (David), Porteous, M.E. (Mary), Drummond, S. (Sarah), Brewer, C. (Carole), Kivuva, E. (Emma), Searle, A. (Anne), Goodman, S. (Selina), Davidson, R. (Rosemarie), Murday, V. (Victoria), Bradshaw, N. (Nicola), Snadden, L. (Lesley), Longmuir, M. (Mark), Watt, C. (Catherine), Gibson, S. (Sarah), Haque, E. (Eshika), Tobias, E. (Ed), Duncan, A. (Alexis), Jacobs, C. (Chris), Langman, C. (Caroline), Brady, A.F. (Angela), Melville, S.A. (Scott), Randhawa, K. (Kashmir), Barwell, J. (Julian), Serra-Feliu, G. (Gemma), Ellis, I.O. (Ian), Lalloo, F. (Fiona), Taylor, J. (James), Male, A. (Alison), Berlin, C. (Cheryl), Collier, R. (Rebecca), Claber, O. (Oonagh), Jobson, I. (Irene), Walker, L.J. (Lisa), McLeod, D. (Diane), Halliday, D. (Dorothy), Durell, S. (Sarah), Stayner, B. (Barbara), Shanley, S. (Susan), Rahman, N. (Nazneen), Houlston, R. (Richard), Stormorken, A. (Astrid), Bancroft, E.K. (Elizabeth), Page, E. (Elizabeth), Ardern-Jones, A. (Audrey), Kohut, K. (Kelly), Wiggins, J. (Jennifer), Castro, E. (Elena), Killick, S.R., Martin, S. (Sue), Rea, D. (Dan), Kulkarni, A. (Anjana), Quarrell, O. (Oliver), Bardsley, C. (Cathryn), Goff, S. (Sheila), Brice, G. (Glen), Winchester, L. (Lizzie), Eddy, C. (Charlotte), Tripathi, V. (Vishakha), Attard, V. (Virginia), Lehmann, A. (Anna), Lucassen, A. (Anneke), Crawford, G. (Gabe), McBride, D. (Donna), Smalley, S. (Sarah), Barjhoux, L. (Laure), Verny-Pierre, C. (Carole), Giraud, S. (Sophie), Buecher, B. (Bruno), Moncoutier, V. (Virginie), Belotti, M. (Muriel), Tirapo, C. (Carole), Pauw, A. (Antoine) de, Bressac-de Paillerets, B. (Brigitte), Caron, O. (Olivier), Uhrhammer, N. (Nancy), Bonadona, V. (Valérie), Handallou, S. (Sandrine), hardouin, A. (Agnès), Bourdon, V. (Violaine), Noguchi, T. (Tetsuro), Remenieras, A. (Audrey), Eisinger, F. (François), Peyrat, J.-P., Fournier, J. (Joëlle), Révillion, F. (Françoise), Vennin, P. (Philippe), Adenis, C. (Claude), Lidereau, R. (Rosette), Demange, L. (Liliane), Muller, D.W. (Danièle), Fricker, J.P. (Jean Pierre), Barouk-Simonet, E. (Emmanuelle), Bonnet, F. (Françoise), Bubien, V. (Virginie), Sevenet, N. (Nicolas), Longy, M. (Michel), Toulas, C. (Christine), Guimbaud, R. (Rosine), Gladieff, L. (Laurence), Feillel, V. (Viviane), Dreyfus, H. (Hélène), Rebischung, C. (Christine), Peysselon, M. (Magalie), Coron, F. (Fanny), Faivre, L. (Laurence), Lebrun, M. (Marine), Kientz, C. (Caroline), Ferrer, S.F., Frenay, M. (Marc), Mortemousque, I. (Isabelle), Coulet, F. (Florence), Colas, C. (Chrystelle), Soubrier, F., Sokolowska, J. (Johanna), Bronner, M. (Myriam), Lynch, H. (Henry), Snyder, C.L. (Carrie), Angelakos, M. (Maggie), Maskiell, J. (Judi), Dite, G.S. (Gillian), Couch, F.J. (Fergus), McGuffog, L. (Lesley), Lee, A. (Andrew), Olswold, C. (Curtis), Kuchenbaecker, K.B. (Karoline), Soucy, P. (Penny), Fredericksen, Z. (Zachary), Barrowdale, D. (Daniel), Dennis, J. (Joe), Gaudet, M.M. (Mia), Dicks, E. (Ed), Kosel, M. (Matthew), Healey, S. (Sue), Sinilnikova, O. (Olga), Bacot, F. (Francois), Vincent, D. (Daniel), Hogervorst, F.B.L. (Frans), Peock, S. (Susan), Stoppa-Lyonnet, D. (Dominique), Jakubowska, A. (Anna), Radice, P. (Paolo), Schmutzler, R.K. (Rita), Domchek, S.M. (Susan), Piedmonte, M. (Marion), Singer, C.F. (Christian), Friedman, E. (Eitan), Thomassen, M. (Mads), Hansen, T.V.O. (Thomas), Neuhausen, S.L. (Susan), Szabo, C. (Csilla), Blanco, I. (Ignacio), Greene, M.H. (Mark), Karlan, B.Y. (Beth), Garber, J., Phelan, C. (Catherine), Weitzel, J.N. (Jeffrey), Montagna, M. (Marco), Olah, E., Andrulis, I.L. (Irene), Godwin, A.K. (Andrew), Yannoukakos, D. (Drakoulis), Goldgar, D. (David), Caldes, T. (Trinidad), Nevanlinna, H. (Heli), Osorio, A. (Ana), Terry, M.-B. (Mary-Beth), Daly, M.B. (Mary), Rensburg, E.J. (Elizabeth) van, Hamann, U. (Ute), Ramus, S.J. (Susan), Ewart-Toland, A. (Amanda), Caligo, M.A. (Maria), Olopade, O.I. (Olofunmilayo), Tung, N. (Nadine), Claes, K. (Kathleen), Beattie, M.S. (Mary), Southey, M.C. (Melissa), Imyanitov, E.N. (Evgeny), Tischkowitz, M. (Marc), Janavicius, R. (Ramunas), John, E.M. (Esther), Kwong, A. (Ava), Diez, O. (Orland), Balmana, J. (Judith), Barkardottir, R.B. (Rosa), Arun, B.K. (Banu), Rennert, G. (Gad), Teo, S.-H. (Soo-Hwang), Ganz, P.A. (Patricia), Campbell, I. (Ian), Hout, A.H. (Annemarie) van der, Deurzen, C.H.M. (Carolien) van, Seynaeve, C.M. (Caroline), Gómez García, E.B. (Encarna), Leeuwen, F.E. (Flora) van, Meijers-Heijboer, H. (Hanne), Gille, J.J. (Johan), Ausems, M.G.E.M. (Margreet), Blok, M.J. (Marinus), Ligtenberg, M.J. (Marjolijn), Rookus, M.A. (Matti), Devilee, P. (Peter), Verhoef, S., Os, T.A.M. (Theo) van, Wijnen, J.T. (Juul), Frost, D. (Debra), Ellis, S. (Steve), Fineberg, E. (Elena), Platte, R. (Radka), Evans, D.G. (Gareth), Izatt, L. (Louise), Eeles, R. (Rosalind), Adlard, J.W. (Julian), Eccles, D. (Diana), Cook, J. (Jackie), Brewer, C. (C.), Douglas, F. (Fiona), Hodgson, S.V. (Shirley), Morrison, P.J. (Patrick), Side, L. (Lucy), Donaldson, A. (Alan), Houghton, C. (Catherine), Rogers, M.T. (Mark), Dorkins, H. (Huw), Eason, J. (Jacqueline), Gregory, H. (Helen), McCann, E. (Emma), Murray, A. (Alexandra), Calender, A. (Alain), Hardouin, A. (Agnès), Berthet, P. (Pascaline), Delnatte, C.D. (Capucine), Nogues, C. (Catherine), Lasset, C. (Christine), Houdayer, C. (Claude), Leroux, D. (Dominique), Rouleau, E. (Etienne), Prieur, F. (Fabienne), Damiola, F. (Francesca), Sobol, H. (Hagay), Coupier, I. (Isabelle), Vénat-Bouvet, L. (Laurence), Castera, L. (Laurent), Gauthier-Villars, M. (Marion), Léone, M. (Mélanie), Pujol, P. (Pascal), Mazoyer, S. (Sylvie), Bignon, Y.-J. (Yves-Jean), Złowocka-Perłowska, E. (Elzbieta), Gronwald, J. (Jacek), Lubinski, J. (Jan), Durda, K. (Katarzyna), Jaworska, K. (Katarzyna), Huzarski, T. (Tomasz), Spurdle, A.B. (Amanda), Viel, A. (Alessandra), Peissel, B. (Bernard), Bonnani, B. (Bernardo), Melloni, G. (Giulia), Ottini, L. (Laura), Papi, L. (Laura), Varesco, L. (Liliana), Tibiletti, M.G. (Maria Grazia), Peterlongo, P. (Paolo), Volorio, S. (Sara), Manoukian, S. (Siranoush), Pensotti, V. (Valeria), Arnold, N. (Norbert), Engel, C. (Christoph), Deissler, H. (Helmut), Gadzicki, D. (Dorothea), Gehrig, P.A. (Paola A.), Kast, K. (Karin), Rhiem, K. (Kerstin), Meindl, A. (Alfons), Niederacher, D. (Dieter), Ditsch, N. (Nina), Plendl, H. (Hansjoerg), Preisler-Adams, S. (Sabine), Engert, S. (Stefanie), Sutter, C. (Christian), Varon-Mateeva, R. (Raymonda), Wapenschmidt, B. (Barbara), Weber, B.H.F. (Bernhard), Arver, B. (Brita Wasteson), Stenmark-Askmalm, M. (M.), Loman, N. (Niklas), Rosenquist, R. (R.), Einbeigi, Z. (Zakaria), Nathanson, K.L. (Katherine), Rebbeck, R. (Timothy), Blank, S.V. (Stephanie), Cohn, D.E. (David), Rodriguez, G.C. (Gustavo), Small, L. (Laurie), Friedlander, M. (Michael), Bae-Jump, V.L. (Victoria L.), Fink-Retter, A. (Anneliese), Rappaport, C. (Christine), Gschwantler-Kaulich, D. (Daphne), Pfeiler, G. (Georg), Tea, M.-K., Lindor, N.M. (Noralane), Kaufman, B. (Bella), Shimon Paluch, S. (Shani), Laitman, Y. (Yael), Skytte, A.-B. (Anne-Bine), Gerdes, A-M. (Anne-Marie), Pedersen, I.S. (Inge Sokilde), Moeller, S.T. (Sanne Traasdahl), Kruse, T.A. (Torben), Jensen, U.B., Vijai, J. (Joseph), Sarrel, K. (Kara), Robson, M. (Mark), Kauff, N. (Noah), Mulligan, A.M. (Anna Marie), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Ejlertsen, B. (Bent), Nielsen, F.C. (Finn), Jønson, L. (Lars), Andersen, M.K. (Mette), Ding, Y.C. (Yuan), Steele, L. (Linda), Foretova, L. (Lenka), Teulé, A. (A.), Lázaro, C. (Conxi), Brunet, J. (Joan), Pujana, M.A. (Miguel), Mai, P.L. (Phuong), Loud, J.T. (Jennifer), Walsh, C.S. (Christine), Lester, K.J. (Kathryn), Orsulic, S. (Sandra), Narod, S. (Steven), Herzog, J. (Josef), Sand, S.R. (Sharon), Tognazzo, S. (Silvia), Agata, S. (Simona), Vaszko, T. (Tibor), Weaver, J. (JoEllen), Stavropoulou, A. (Alexandra), Buys, S.S. (Saundra), Romero, A. (Alfonso), Hoya, M. (Miguel) de La, Aittomäki, K. (Kristiina), Muranen, T.A. (Taru), Durán, M. (Mercedes), Chung, W.K. (Wendy), Lasa, A. (Adriana), Dorfling, C.M. (Cecelia), Miron, A. (Alexander), Benítez, J. (Javier), Senter, L. (Leigha), Huo, D. (Dezheng), Chan, S. (Salina), Sokolenko, A. (Anna), Chiquette, J. (Jocelyne), Tihomirova, L. (Laima), Friebel, M.O.W. (Mark ), Agnarsson, B.A. (Bjarni), Lu, K.H. (Karen), Lejbkowicz, F. (Flavio), James, P.A. (Paul ), Hall, A.S. (Alistair), Dunning, A.M. (Alison), Tessier, Y. (Yann), Cunningham, J. (Jane), Slager, S. (Susan), Wang, C. (Chen), Hart, S. (Stewart), Stevens, K. (Kristen), Simard, J. (Jacques), Pastinen, T. (Tomi), Pankratz, V.S. (Shane), Offit, K. (Kenneth), Easton, D.F. (Douglas), Chenevix-Trench, G. (Georgia), Antoniou, A.C. (Antonis), Thorne, H. (Heather), Niedermayr, E. (Eveline), Borg, Å. (Åke), Olsson, H., Jernström, H. (H.), Henriksson, K. (Karin), Harbst, K. (Katja), Soller, M. (Maria), Kristoffersson, U. (Ulf), Wang, X. (Xianshu), Öfverholm, A. (Anna), Nordling, M. (Margareta), Karlsson, P. (Per), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Lindblom, A. (Annika), Bustinza, G.B., Rantala, J. (Johanna), Melin, B. (Beatrice), Ardnor, C.E. (Christina Edwinsdotter), Emanuelsson, M. (Monica), Ehrencrona, H. (Hans), Pigg, M.H. (Maritta ), Liedgren, S. (Sigrun), Rookus, M.A. (M.), Verhoef, S. (S.), Schmidt, M.K. (Marjanka), Lange, J.L. (J.) de, Collée, J.M. (Margriet), Ouweland, A.M.W. (Ans) van den, Hooning, M.J. (Maartje), Asperen, C.J. (Christi) van, Tollenaar, R.A.E.M. (Rob), Cronenburg, T.C.T.E.F. van, Kets, C.M. (Marleen), Mensenkamp, A.R. (Arjen), Luijt, R.B. (Rob) van der, Aalfs, C.M. (Cora), Waisfisz, Q. (Quinten), Meijers-Heijboer, E.J. (Hanne), Gomez Garcia, E.B. (Encarna), Oosterwijk, J.C. (Jan), Mourits, M.J. (Marjan), Bock, G.H. (Geertruida) de, Ellis, S.D. (Steve), Miedzybrodzka, Z. (Zosia), Jeffers, L. (Lisa), Cole, T.J. (Trevor), Ong, K.-R. (Kai-Ren), Hoffman, J. (Jonathan), James, M. (Margaret), Paterson, J. (Joan), Taylor, A. (Amy), Murray, A. (Anna), Kennedy, M.J. (John), Barton, D.E. (David), Porteous, M.E. (Mary), Drummond, S. (Sarah), Brewer, C. (Carole), Kivuva, E. (Emma), Searle, A. (Anne), Goodman, S. (Selina), Davidson, R. (Rosemarie), Murday, V. (Victoria), Bradshaw, N. (Nicola), Snadden, L. (Lesley), Longmuir, M. (Mark), Watt, C. (Catherine), Gibson, S. (Sarah), Haque, E. (Eshika), Tobias, E. (Ed), Duncan, A. (Alexis), Jacobs, C. (Chris), Langman, C. (Caroline), Brady, A.F. (Angela), Melville, S.A. (Scott), Randhawa, K. (Kashmir), Barwell, J. (Julian), Serra-Feliu, G. (Gemma), Ellis, I.O. (Ian), Lalloo, F. (Fiona), Taylor, J. (James), Male, A. (Alison), Berlin, C. (Cheryl), Collier, R. (Rebecca), Claber, O. (Oonagh), Jobson, I. (Irene), Walker, L.J. (Lisa), McLeod, D. (Diane), Halliday, D. (Dorothy), Durell, S. (Sarah), Stayner, B. (Barbara), Shanley, S. (Susan), Rahman, N. (Nazneen), Houlston, R. (Richard), Stormorken, A. (Astrid), Bancroft, E.K. (Elizabeth), Page, E. (Elizabeth), Ardern-Jones, A. (Audrey), Kohut, K. (Kelly), Wiggins, J. (Jennifer), Castro, E. (Elena), Killick, S.R., Martin, S. (Sue), Rea, D. (Dan), Kulkarni, A. (Anjana), Quarrell, O. (Oliver), Bardsley, C. (Cathryn), Goff, S. (Sheila), Brice, G. (Glen), Winchester, L. (Lizzie), Eddy, C. (Charlotte), Tripathi, V. (Vishakha), Attard, V. (Virginia), Lehmann, A. (Anna), Lucassen, A. (Anneke), Crawford, G. (Gabe), McBride, D. (Donna), Smalley, S. (Sarah), Barjhoux, L. (Laure), Verny-Pierre, C. (Carole), Giraud, S. (Sophie), Buecher, B. (Bruno), Moncoutier, V. (Virginie), Belotti, M. (Muriel), Tirapo, C. (Carole), Pauw, A. (Antoine) de, Bressac-de Paillerets, B. (Brigitte), Caron, O. (Olivier), Uhrhammer, N. (Nancy), Bonadona, V. (Valérie), Handallou, S. (Sandrine), hardouin, A. (Agnès), Bourdon, V. (Violaine), Noguchi, T. (Tetsuro), Remenieras, A. (Audrey), Eisinger, F. (François), Peyrat, J.-P., Fournier, J. (Joëlle), Révillion, F. (Françoise), Vennin, P. (Philippe), Adenis, C. (Claude), Lidereau, R. (Rosette), Demange, L. (Liliane), Muller, D.W. (Danièle), Fricker, J.P. (Jean Pierre), Barouk-Simonet, E. (Emmanuelle), Bonnet, F. (Françoise), Bubien, V. (Virginie), Sevenet, N. (Nicolas), Longy, M. (Michel), Toulas, C. (Christine), Guimbaud, R. (Rosine), Gladieff, L. (Laurence), Feillel, V. (Viviane), Dreyfus, H. (Hélène), Rebischung, C. (Christine), Peysselon, M. (Magalie), Coron, F. (Fanny), Faivre, L. (Laurence), Lebrun, M. (Marine), Kientz, C. (Caroline), Ferrer, S.F., Frenay, M. (Marc), Mortemousque, I. (Isabelle), Coulet, F. (Florence), Colas, C. (Chrystelle), Soubrier, F., Sokolowska, J. (Johanna), Bronner, M. (Myriam), Lynch, H. (Henry), Snyder, C.L. (Carrie), Angelakos, M. (Maggie), Maskiell, J. (Judi), and Dite, G.S. (Gillian)
Abstract: BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associati
Published: 2013
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15. Characterization of MYG1 gene and protein: Subcellular distribution and function

Author: Philips, M-A, Vikeså, J., Luuk, H., Jønson, L., Lilleväli, K., Rehfeld, J.F., Vasar, E., Kõks, S., Nielsen, F.C., Philips, M-A, Vikeså, J., Luuk, H., Jønson, L., Lilleväli, K., Rehfeld, J.F., Vasar, E., Kõks, S., and Nielsen, F.C.
Abstract: Background information. MYG1 [Melanocyte proliferating gene 1, also known as Gamm1 (NM_021640)] is a recently described gene of unknown function. MYG1 orthologues are found in simple as well as complex eukaryotes. According to sequence homology, MYG1 is considered to have a metal‐dependent protein hydrolase (UPF0160) domain. The purpose of the present study was to determine the expression and subcellular localization of MYG1 protein and to identify physiological processes connected to MYG1 function. Results. Human and mouse MYG1 is ubiquitously expressed, with the highest level in the testis. Analysis of mouse embryos moreover revealed a uniform Myg1 expression at E (embryonic day) 8.5, but at E11.75 expression becomes restricted predominantly to the developing brain and eye, limb buds and tail region. MYG1 exhibits a mitochondrial targeting signal in the N‐terminal region and a Pat7‐type nuclear localization signal in the region between amino acids 33–39 and localizes to these compartments. No active shuttling of MYG1 between the nucleus and the mitochondria was detected and the distribution of MYG1 was not dependent on the phase of the cell cycle. Immunoprecipitation of C‐terminally FLAG‐tagged MYG1 from HeLa cells did not identify any co‐precipitated proteins. siRNA (short interfering RNA)‐mediated knockdown of MYG1 mRNA was mainly followed by changes in the level of transcripts encoding factors involved in developmental tissue patterning and growth as well as immune‐related processes. Conclusions. Taken together, we infer that MYG1 is a ubiquitous nucleo‐mitochondrial protein, with differential pattern and level of expression during embryonic development. MYG1 expression in normal adult tissues is stable and our data suggest MYG1 involvement in early developmental processes and also in adult stress/illness conditions.
Published: 2012

16. Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers

Author: Antoniou, A.C. (Antonis), Kartsonaki, C. (Christiana), Sinilnikova, O. (Olga), Soucy, P. (Penny), McGuffog, L. (Lesley), Healey, S. (Sue), Lee, A. (Andrew), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Cattaneo, E. (Elisa), Barile, M. (Monica), Pensotti, V. (Valeria), Pasini, B. (Barbara), Dolcetti, R. (Riccardo), Giannini, G. (Giuseppe), Putignano, A.L., Varesco, L. (Liliana), Radice, P. (Paolo), Mai, P.L. (Phuong), Greene, M.H. (Mark), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Gerdes, A-M. (Anne-Marie), Kruse, T.A. (Torben), Jensen, U.B., Cruger, D. (Dorthe), Caligo, M.A. (Maria), Laitman, Y. (Yael), Milgrom, R. (Roni), Kaufman, B. (Bella), Paluch-Shimon, S. (Shani), Friedman, E. (Eitan), Loman, N. (Niklas), Harbst, K. (Katja), Lindblom, A. (Annika), Melin, B. (Beatrice), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Rebbeck, R. (Timothy), Jakubowska, A. (Anna), Lubinski, J. (Jan), Gronwald, J. (Jacek), Huzarski, T. (Tomasz), Byrski, T. (Tomasz), Cybulski, C. (Cezary), Górski, B. (Bohdan), Osorio, A. (Ana), Cajal, T.R., Fostira, F. (Florentia), Andres, R. (Raquel), Benitez, J. (Javier), Hamann, U. (Ute), Hogervorst, F.B.L. (Frans), Rookus, M.A. (Matti), Hooning, M.J. (Maartje), Nelen, M.R. (Marcel), Luijt, R.B. (Rob) van der, Os, T.A.M. (Theo) van, Asperen, C.J. (Christi) van, Devilee, P. (Peter), Meijers-Heijboer, H. (Hanne), Garcia, E.B.G., Peock, S. (Susan), Cook, M. (Margaret), Frost, D., Platte, R. (Radka), Leyland, J. (Jean), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Izatt, L. (Louise), Davidson, R. (Rosemarie), Eccles, D. (Diana), Ong, K.-R., Douglas, F. (Fiona), Paterson, J. (Joan), Kennedy, M.J. (John), Miedzybrodzka, Z. (Zosia), Godwin, A.K. (Andrew), Stoppa-Lyonnet, D. (Dominique), Buecher, B. (Bruno), Belotti, M. (Muriel), Tirapo, C. (Carole), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Lasset, C. (Christine), Leroux, D. (Dominique), Faivre, L. (Laurence), Bronner, M. (Myriam), Prieur, F. (Fabienne), Nogues, C. (Catherine), Rouleau, E. (Etienne), Pujol, P. (Pascal), Coupier, I. (Isabelle), Frenay, M. (Marc), Hopper, J. (John), Daly, M.J. (Mark), Terry, M-B. (Mary-beth), John, E.M. (Esther), Buys, S.S. (Saundra), Yassin, Y. (Yosuf), Miron, A. (Alexander), Goldgar, D. (David), Singer, C.F. (Christian), Tea, M.-K., Pfeiler, G. (Georg), Dressler, C. (Catherina), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Ejlertsen, B. (Bent), Barkardottir, R.B. (Rosa), Kircchoff, T. (Tomas), Offit, K. (Kenneth), Piedmonte, M. (Marion), Rodriguez, G.C. (Gustavo), Small, L. (Laurie), Boggess, J.F. (John), Blank, S.V. (Stephanie), Basil, J. (Jack), Azodi, M. (Masoud), Toland, A.E. (Amanda), Montagna, M. (Marco), Tognazzo, S. (Silvia), Agata, S. (Simona), Imyanitov, E.N. (Evgeny), Janavicius, R. (Ramunas), Lázaro, C. (Conxi), Blanco, I. (Ignacio), Pharoah, P.D.P. (Paul), Sucheston, L. (Lara), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Olah, E. (Edith), Bozsik, A. (Aniko), Teo, S.-H. (Soo-Hwang), Seldon, J.L. (Joyce), Beattie, M.S. (Mary), Rensburg, E.J. (Elizabeth) van, Sluiter, M.D. (Michelle), Diez, O. (Orland), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Engel, C. (Christoph), Meindl, A. (Alfons), Ruehl, I. (Ina), Varon-Mateeva, R. (Raymonda), Kast, K. (Karin), Deissler, H. (Helmut), Niederacher, D. (Dieter), Arnold, N. (Norbert), Gadzicki, D. (Dorothea), Schönbuchner, I. (Ines), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Dumont, M. (Martine), Chiquette, J. (Jocelyne), Tischkowitz, M. (Marc), Chenevix-Trench, G. (Georgia), Beesley, J. (Jonathan), Spurdle, A.B. (Amanda), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Fredericksen, Z. (Zachary), Wang, X. (Xing), Pankratz, V.S. (Shane), Couch, F.J. (Fergus), Simard, J. (Jacques), Easton, D.F. (Douglas), Karlsson, P. (Per), Nordling, M. (Margareta), Bergman, A. (Annika), Einbeigi, Z. (Zakaria), Stenmark-Askmalm, M. (M.), Liedgren, S. (Sigrun), Borg, Å. (Åke), Olsson, H. (Hans), Kristoffersson, U. (Ulf), Jernström, H. (H.), Henriksson, K. (Karin), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Barbany-Bustinza, G. (Gisela), Rantala, J. (Johanna), Grönberg, H. (Henrik), Stattin, E.-L., Emanuelsson, M. (Monica), Brandell, R.R., Dahl, N. (Niklas), Verhoef, S., Verheus, M. (Martijn), Veer, L.J. (Laura) van 't, Leeuwen, F.E. (Flora) van, Collée, J.M. (Margriet), Ouweland, A.M.W. (Ans) van den, Jager, A. (Agnes), Tilanus-Linthorst, M.M.A. (Madeleine), Seynaeve, C.M. (Caroline), Wijnen, J.T. (Juul), Vreeswijk, M.P. (Maaike), Tollenaar, R.A.E.M. (Rob), Ligtenberg, M.J. (Marjolijn), Hoogerbrugge, N. (Nicoline), Ausems, M.G.E.M. (Margreet), Aalfs, C.M. (Cora), Gille, J.J.P. (Jan), Waisfisz, Q. (Quinten), Gómez García, E.B. (Encarna), Roozendaal, C.E. (Cees) van, Blok, M.J. (Marinus), Caanen, B., Oosterwijk, J.C., Hout, A.H. (Annemarie) van der, Mourits, M.J., Vasen, H.F. (Hans), Gregory, H. (Helen), Morrison, P.J. (Patrick), Jeffers, L. (Lisa), Cole, T.J. (Trevor), McKeown, C. (Carole), Hoffman, J. (Jonathan), Donaldson, A. (Alan), Downing, S. (Sarah), Taylor, A. (Amy), Murray, A. (Alexandra), Rogers, M.T. (Mark), McCann, E. (Emma), Porteous, M.E. (Mary), Drummond, S. (Sarah), Brewer, C. (Carole), Kivuva, E. (Emma), Searle, A. (Anne), Goodman, S. (Selina), Hill, K. (Kathryn), Murday, V. (Victoria), Bradshaw, N. (Nicola), Snadden, L. (Lesley), Longmuir, M. (Mark), Watt, C. (Catherine), Gibson, S. (Sarah), Haque, E. (Eshika), Tobias, E. (Ed), Duncan, A. (Alexis), Jacobs, C. (Chris), Langman, C. (Caroline), Whaite, A. (Anna), Dorkins, H. (Huw), Barwell, J. (Julian), Chu, C. (Chengbin), Miller, J. (Julie), Ellis, I.O. (Ian), Houghton, C. (Catherine), Side, L. (Lucy), Male, A. (Alison), Berlin, C. (Cheryl), Eason, J. (Jacqueline), Collier, R. (Rebecca), Claber, O. (Oonagh), Jobson, I. (Irene), Walker, L.J. (Lisa), McLeod, D. (Diane), Halliday, D. (Dorothy), Durell, S. (Sarah), Stayner, B. (Barbara), Shanley, S. (Susan), Rahman, N. (Nazneen), Houlston, R. (Richard), Bancroft, E.K. (Elizabeth), D'Mello, L. (Lucia), Page, E. (Elizabeth), Ardern-Jones, A. (Audrey), Kohut, K. (Kelly), Wiggins, J. (Jennifer), Castro, E. (Elena), Mitra, A. (Anita), Robertson, L. (Lisa), Quarrell, O. (Oliver), Bardsley, C. (Cathryn), Ehrencrona, H. (Hans), Hodgson, S.V. (Shirley), Barton, D.E. (David), Goff, S. (Sheila), Brice, G. (Glen), Winchester, L. (Lizzie), Eddy, C. (Charlotte), Tripathi, V. (Vishakha), Attard, V. (Virginia), Lucassen, A. (Anneke), Crawford, G. (Gillian), McBride, D. (Donna), Smalley, S. (Sarah), Adlard, J.W. (Julian), Arver, B. (Brita Wasteson), Antoniou, A.C. (Antonis), Kartsonaki, C. (Christiana), Sinilnikova, O. (Olga), Soucy, P. (Penny), McGuffog, L. (Lesley), Healey, S. (Sue), Lee, A. (Andrew), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Cattaneo, E. (Elisa), Barile, M. (Monica), Pensotti, V. (Valeria), Pasini, B. (Barbara), Dolcetti, R. (Riccardo), Giannini, G. (Giuseppe), Putignano, A.L., Varesco, L. (Liliana), Radice, P. (Paolo), Mai, P.L. (Phuong), Greene, M.H. (Mark), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Gerdes, A-M. (Anne-Marie), Kruse, T.A. (Torben), Jensen, U.B., Cruger, D. (Dorthe), Caligo, M.A. (Maria), Laitman, Y. (Yael), Milgrom, R. (Roni), Kaufman, B. (Bella), Paluch-Shimon, S. (Shani), Friedman, E. (Eitan), Loman, N. (Niklas), Harbst, K. (Katja), Lindblom, A. (Annika), Melin, B. (Beatrice), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Rebbeck, R. (Timothy), Jakubowska, A. (Anna), Lubinski, J. (Jan), Gronwald, J. (Jacek), Huzarski, T. (Tomasz), Byrski, T. (Tomasz), Cybulski, C. (Cezary), Górski, B. (Bohdan), Osorio, A. (Ana), Cajal, T.R., Fostira, F. (Florentia), Andres, R. (Raquel), Benitez, J. (Javier), Hamann, U. (Ute), Hogervorst, F.B.L. (Frans), Rookus, M.A. (Matti), Hooning, M.J. (Maartje), Nelen, M.R. (Marcel), Luijt, R.B. (Rob) van der, Os, T.A.M. (Theo) van, Asperen, C.J. (Christi) van, Devilee, P. (Peter), Meijers-Heijboer, H. (Hanne), Garcia, E.B.G., Peock, S. (Susan), Cook, M. (Margaret), Frost, D., Platte, R. (Radka), Leyland, J. (Jean), Evans, D.G. (Gareth), Lalloo, F. (Fiona), Eeles, R. (Rosalind), Izatt, L. (Louise), Davidson, R. (Rosemarie), Eccles, D. (Diana), Ong, K.-R., Douglas, F. (Fiona), Paterson, J. (Joan), Kennedy, M.J. (John), Miedzybrodzka, Z. (Zosia), Godwin, A.K. (Andrew), Stoppa-Lyonnet, D. (Dominique), Buecher, B. (Bruno), Belotti, M. (Muriel), Tirapo, C. (Carole), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Lasset, C. (Christine), Leroux, D. (Dominique), Faivre, L. (Laurence), Bronner, M. (Myriam), Prieur, F. (Fabienne), Nogues, C. (Catherine), Rouleau, E. (Etienne), Pujol, P. (Pascal), Coupier, I. (Isabelle), Frenay, M. (Marc), Hopper, J. (John), Daly, M.J. (Mark), Terry, M-B. (Mary-beth), John, E.M. (Esther), Buys, S.S. (Saundra), Yassin, Y. (Yosuf), Miron, A. (Alexander), Goldgar, D. (David), Singer, C.F. (Christian), Tea, M.-K., Pfeiler, G. (Georg), Dressler, C. (Catherina), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Ejlertsen, B. (Bent), Barkardottir, R.B. (Rosa), Kircchoff, T. (Tomas), Offit, K. (Kenneth), Piedmonte, M. (Marion), Rodriguez, G.C. (Gustavo), Small, L. (Laurie), Boggess, J.F. (John), Blank, S.V. (Stephanie), Basil, J. (Jack), Azodi, M. (Masoud), Toland, A.E. (Amanda), Montagna, M. (Marco), Tognazzo, S. (Silvia), Agata, S. (Simona), Imyanitov, E.N. (Evgeny), Janavicius, R. (Ramunas), Lázaro, C. (Conxi), Blanco, I. (Ignacio), Pharoah, P.D.P. (Paul), Sucheston, L. (Lara), Karlan, B.Y. (Beth), Walsh, C.S. (Christine), Olah, E. (Edith), Bozsik, A. (Aniko), Teo, S.-H. (Soo-Hwang), Seldon, J.L. (Joyce), Beattie, M.S. (Mary), Rensburg, E.J. (Elizabeth) van, Sluiter, M.D. (Michelle), Diez, O. (Orland), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Engel, C. (Christoph), Meindl, A. (Alfons), Ruehl, I. (Ina), Varon-Mateeva, R. (Raymonda), Kast, K. (Karin), Deissler, H. (Helmut), Niederacher, D. (Dieter), Arnold, N. (Norbert), Gadzicki, D. (Dorothea), Schönbuchner, I. (Ines), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Dumont, M. (Martine), Chiquette, J. (Jocelyne), Tischkowitz, M. (Marc), Chenevix-Trench, G. (Georgia), Beesley, J. (Jonathan), Spurdle, A.B. (Amanda), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Fredericksen, Z. (Zachary), Wang, X. (Xing), Pankratz, V.S. (Shane), Couch, F.J. (Fergus), Simard, J. (Jacques), Easton, D.F. (Douglas), Karlsson, P. (Per), Nordling, M. (Margareta), Bergman, A. (Annika), Einbeigi, Z. (Zakaria), Stenmark-Askmalm, M. (M.), Liedgren, S. (Sigrun), Borg, Å. (Åke), Olsson, H. (Hans), Kristoffersson, U. (Ulf), Jernström, H. (H.), Henriksson, K. (Karin), Wachenfeldt, A. (Anna) von, Liljegren, A. (Annelie), Barbany-Bustinza, G. (Gisela), Rantala, J. (Johanna), Grönberg, H. (Henrik), Stattin, E.-L., Emanuelsson, M. (Monica), Brandell, R.R., Dahl, N. (Niklas), Verhoef, S., Verheus, M. (Martijn), Veer, L.J. (Laura) van 't, Leeuwen, F.E. (Flora) van, Collée, J.M. (Margriet), Ouweland, A.M.W. (Ans) van den, Jager, A. (Agnes), Tilanus-Linthorst, M.M.A. (Madeleine), Seynaeve, C.M. (Caroline), Wijnen, J.T. (Juul), Vreeswijk, M.P. (Maaike), Tollenaar, R.A.E.M. (Rob), Ligtenberg, M.J. (Marjolijn), Hoogerbrugge, N. (Nicoline), Ausems, M.G.E.M. (Margreet), Aalfs, C.M. (Cora), Gille, J.J.P. (Jan), Waisfisz, Q. (Quinten), Gómez García, E.B. (Encarna), Roozendaal, C.E. (Cees) van, Blok, M.J. (Marinus), Caanen, B., Oosterwijk, J.C., Hout, A.H. (Annemarie) van der, Mourits, M.J., Vasen, H.F. (Hans), Gregory, H. (Helen), Morrison, P.J. (Patrick), Jeffers, L. (Lisa), Cole, T.J. (Trevor), McKeown, C. (Carole), Hoffman, J. (Jonathan), Donaldson, A. (Alan), Downing, S. (Sarah), Taylor, A. (Amy), Murray, A. (Alexandra), Rogers, M.T. (Mark), McCann, E. (Emma), Porteous, M.E. (Mary), Drummond, S. (Sarah), Brewer, C. (Carole), Kivuva, E. (Emma), Searle, A. (Anne), Goodman, S. (Selina), Hill, K. (Kathryn), Murday, V. (Victoria), Bradshaw, N. (Nicola), Snadden, L. (Lesley), Longmuir, M. (Mark), Watt, C. (Catherine), Gibson, S. (Sarah), Haque, E. (Eshika), Tobias, E. (Ed), Duncan, A. (Alexis), Jacobs, C. (Chris), Langman, C. (Caroline), Whaite, A. (Anna), Dorkins, H. (Huw), Barwell, J. (Julian), Chu, C. (Chengbin), Miller, J. (Julie), Ellis, I.O. (Ian), Houghton, C. (Catherine), Side, L. (Lucy), Male, A. (Alison), Berlin, C. (Cheryl), Eason, J. (Jacqueline), Collier, R. (Rebecca), Claber, O. (Oonagh), Jobson, I. (Irene), Walker, L.J. (Lisa), McLeod, D. (Diane), Halliday, D. (Dorothy), Durell, S. (Sarah), Stayner, B. (Barbara), Shanley, S. (Susan), Rahman, N. (Nazneen), Houlston, R. (Richard), Bancroft, E.K. (Elizabeth), D'Mello, L. (Lucia), Page, E. (Elizabeth), Ardern-Jones, A. (Audrey), Kohut, K. (Kelly), Wiggins, J. (Jennifer), Castro, E. (Elena), Mitra, A. (Anita), Robertson, L. (Lisa), Quarrell, O. (Oliver), Bardsley, C. (Cathryn), Ehrencrona, H. (Hans), Hodgson, S.V. (Shirley), Barton, D.E. (David), Goff, S. (Sheila), Brice, G. (Glen), Winchester, L. (Lizzie), Eddy, C. (Charlotte), Tripathi, V. (Vishakha), Attard, V. (Virginia), Lucassen, A. (Anneke), Crawford, G. (Gillian), McBride, D. (Donna), Smalley, S. (Sarah), Adlard, J.W. (Julian), and Arver, B. (Brita Wasteson)
Abstract: Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r2= 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 × 10-9for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 × 10-8for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.
Published: 2011
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17. Genetic variation at 9p22.2 and ovarian cancer risk for BRCA1 and BRCA2 mutation carriers

Author: Ramus, S.J. (Susan), Kartsonaki, C. (Christiana), Gayther, S.A. (Simon), Pharoah, P.D.P. (Paul), Sinilnikova, O. (Olga), Beesley, J. (Jonathan), Chenevix-Trench, G. (Georgia), McGuffog, L. (Lesley), Healey, S. (Sue), Couch, F.J. (Fergus), Wang, X. (Xing), Fredericksen, Z. (Zachary), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Roversi, G. (Gaia), Barile, M. (Monica), Viel, A. (Alessandra), Allavena, A. (Anna), Ottini, L. (Laura), Papi, L. (Laura), Gismondi, V. (Viviana), Capra, F. (Fabio), Radice, P. (Paolo), Greene, M.H. (Mark), Mai, P.L. (Phuong), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Gerdes, A-M. (Anne-Marie), Kruse, T.A. (Torben), Cruger, D. (Dorthe), Jensen, U.B., Caligo, M.A. (Maria), Olsson, H. (Hkan), Kristoffersson, U. (Ulf), Lindblom, A. (Annika), Arver, B. (Brita Wasteson), Karlsson, P. (Per), Stenmark-Askmalm, M. (M.), Borg, Å. (Åke), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Jakubowska, A. (Anna), Lubinski, J. (Jan), Huzarski, T. (Tomasz), Byrski, T. (Tomasz), Gronwald, J. (Jacek), Górski, B. (Bohdan), Cybulski, C. (Cezary), Dbniak, T. (Tadeusz), Osorio, A. (Ana), Durán, M. (Mercedes), Tejada, M.-I., Benitez, J. (Javier), Hamann, U. (Ute), Rookus, M.A. (Matti), Verhoef, S., Tilanus-Linthorst, M.M.A. (Madeleine), Vreeswijk, M.P. (Maaike), Bodmer, D. (Danielle), Ausems, M.G.E.M. (Margreet), Os, T.A.M. (Theo) van, Blok, M.J. (Marinus), Meijers-Heijboer, H. (Hanne), Peock, S. (Susan), Cook, M. (Margaret), Oliver, C.T. (Clare), Frost, D. (Debra), Dunning, A.M. (Alison), Evans, D.G. (Gareth), Eeles, R. (Rosalind), Pichert, G. (Gabriella), Cole, T.J. (Trevor), Hodgson, S.V. (Shirley), Brewer, C. (Carole), Morrison, P.J. (Patrick), Porteous, M.E. (Mary), Kennedy, M.J. (John), Rogers, M.T. (Mark), Side, L. (Lucy), Donaldson, A. (Alan), Gregory, H. (Helen), Godwin, A.K. (Andrew), Stoppa-Lyonnet, D. (Dominique), Moncoutier, V. (Virginie), Castera, L. (Laurent), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Bonadona, V. (Valérie), Leroux, D. (Dominique), Faivre, L. (Laurence), Lidereau, R. (Rosette), Nogues, C. (Catherine), Bignon, Y.-J. (Yves-Jean), Prieur, F. (Fabienne), Collonge-Rame, M.-A., Vénat-Bouvet, L. (Laurence), Fert-Ferrer, S. (Sandra), Miron, A. (Alexander), Buys, S.S. (Saundra), Hopper, J. (John), Daly, M.J. (Mark), John, E.M. (Esther), Terry, M-B. (Mary-beth), Goldgar, D. (David), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Agnarsson, B.A. (Bjarni), Offit, K. (Kenneth), Kircchoff, T. (Tomas), Vijai, J. (Joseph), Dutra-Clarke, A. (Ana), Przybylo, J.A. (Jennifer), Montagna, M. (Marco), Casella, C. (Cinzia), Imyanitov, E.N. (Evgeny), Janavicius, R. (Ramunas), Blanco, I. (Ignacio), Lázaro, C. (Conxi), Moysich, K.B. (Kirsten), Karlan, B.Y. (Beth), Gross, J. (Jenny), Beattie, M.S. (Mary), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Meindl, A. (Alfons), Ruehl, I. (Ina), Fiebig, B. (Britta), Sutter, C. (Christian), Arnold, N. (Norbert), Deissler, H. (Helmut), Varon-Mateeva, R. (Raymonda), Kast, K. (Karin), Niederacher, D. (Dieter), Gadzicki, D. (Dorothea), Ejlertsen, B. (Bent), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Simard, J. (Jacques), Soucy, P. (Penny), Spurdle, A.B. (Amanda), Holland, H. (Helene), Easton, D.F. (Douglas), Antoniou, A.C. (Antonis), Asperen, C.J. (Christi) van, Ramus, S.J. (Susan), Kartsonaki, C. (Christiana), Gayther, S.A. (Simon), Pharoah, P.D.P. (Paul), Sinilnikova, O. (Olga), Beesley, J. (Jonathan), Chenevix-Trench, G. (Georgia), McGuffog, L. (Lesley), Healey, S. (Sue), Couch, F.J. (Fergus), Wang, X. (Xing), Fredericksen, Z. (Zachary), Peterlongo, P. (Paolo), Manoukian, S. (Siranoush), Peissel, B. (Bernard), Zaffaroni, D. (D.), Roversi, G. (Gaia), Barile, M. (Monica), Viel, A. (Alessandra), Allavena, A. (Anna), Ottini, L. (Laura), Papi, L. (Laura), Gismondi, V. (Viviana), Capra, F. (Fabio), Radice, P. (Paolo), Greene, M.H. (Mark), Mai, P.L. (Phuong), Andrulis, I.L. (Irene), Glendon, G. (Gord), Ozcelik, H. (Hilmi), Thomassen, M. (Mads), Gerdes, A-M. (Anne-Marie), Kruse, T.A. (Torben), Cruger, D. (Dorthe), Jensen, U.B., Caligo, M.A. (Maria), Olsson, H. (Hkan), Kristoffersson, U. (Ulf), Lindblom, A. (Annika), Arver, B. (Brita Wasteson), Karlsson, P. (Per), Stenmark-Askmalm, M. (M.), Borg, Å. (Åke), Neuhausen, S.L. (Susan), Ding, Y.C. (Yuan), Nathanson, K.L. (Katherine), Domchek, S.M. (Susan), Jakubowska, A. (Anna), Lubinski, J. (Jan), Huzarski, T. (Tomasz), Byrski, T. (Tomasz), Gronwald, J. (Jacek), Górski, B. (Bohdan), Cybulski, C. (Cezary), Dbniak, T. (Tadeusz), Osorio, A. (Ana), Durán, M. (Mercedes), Tejada, M.-I., Benitez, J. (Javier), Hamann, U. (Ute), Rookus, M.A. (Matti), Verhoef, S., Tilanus-Linthorst, M.M.A. (Madeleine), Vreeswijk, M.P. (Maaike), Bodmer, D. (Danielle), Ausems, M.G.E.M. (Margreet), Os, T.A.M. (Theo) van, Blok, M.J. (Marinus), Meijers-Heijboer, H. (Hanne), Peock, S. (Susan), Cook, M. (Margaret), Oliver, C.T. (Clare), Frost, D. (Debra), Dunning, A.M. (Alison), Evans, D.G. (Gareth), Eeles, R. (Rosalind), Pichert, G. (Gabriella), Cole, T.J. (Trevor), Hodgson, S.V. (Shirley), Brewer, C. (Carole), Morrison, P.J. (Patrick), Porteous, M.E. (Mary), Kennedy, M.J. (John), Rogers, M.T. (Mark), Side, L. (Lucy), Donaldson, A. (Alan), Gregory, H. (Helen), Godwin, A.K. (Andrew), Stoppa-Lyonnet, D. (Dominique), Moncoutier, V. (Virginie), Castera, L. (Laurent), Mazoyer, S. (Sylvie), Barjhoux, L. (Laure), Bonadona, V. (Valérie), Leroux, D. (Dominique), Faivre, L. (Laurence), Lidereau, R. (Rosette), Nogues, C. (Catherine), Bignon, Y.-J. (Yves-Jean), Prieur, F. (Fabienne), Collonge-Rame, M.-A., Vénat-Bouvet, L. (Laurence), Fert-Ferrer, S. (Sandra), Miron, A. (Alexander), Buys, S.S. (Saundra), Hopper, J. (John), Daly, M.J. (Mark), John, E.M. (Esther), Terry, M-B. (Mary-beth), Goldgar, D. (David), Hansen, T.V.O. (Thomas), Jønson, L. (Lars), Agnarsson, B.A. (Bjarni), Offit, K. (Kenneth), Kircchoff, T. (Tomas), Vijai, J. (Joseph), Dutra-Clarke, A. (Ana), Przybylo, J.A. (Jennifer), Montagna, M. (Marco), Casella, C. (Cinzia), Imyanitov, E.N. (Evgeny), Janavicius, R. (Ramunas), Blanco, I. (Ignacio), Lázaro, C. (Conxi), Moysich, K.B. (Kirsten), Karlan, B.Y. (Beth), Gross, J. (Jenny), Beattie, M.S. (Mary), Schmutzler, R.K. (Rita), Wapenschmidt, B. (Barbara), Meindl, A. (Alfons), Ruehl, I. (Ina), Fiebig, B. (Britta), Sutter, C. (Christian), Arnold, N. (Norbert), Deissler, H. (Helmut), Varon-Mateeva, R. (Raymonda), Kast, K. (Karin), Niederacher, D. (Dieter), Gadzicki, D. (Dorothea), Ejlertsen, B. (Bent), Caldes, T. (Trinidad), Hoya, M. (Miguel) de La, Nevanlinna, H. (Heli), Aittomäki, K. (Kristiina), Simard, J. (Jacques), Soucy, P. (Penny), Spurdle, A.B. (Amanda), Holland, H. (Helene), Easton, D.F. (Douglas), Antoniou, A.C. (Antonis), and Asperen, C.J. (Christi) van
Abstract: Background Germline mutations in the BRCA1 and BRCA2 genes are associated with increased risks of breast and ovarian cancers. Although several common variants have been associated with breast cancer susceptibility in mutation carriers, none have been associated with ovarian cancer susceptibility. A genome-wide association study recently identified an association between the rare allele of the single-nucleotide polymorphism (SNP) rs3814113 (ie, the C allele) at 9p22.2 and decreased risk of ovarian cancer for women in the general population. We evaluated the association of this SNP with ovarian cancer risk among BRCA1 or BRCA2 mutation carriers by use of data from the Consortium of Investigators of Modifiers of BRCA1/2. Method sWe genotyped rs3814113 in 10029 BRCA1 mutation carriers and 5837 BRCA2 mutation carriers. Associations with ovarian and breast cancer were assessed with a retrospective likelihood approach. All statistical tests were two-sided. Results The minor allele of rs3814113 was associated with a reduced risk of ovarian cancer among BRCA1 mutation carriers (per-allele hazard ratio of ovarian cancer = 0.78, 95% confidence interval = 0.72 to 0.85; P = 4.8 × 10-9) and BRCA2 mutation carriers (hazard ratio of ovarian cancer = 0.78, 95% confidence interval = 0.67 to 0.90; P = 5.5 × 10-4). This SNP was not associated with breast cancer risk among either BRCA1 or BRCA2 mutation carriers. BRCA1 mutation carriers with the TT genotype at SNP rs3814113 were predicted to have an ovarian cancer risk to age 80 years of 48%, and those with the CC genotype were predicted to have a risk of 33%. Conclusion Common genetic variation at the 9p22.2 locus was associated with decreased risk of ovarian cancer for carriers of a BRCA1 or BRCA2 mutation.
Published: 2011
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18. Genetic variation at 9p22.2 and ovarian cancer risk for BRCA1 and BRCA2 mutation carriers

Author: Ramus, S, Kartsonaki, C, Gayther, S, Pharoah, P, Sinilnikova, O, Beesley, J, Chen, X, Mcguffog, L, Healey, S, Couch, F, Wang, X, Fredericksen, Z, Peterlongo, P, Manoukian, S, Peissel, B, Zaffaroni, D, Roversi, G, Barile, M, Viel, A, Allavena, A, Ottini, L, Papi, L, Gismondi, V, Capra, F, Radice, P, Greene, M, Mai, P, Andrulis, I, Glendon, G, Ozcelik, H, Thomassen, M, Gerdes, A, Kruse, T, Cruger, D, Jensen, U, Caligo, M, Olsson, H, Kristoffersson, U, Lindblom, A, Arver, B, Karlsson, P, Stenmark Askmalm, M, Borg, A, Neuhausen, S, Ding, Y, Nathanson, K, Domchek, S, Jakubowska, A, Lubiński, J, Huzarski, T, Byrski, T, Gronwald, J, Górski, B, Cybulski, C, Dębniak, T, Osorio, A, Durán, M, Tejada, M, Benítez, J, Hamann, U, Rookus, M, Verhoef, S, Tilanus Linthorst, M, Vreeswijk, M, Bodmer, D, Ausems, M, van Os, T, Asperen, C, Blok, M, Meijers Heijboer, H, Peock, S, Cook, M, Oliver, C, Frost, D, Dunning, A, Evans, D, Eeles, R, Pichert, G, Cole, T, Hodgson, S, Brewer, C, Morrison, P, Porteous, M, Kennedy, M, Rogers, M, Side, L, Donaldson, A, Gregory, H, Godwin, A, Stoppa Lyonnet, D, Moncoutier, V, Castera, L, Mazoyer, S, Barjhoux, L, Bonadona, V, Leroux, D, Faivre, L, Lidereau, R, Nogues, C, Bignon, Y, Prieur, F, Collonge Rame, M, Venat Bouvet, L, Fert Ferrer, S, Miron, A, Buys, S, Hopper, J, Daly, M, John, E, Terry, M, Goldgar, D, Hansen, T, Jønson, L, Ejlertsen, B, Agnarsson, B, Offit, K, Kirchhoff, T, Vijai, J, Dutra Clarke, A, Przybylo, J, Montagna, M, Casella, C, Imyanitov, E, Janavicius, R, Blanco, I, Lázaro, C, Moysich, K, Karlan, B, Gross, J, Beattie, M, Schmutzler, R, Wappenschmidt, B, Meindl, A, Ruehl, I, Fiebig, B, Sutter, C, Arnold, N, Deissler, H, Varon Mateeva, R, Kast, K, Niederacher, D, Gadzicki, D, Caldes, T, de la Hoya, M, Nevanlinna, H, Aittomäki, K, Simard, J, Soucy, P, Spurdle, A, Holland, H, Chenevix Trench, G, Easton, D, Antoniou, A, Ramus, SJ, Gayther, SA, Pharoah, PDP, Sinilnikova, OM, McGuffog, L, Couch, FJ, Greene, MH, Mai, PL, Andrulis, IL, Kruse, TA, Jensen, UB, Caligo, MA, Neuhausen, SL, Ding, YC, Nathanson, KL, Domchek, SM, Rookus, MA, Tilanus Linthorst, MA, Vreeswijk, MP, Ausems, MGEM, van Os, TA, Asperen, CJ, Blok, MJ, Meijers Heijboer, HEJ, Dunning, AM, Evans, DG, Morrison, PJ, Kennedy, MJ, Rogers, MT, Side, LE, Buys, SS, Hopper, JL, Daly, MB, John, EM, Terry, MB, Hansen, TvO, Agnarsson, BA, Dutra Clarke, AVC, Przybylo, JA, Imyanitov, EN, Moysich, KB, Karlan, BY, Beattie, MS, Spurdle, AB, Easton, DF, Antoniou, AC, ROVERSI, GAIA, Ramus, S, Kartsonaki, C, Gayther, S, Pharoah, P, Sinilnikova, O, Beesley, J, Chen, X, Mcguffog, L, Healey, S, Couch, F, Wang, X, Fredericksen, Z, Peterlongo, P, Manoukian, S, Peissel, B, Zaffaroni, D, Roversi, G, Barile, M, Viel, A, Allavena, A, Ottini, L, Papi, L, Gismondi, V, Capra, F, Radice, P, Greene, M, Mai, P, Andrulis, I, Glendon, G, Ozcelik, H, Thomassen, M, Gerdes, A, Kruse, T, Cruger, D, Jensen, U, Caligo, M, Olsson, H, Kristoffersson, U, Lindblom, A, Arver, B, Karlsson, P, Stenmark Askmalm, M, Borg, A, Neuhausen, S, Ding, Y, Nathanson, K, Domchek, S, Jakubowska, A, Lubiński, J, Huzarski, T, Byrski, T, Gronwald, J, Górski, B, Cybulski, C, Dębniak, T, Osorio, A, Durán, M, Tejada, M, Benítez, J, Hamann, U, Rookus, M, Verhoef, S, Tilanus Linthorst, M, Vreeswijk, M, Bodmer, D, Ausems, M, van Os, T, Asperen, C, Blok, M, Meijers Heijboer, H, Peock, S, Cook, M, Oliver, C, Frost, D, Dunning, A, Evans, D, Eeles, R, Pichert, G, Cole, T, Hodgson, S, Brewer, C, Morrison, P, Porteous, M, Kennedy, M, Rogers, M, Side, L, Donaldson, A, Gregory, H, Godwin, A, Stoppa Lyonnet, D, Moncoutier, V, Castera, L, Mazoyer, S, Barjhoux, L, Bonadona, V, Leroux, D, Faivre, L, Lidereau, R, Nogues, C, Bignon, Y, Prieur, F, Collonge Rame, M, Venat Bouvet, L, Fert Ferrer, S, Miron, A, Buys, S, Hopper, J, Daly, M, John, E, Terry, M, Goldgar, D, Hansen, T, Jønson, L, Ejlertsen, B, Agnarsson, B, Offit, K, Kirchhoff, T, Vijai, J, Dutra Clarke, A, Przybylo, J, Montagna, M, Casella, C, Imyanitov, E, Janavicius, R, Blanco, I, Lázaro, C, Moysich, K, Karlan, B, Gross, J, Beattie, M, Schmutzler, R, Wappenschmidt, B, Meindl, A, Ruehl, I, Fiebig, B, Sutter, C, Arnold, N, Deissler, H, Varon Mateeva, R, Kast, K, Niederacher, D, Gadzicki, D, Caldes, T, de la Hoya, M, Nevanlinna, H, Aittomäki, K, Simard, J, Soucy, P, Spurdle, A, Holland, H, Chenevix Trench, G, Easton, D, Antoniou, A, Ramus, SJ, Gayther, SA, Pharoah, PDP, Sinilnikova, OM, McGuffog, L, Couch, FJ, Greene, MH, Mai, PL, Andrulis, IL, Kruse, TA, Jensen, UB, Caligo, MA, Neuhausen, SL, Ding, YC, Nathanson, KL, Domchek, SM, Rookus, MA, Tilanus Linthorst, MA, Vreeswijk, MP, Ausems, MGEM, van Os, TA, Asperen, CJ, Blok, MJ, Meijers Heijboer, HEJ, Dunning, AM, Evans, DG, Morrison, PJ, Kennedy, MJ, Rogers, MT, Side, LE, Buys, SS, Hopper, JL, Daly, MB, John, EM, Terry, MB, Hansen, TvO, Agnarsson, BA, Dutra Clarke, AVC, Przybylo, JA, Imyanitov, EN, Moysich, KB, Karlan, BY, Beattie, MS, Spurdle, AB, Easton, DF, Antoniou, AC, and ROVERSI, GAIA
Abstract: Germline mutations in the BRCA1 and BRCA2 genes are associated with increased risks of breast and ovarian cancers. Although several common variants have been associated with breast cancer susceptibility in mutation carriers, none have been associated with ovarian cancer susceptibility. A genome-wide association study recently identified an association between the rare allele of the single-nucleotide polymorphism (SNP) rs3814113 (ie, the C allele) at 9p22.2 and decreased risk of ovarian cancer for women in the general population. We evaluated the association of this SNP with ovarian cancer risk among BRCA1 or BRCA2 mutation carriers by use of data from the Consortium of Investigators of Modifiers of BRCA1/2.
Published: 2011

19. Kajian Lahan Potensial untuk Budidaya Perikanan dari Citra Satelit di Pantai Timur Belitung

Author: Jonson Lumban-Gaol, Nyoman Metta N. Natih, and Marlis Yulianto
Subjects: budidaya, perikanan, satelit, penggunaan lahan, topografi, Geography (General), G1-922
Abstract: Pemetaan lahan yang potensial untuk budidaya perikanan dilakukan melalui pemetaan topografi dan tutupan lahan dari citra satelit serta survei lapang di perairan pantai Timur Belitung. Peta Topografi estimasi dari citra satelit mempunyai pola yang sama dengan hasil pengukuran terestris dimana ketinggian lahan semakin meningkat mulai dari garis pantai menuju daratan. Data hasil pengukuran topografi secara terestris lebih tinggi dari data topografi estimasi dari data satelit. Tipe pasut di perairan pantai Belitung timur adalah tipe tunggal. Data pasut ini digunakan menjadi acuan untuk pengukuran topografi secara terestris. Peta tutupan lahan hasil intrepretasi dari citra satelit diklasifikasikan menjadi kelas: hutan primer, hutan sekunder, belukar, rawa/air, lahan terbuka, permukiman dan galian tambang. Berdasarkan peta topografi, peta tutupan lahan dan data pasang surut maka lahan di wilayah kajian pesisir pantai Timur Belitung potensial dikembangkan untuk budidaya perikanan seluas 9.000 ha. ABSTRACT Mapping potential land for aquaculture was done through topography, and land cover mapping derived satellite imagery and field survey in the east coast of Belitung. Topographic data derived satellite, and terrestrial measurement shows that topographic patterns increase as we move from the coastal line to inland. Topographic data from the terrestrial measurement was higher than satellite estimations. The type of tide in the east coast Belitung’s is the diurnal type. Within this research, tidal data was used as a reference terrestrial topographic measurement. Land coverage maps from satellite images were classified into primary and secondary forests, grove forests, marsh/water lands, open land, inhabited land, and mining areas. According to topographic, land cover map, and tide pattern it can be confirmed that the eastern coastal area of Belitung has the potential to be developed into an aquaculture fishery area of 9,000 ha.
Published: 2018
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20. PEMETAAN GEOMORFOLOGI TERUMBU KARANG PULAU TUNDA MENGGUNAKAN KLASIFIKASI BERBASIS OBJEK

Author: Fahriansyah, Jonson Lumban Gaol, and James P Panjaitan
Subjects: Aquaculture. Fisheries. Angling, SH1-691
Abstract: Pemetaan zona geomorfologi terumbu karang di Pulau Tunda ini belum pernah dilakukan khususnya menggunakan klasifikasi citra berbasis objek. Hasil pemetaan ini dapat digunakan sebagai dasar informasi perencanaan dan pengembangan suatu kawasan menuju pemanfaatan yang optimal seperti contoh pemanfaatan sebagai kawasan ekowisata bahari. Penelitian ini bertujuan untuk memetakan zona geomorfologi terumbu karang Pulau Tunda denganmenggunakan klasifikasi berbasis objek. Bahan analisis menggunakan citra multispektral Worldview-2 dengan akuisisi data tanggal 25 Agustus 2013 dan profil batimetri. Klasifikasi memakai algoritma segmentasi multiresolusi. Klasifikasi dibagi kedalam 2 level klasifikasi. Parameter klasifikasi level 1 menggunakan scale sebesar 200, shape 0.6 dan compactness 0.4. Segmentasi level 2 menggunakan scale 30, shape 0.6 dan compactness 0.4. Klasifikasi segmentasi objek ini mampu menghasilkan peta dengan tingkat akurasi yang tinggi pada setiap level. Akurasi klasifikasi level 1 adalah sebesar 97% dan level 2 sebesar 91%.
Published: 2018
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21. ALGORITMA UNTUK DETEKSI TUMPAHAN MINYAK DI LAUT TIMOR MENGGUNAKAN CITRA MODIS

Author: Muhammad Sudibjo, Vincentius P. Siregar, and Jonson Lumban Gaol
Subjects: Aquaculture. Fisheries. Angling, SH1-691
Abstract: Tumpahan minyak di Laut Timor yang terjadi pada tahun 2009 telah menyebarkan minyak seluas 10.842.81 km2.Tumpahan minyak ini berhasil dideteksi oleh satelit Moderate Resolution Imaging Spectroradiometer (MODIS). Tujuan dari penelitian ini adalah membandingkan hasil deteksi tumpahan minyak dari beberapa algoritma dengan citra menggunakan citra MODIS dan melihat perbedaan visual yang dihasilkan. Algoritma yang digunakan adalah Oil Spill Index, Fluorescence Index, Principal Component Analysis (PCA), Normalized Difference Vegetation Index (NDVI). Visualisasi tumpahan minyak yang terlihat pada citra MODIS dengan algoritma oil spill indeks dan fluorescence index lebih cerah dibandingkan dengan badan air disekitarnya dan juga memiliki nilai piksel lebih tinggi, sedangkan visualisasi minyak menggunakan algoritma PCA dan NDVI lebih gelap dibandingkan dengan badan air disekitarnya dan juga memiliki nilai piksel yang lebih rendah. Hasil uji akurasi yang dilakukan terhadap algoritma oil splill index, fluorescence index, PCA, NDVI berturut-turut sebagai berikut 41%, 46%, 41%, dan 60%
Published: 2017
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22. HUBUNGAN KONSENTRASI KLOROFIL-A DAN SUHU PERMUKAAN LAUT DENGAN HASIL TANGKAPAN IKAN PELAGIS UTAMA DI PERAIRAN LAUT JAWA DARI CITRA SATELIT MODIS

Author: Ega Putra, Jonson Lumban Gaol, and Vincentius P. Siregar
Subjects: Aquaculture. Fisheries. Angling, SH1-691
Abstract: Penelitian ini bertujuan untuk mempelajari variasi spasial dan temporal konsentrasi klorofil-a dan suhu permukaan laut serta hubungannya dengan hasil tangkapan ikan pelagis di Laut Jawa. Hasil penelitian menunjukkan dalam tahun 2006-2010 terjadi kenaikan suhu permukan laut sebesar 1°C dimana suhu permukan laut rata-rata bulanan berkisar antara 27,9°C – 31,4°C. Suhu permukaan laut relatif lebih tinggi pada saat musim peralihan dibandingkan dengan musim barat dan musim timur. Konsentrasi klorofil-a pada wilayah penelitian berkisar antara 0,22 mg/m³- 1,15 mg/m³. Nilai konsentrasi klorofil-a setiap bulannya berfluktuasi mengikuti musim angin yang sedang berlangsung. Nilai maksimum konsentrasi klorofil-a terjadi pada musim Barat dan nilai minimumnya terjadi pada musim peralihan 2. Ikan layang, banyar dan tembang memiliki respon yang negatif terhadap suhu permukaan laut terutama pada musim timur. Sedangkan untuk ikan lemuru dan ikan tembang menunjukkan tidak adanya hubungan langsung antara suhu permukaan laut dengan nilai CPUE hasil tangkapan. Ikan lemuru dan ikan tembang menunjukkan adanya respon positif terhadap naiknya konsentrasi klorofil-a, sedangkan untuk ikan layang, banyar dan tongkol kenaikan nilai konsentrasi klorofil tidak berdampak langsung pada naiknya nilai CPUE ketiga jenis ikan ini
Published: 2017
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23. Perbandingan Klasifikasi SVM dan Decision Tree untuk Pemetaan Mangrove Berbasis Objek Menggunakan Citra Satelit Sentinel-2B di Gili Sulat, Lombok Timur

Author: Septiyan Firmansyah, Jonson Lumban Gaol, and Setyo Budi Susilo
Subjects: Environmental sciences, GE1-350
Abstract: Mangrove is one of the most important objects in wetland ecosystems. Mangrove research has been done, one of them is using remote sensing technology. This study aims to assess accuracy of object based image analysis (OBIA) approach on both Support Vector Machine (SVM) and Decision Tree classification methods to classify mangrove and estimate mangrove area in the field study. We selected Kawasan Konservasi Laut Daerah (KKLD) Gili Sulat as a research site. This research used Sentinel-2B satellite imagery. We took field data using stratified random sampling and the amount of the data we collected were 121 points. The classification analysis result with object based showed that SVM had an overall accuracy of 95 % (kappa = 0.86) and Decision Tree classification had an overall accuracy of 93 % (kappa = 0.82). It is caused SVM can reduce the error of classification than Decision Tree. Estimation result based on assessment showed that mangrove using SVM had 634.62 Ha while using Decision Tree had 590.47 Ha
Published: 2019
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24. ESTIMASI INTENSITAS UPWELLING PANTAI DARI SATELIT AQUAMODIS DI PERAIRAN SELATAN JAWA DAN BARAT SUMATERA

Author: Dortje Theodora Silubun, Jonson Lumban Gaol, and Yuli Naulita
Subjects: Aquaculture. Fisheries. Angling, SH1-691
Abstract: Upwelling musiman pada umumnya terjadi di sepanjang selatan jawa hingga barat Sumatera. Penelitian ini bertujuan untuk mengestimasi intensitas upwelling dari data SPL dan konsentrasi klorofil-a dari sensor satelit. Data SPL dan Klorofil-a yang digunakan adalah data satelit Aqua-MODIS level-3 dan data angin dari satelit Quikscat pada bulan Juli 2002 sampai Juni 2011. Indeks upwelling diperoleh dengan formula Coastal Upwelling Index (CUIx). Analisis statistik digunakan untuk melihat hubungan antara SPL dan klorofil dengan CUIx. Hasil penelitian menunjukan bahwa secara temporal upwelling terjadi pada musim timur, dengan kisaran SPL 25.10 – 27.30 °C dan konsentrasi klorofil-a 0.30 – 0.67 mg m-3. Namun pada tahun 2006 terjadi anomali intensitas upwelling yang ditandai dengan SPL yang turun mencapai 24.98 °C (Selatan Jawa) dan 25.97 °C (Barat Sumatera), konsentrasi klorofil-a meningkat 1.33 mg m-3 (Barat Sumatera) dan 3.71 mg m-3 (Selatan Jawa). Hasil analisis menunjukkan bahwa SPL memiliki hubungan yang sangat kuat dengan CUIx di Barat Sumatra (r=0.84). Sementara di perairan selatan Jawa, kedua parameter (SPL dan klorofil-a) menunjukkan hubungan yang sangat kuat dengan CUIx (r=0.86 yang untuk SPL dan r = 0.81 untuk klorofil-a).
Published: 2016
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25. Seagrass Mapping Based on Satellite Image Worldview-2 by Using Depth Invariant Index Method

Author: Agnestesya Manuputty, Jonson Lumban Gaol, and Syamsul Bahri Agus
Subjects: Oceanography, GC1-1581, Biology (General), QH301-705.5
Abstract: Seagrass has an important role in coastal areas, so it’s sustainability need to be maintained. One effort to preserve it is sustainable manner management of segrass based on the spatial data using remote sensing techniques. The aim of this study was to map seagrass ecosystems and to determining the accuracy level from classification results that obtained by the WorldView-2 images. This study was conducted in Karang Bongkok and Kotok Islands in August 2014 and March 2015. The satellite images data used on this study was WorldView-2 satellite images at the acquisition date of October 5, 2013. The method used to conduct image processing data is Depth Invariant Index (DII) using Support Vector Machine (SVM) classification. The result shows that seagrass mapping in Karang Bongkok and Kotok Islands using DII transformation has 19.5112 ha areas with 72% accuracy on Karang Bongkok Island and 2.5704 ha areas with of 83% accuracy on Kotok Island. Key words: Seagrass mapping, DII, SVM, Karang Bongkok, Kotok Island.
Published: 2015
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26. Reconstruction of sea level change in Southeast Asia waters using combined coastal sea level data and satellite altimetry data

Author: Parluhutan Manurung, Robert R Leben, Stefano Vignudelli, Jonson Lumban Gaol, Benjamin Hamlington, and Tong Phuoc Hoang Son
Subjects: Science (General), Q1-390, Environmental sciences, GE1-350
Published: 2014
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27. PEMETAAN SUMBER DAYA LAUT PULAU NIAS DENGAN TEKNOLOGI PENGINDERAAN JAUH SATELIT PASCA-TSUNAMI 2004

Author: Jonson Lumban Gaol, Risti Endriani Arhatin, Djisman Manurung, and Mujizat Kawaroe
Subjects: remote sensing, satellite, Nias, tsunami, chorophyll-a, coral reef, mangrove, Agriculture, Agriculture (General), S1-972
Abstract: Accurate and up-to-date information of marine resources is needed for optimum resource utilization. If the required information cannot be obtained with traditional field surveys, remote sensing as a tool for providing fast, efficient, and accurate information is used to detect the changes. The study aims to use remote sensing data for assessing distribustion and condition of marine resources in Nias water's before and after tsunami. Marine resources pararameter derived remote sensing data are sea surface temperature (SST), suspended solid matter, chlorphyll-a concentration, coral reef and mangrove distributions. Mapping and differences in coral reef and mangrove distribution were evaluated using two scans of Landsat image in 1989 and 2005. Sea surface temperature was derived from NOAA-AVHRR data, and chlorophyll-a concentration was derived from SeaWiFS data. The study showed that there were no significant changes of coral reef and mangrove distribution, SST, chlorophyll-a concentration after and before tsunami. Spectral analysis of SST and chlorophyll-a showed that the variability of the parameters was affected by monsoon system and global climate change, namely El Nino Southern Oscillation and Indian Ocean Dipole
Published: 2007

28. Jak3, STAT3, and STAT5 inhibit expression of miR-22, a novel tumor suppressor microRNA, in cutaneous T-Cell lymphoma

Author: Na, Sibbesen, Kl, Kopp, Iv, Litvinov, Jønson L, Willerslev-Olsen A, Fredholm S, Dl, Petersen, Nastasi C, Krejsgaard T, Lm, Lindahl, Gniadecki R, Np, Mongan, Sasseville D, Ma, Wasik, Iversen L, Cm, Bonefeld, Carsten Geisler, Woetmann A, and Odum N

29. Novel de novo BRCA2 mutation in a patient with a family history of breast cancer

Author: Eiberg Hans, Filtenborg-Barnkob Bettina, Albrechtsen Anders, Jønson Lars, Bisgaard Marie, Hansen Thomas, Ejlertsen Bent, and Nielsen Finn C
Subjects: Internal medicine, RC31-1245, Genetics, QH426-470
Abstract: Abstract Background BRCA2 germ-line mutations predispose to breast and ovarian cancer. Mutations are widespread and unclassified splice variants are frequently encountered. We describe the parental origin and functional characterization of a novel de novo BRCA2 splice site mutation found in a patient exhibiting a ductal carcinoma at the age of 40. Methods Variations were identified by denaturing high performance liquid chromatography (dHPLC) and sequencing of the BRCA1 and BRCA2 genes. The effect of the mutation on splicing was examined by exon trapping in COS-7 cells and by RT-PCR on RNA isolated from whole blood. The paternity was determined by single nucleotide polymorphism (SNP) microarray analysis. Parental origin of the de novo mutation was determined by establishing mutation-SNP haplotypes by variant specific PCR, while de novo and mosaic status was investigated by sequencing of DNA from leucocytes and carcinoma tissue. Results A novel BRCA2 variant in the splice donor site of exon 21 (nucleotide 8982+1 G→A/c.8754+1 G→A) was identified. Exon trapping showed that the mutation activates a cryptic splice site 46 base pairs 3' of exon 21, resulting in the inclusion of a premature stop codon and synthesis of a truncated BRCA2 protein. The aberrant splicing was verified by RT-PCR analysis on RNA isolated from whole blood of the affected patient. The mutation was not found in any of the patient's parents or in the mother's carcinoma, showing it is a de novo mutation. Variant specific PCR indicates that the mutation arose in the male germ-line. Conclusion We conclude that the novel BRCA2 splice variant is a de novo mutation introduced in the male spermatozoa that can be classified as a disease causing mutation.
Published: 2008
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30. Genetic variation at 9p22.2 and ovarian cancer risk for BRCA1 and BRCA2 mutation carriers

Author: Thomas v O Hansen, Amanda B. Spurdle, Anne-Marie Gerdes, Sue Healey, Per Karlsson, Tomasz Huzarski, Mary B. Daly, Mary Porteous, T. Caldes, Ulf Kristoffersson, Ignacio Blanco, A. Miron, Laurence Faivre, Barbara Wappenschmidt, Laurence Venat-Bouvet, Marie Stenmark Askmalm, Olga M. Sinilnikova, Susan Peock, Alessandra Viel, Conxi Lázaro, Katherine L. Nathanson, Laurent Castera, Douglas F. Easton, Susan L. Neuhausen, Jan Lubinski, Phuong L. Mai, Virginie Moncoutier, Paolo Radice, Heli Nevanlinna, Christi J Asperen, Xianshu Wang, Brita Arver, Christian Sutter, Senno Verhoef, Rosette Lidereau, Mary S Beattie, Bjarni A Agnarsson, Ina Ruehl, Monica Barile, Bent Ejlertsen, Laura Ottini, Catherine Noguès, Jennifer A. Przybylo, Cinzia Casella, Trevor Cole, Norbert Arnold, Sandra Fert-Ferrer, Hilmi Ozcelik, Irene L. Andrulis, Susan M. Domchek, Valérie Bonadona, Kirsten B. Moysich, David E. Goldgar, Anna Jakubowska, Paul D.P. Pharoah, Beth Y. Karlan, Jenny Gross, Gaia Roversi, Tadeusz Dębniak, Hanne Meijers-Heijboer, Susan J. Ramus, Dorthe G. Crüger, Zachary S. Fredericksen, Siranoush Manoukian, Viviana Gismondi, Maria A. Caligo, Helene Holland, Laure Barjhoux, Gord Glendon, Ana Osorio, Jacques Simard, John L. Hopper, Mercedes Durán, Kristiina Aittomäki, Håkan Olsson, Mads Thomassen, Fabio Capra, Patrick J. Morrison, Britta Fiebig, Mary Beth Terry, Marinus J. Blok, Evgeny N. Imyanitov, Joseph Vijai, Javier Benitez, Mark T. Rogers, D. Gareth Evans, Helmut Deissler, Tomasz Byrski, Sylvie Mazoyer, Laura Papi, Dominique Stoppa-Lyonnet, Marco Montagna, Kenneth Offit, Cezary Cybulski, Dominique Leroux, Georgia Chenevix-Trench, Danielle Bodmer, Lucy Side, Margaret Cook, Ros Eeles, Alan Donaldson, Christiana Kartsonaki, Carole Brewer, Matti A. Rookus, Jacek Gronwald, Dorothea Gadzicki, Shirley Hodgson, Jonathan Beesley, Gabriella Pichert, Andrew K. Godwin, Dieter Niederacher, Yuan Chun Ding, Torben A Kruse, Paolo Peterlongo, Rita K. Schmutzler, Xiaoqing Chen, Annika Lindblom, Fergus J. Couch, Maaike P.G. Vreeswijk, Mark H. Greene, Esther M. John, Raymonda Varon-Mateeva, Simon A. Gayther, Margreet G. E. M. Ausems, Tomas Kirchhoff, Lars Jønson, Madeleine M. A. Tilanus-Linthorst, Ute Hamann, Marie-Agnès Collonge-Rame, Antonis C. Antoniou, M John Kennedy, Karin Kast, Theo A. M. van Os, Penny Soucy, Debra Frost, Alison M. Dunning, Daniela Zaffaroni, Anna Allavena, Maria-Isabel Tejada, Yves-Jean Bignon, Lesley McGuffog, Bohdan Górski, Åke Borg, Fabienne Prieur, Bernard Peissel, Helen Gregory, Clare Oliver, Saundra S. Buys, Ana Dutra-Clarke, Alfons Meindl, Ramunas Janavicius, Uffe Birk Jensen, Miguel de la Hoya, Ramus, S, Kartsonaki, C, Gayther, S, Pharoah, P, Sinilnikova, O, Beesley, J, Chen, X, Mcguffog, L, Healey, S, Couch, F, Wang, X, Fredericksen, Z, Peterlongo, P, Manoukian, S, Peissel, B, Zaffaroni, D, Roversi, G, Barile, M, Viel, A, Allavena, A, Ottini, L, Papi, L, Gismondi, V, Capra, F, Radice, P, Greene, M, Mai, P, Andrulis, I, Glendon, G, Ozcelik, H, Thomassen, M, Gerdes, A, Kruse, T, Cruger, D, Jensen, U, Caligo, M, Olsson, H, Kristoffersson, U, Lindblom, A, Arver, B, Karlsson, P, Stenmark Askmalm, M, Borg, A, Neuhausen, S, Ding, Y, Nathanson, K, Domchek, S, Jakubowska, A, Lubiński, J, Huzarski, T, Byrski, T, Gronwald, J, Górski, B, Cybulski, C, Dębniak, T, Osorio, A, Durán, M, Tejada, M, Benítez, J, Hamann, U, Rookus, M, Verhoef, S, Tilanus Linthorst, M, Vreeswijk, M, Bodmer, D, Ausems, M, van Os, T, Asperen, C, Blok, M, Meijers Heijboer, H, Peock, S, Cook, M, Oliver, C, Frost, D, Dunning, A, Evans, D, Eeles, R, Pichert, G, Cole, T, Hodgson, S, Brewer, C, Morrison, P, Porteous, M, Kennedy, M, Rogers, M, Side, L, Donaldson, A, Gregory, H, Godwin, A, Stoppa Lyonnet, D, Moncoutier, V, Castera, L, Mazoyer, S, Barjhoux, L, Bonadona, V, Leroux, D, Faivre, L, Lidereau, R, Nogues, C, Bignon, Y, Prieur, F, Collonge Rame, M, Venat Bouvet, L, Fert Ferrer, S, Miron, A, Buys, S, Hopper, J, Daly, M, John, E, Terry, M, Goldgar, D, Hansen, T, Jønson, L, Ejlertsen, B, Agnarsson, B, Offit, K, Kirchhoff, T, Vijai, J, Dutra Clarke, A, Przybylo, J, Montagna, M, Casella, C, Imyanitov, E, Janavicius, R, Blanco, I, Lázaro, C, Moysich, K, Karlan, B, Gross, J, Beattie, M, Schmutzler, R, Wappenschmidt, B, Meindl, A, Ruehl, I, Fiebig, B, Sutter, C, Arnold, N, Deissler, H, Varon Mateeva, R, Kast, K, Niederacher, D, Gadzicki, D, Caldes, T, de la Hoya, M, Nevanlinna, H, Aittomäki, K, Simard, J, Soucy, P, Spurdle, A, Holland, H, Chenevix Trench, G, Easton, D, Antoniou, A, Faculteit Medische Wetenschappen/UMCG, Biostatistiques santé, Département biostatistiques et modélisation pour la santé et l'environnement [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Klinische Genetica, Genetica & Celbiologie, RS: GROW - School for Oncology and Reproduction, Clinical Genetics, Pediatric Surgery, Human genetics, CCA - Oncogenesis, and Human Genetics
Subjects: Oncology, Cancer Research, endocrine system diseases, Genes, BRCA2, Genes, BRCA1, Genome-wide association study, FAMILIES, 0302 clinical medicine, Risk Factors, Retrospective Studie, Genotype, Odds Ratio, skin and connective tissue diseases, POPULATION, Genetics, Ovarian Neoplasms, Aged, 80 and over, Allele, 0303 health sciences, education.field_of_study, Likelihood Functions, Articles, GERMLINE MUTATIONS, Middle Aged, Likelihood Function, female genital diseases and pregnancy complications, 3. Good health, 030220 oncology & carcinogenesis, Female, Chromosomes, Human, Pair 9, Human, Adult, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], medicine.medical_specialty, Heterozygote, SUSCEPTIBILITY LOCI, PROTEINS, Population, Biology, Polymorphism, Single Nucleotide, BASONUCLIN-2, 03 medical and health sciences, Breast cancer, Germline mutation, SDG 3 - Good Health and Well-being, Internal medicine, medicine, BREAST-CANCER, Humans, GENOME-WIDE ASSOCIATION, education, Alleles, Germ-Line Mutation, 030304 developmental biology, Retrospective Studies, Aged, IDENTIFICATION, Risk Factor, Ovarian Neoplasm, Editorials, Cancer, medicine.disease, Minor allele frequency, Ovarian cancer
Abstract: [Background]: Germline mutations in the BRCA1 and BRCA2 genes are associated with increased risks of breast and ovarian cancers. Although several common variants have been associated with breast cancer susceptibility in mutation carriers, none have been associated with ovarian cancer susceptibility. A genome-wide association study recently identified an association between the rare allele of the single-nucleotide polymorphism (SNP) rs3814113 (ie, the C allele) at 9p22.2 and decreased risk of ovarian cancer for women in the general population. We evaluated the association of this SNP with ovarian cancer risk among BRCA1 or BRCA2 mutation carriers by use of data from the Consortium of Investigators of Modifiers of BRCA1/2. [Methods]: We genotyped rs3814113 in 10 029 BRCA1 mutation carriers and 5837 BRCA2 mutation carriers. Associations with ovarian and breast cancer were assessed with a retrospective likelihood approach. All statistical tests were two-sided. [Results]: The minor allele of rs3814113 was associated with a reduced risk of ovarian cancer among BRCA1 mutation carriers (per-allele hazard ratio of ovarian cancer = 0.78, 95% confidence interval = 0.72 to 0.85; P = 4.8 × 10-9) and BRCA2 mutation carriers (hazard ratio of ovarian cancer = 0.78, 95% confidence interval = 0.67 to 0.90; P = 5.5 × 10-4). This SNP was not associated with breast cancer risk among either BRCA1 or BRCA2 mutation carriers. BRCA1 mutation carriers with the TT genotype at SNP rs3814113 were predicted to have an ovarian cancer risk to age 80 years of 48%, and those with the CC genotype were predicted to have a risk of 33%. [Conclusion]: Common genetic variation at the 9p22.2 locus was associated with decreased risk of ovarian cancer for carriers of a BRCA1 or BRCA2 mutation., Spanish National Cancer Center (CNIO) and the Spanish Consortium: Partially supported by Fundación Mutua Madrileña, Asociación Española Contra el Cáncer, and the Spanish Ministry of Science and Innovation (FIS PI08 1120).
Published: 2011
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31. Exome-Based Trio Analysis for Diagnosis of the Cause of Congenital Severe Hemolytic Anemia in a Child.

Author: Rieneck K, Lausen B, Clausen FB, Jønson L, Hansen AT, and Dziegiel MH
Abstract: Inborn hemolytic anemia requiring frequent blood transfusions can be a life-threatening disease. Treatment, besides blood transfusion, includes iron chelation for prevention of iron accumulation due to frequent blood transfusions. We present the results of a clinical investigation where the proband was diagnosed with severe hemolytic anemia of unknown origin soon after birth. Transfusion was required every 4-6 weeks. After whole exome sequencing of the proband and his parents as well as a healthy sibling, we established that the proband had a compound heterozygous state carrying two rare variants in the erythrocytic spectrin gene, SPTA1 . The maternal allele was a stop mutation (rs755630903) and the paternal allele was a missense mutation (rs375506528). The healthy sibling had the paternal variant but not the maternal variant. These rare variants of SPTA1 most likely account for the hemolytic anemia. A severely reduced osmotic resistance in the erythrocytes from the proband was demonstrated. Splenectomy considerably improved the hemolytic anemia and obviated the need for blood transfusion despite the severe clinical presentation., Competing Interests: Lars Jønson is now employed by a private company but at the time of the investigation was employed at a public hospital as were the rest of the authors. Otherwise, the authors have no conflicts of interest to declare., (Copyright © 2022 by The Author(s). Published by S. Karger AG, Basel.)
Published: 2022
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32. Deep targeted sequencing of TP53 in chronic lymphocytic leukemia: clinical impact at diagnosis and at time of treatment.

Author: Brieghel C, Kinalis S, Yde CW, Schmidt AY, Jønson L, Andersen MA, da Cunha-Bang C, Pedersen LB, Geisler CH, Nielsen FC, and Niemann CU
Subjects: Aged, Disease-Free Survival, Female, Humans, Leukemia, Lymphocytic, Chronic, B-Cell metabolism, Male, Middle Aged, Survival Rate, Tumor Suppressor Protein p53 metabolism, Alleles, Gene Frequency, High-Throughput Nucleotide Sequencing, Leukemia, Lymphocytic, Chronic, B-Cell genetics, Leukemia, Lymphocytic, Chronic, B-Cell mortality, Mutation, Tumor Suppressor Protein p53 genetics
Abstract: In chronic lymphocytic leukemia, TP53 mutations and deletion of chromosome 17p are well-characterized biomarkers associated with poor progression-free and overall survival following chemoimmunotherapy. Patients harboring low burden TP53 mutations with variant allele frequencies of 0.3-15% have been shown to have similar dismal outcome as those with high burden mutations. We here describe a highly sensitive deep targeted next-generation sequencing assay allowing for the detection of TP53 mutations as low as 0.2% variant allele frequency. Within a consecutive, single center cohort of 290 newly diagnosed patients with chronic lymphocytic leukemia, deletion of chromosome 17p was the only TP53 aberration significantly associated with shorter overall survival and treatment-free survival. We were unable to demonstrate any impact of TP53 mutations, whether high burden (variant allele frequency >10%) or low burden (variant allele frequency ≤10%), in the absence of deletion of chromosome 17p. In addition, the impact of high burden TP53 aberration (deletion of chromosome 17p and/or TP53 mutation with variant allele frequency >10%) was only evident for patients with IGHV unmutated status; no impact of TP53 aberrations on outcome was seen for patients with IGHV mutated status. In 61 patients at time of treatment, the prognostic impact of TP53 mutations over 1% variant allele frequency could be confirmed. This study furthers the identification of a clinical significant limit of detection for robust TP53 mutation analysis in chronic lymphocytic leukemia. Multicenter studies are needed for validation of ultra-sensitive TP53 mutation assays in order to define and implement a technical as well as a clinical lower limit of detection., (Copyright© 2019 Ferrata Storti Foundation.)
Published: 2019
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33. Next-Generation Sequencing-Based Detection of Germline Copy Number Variations in BRCA1/BRCA2: Validation of a One-Step Diagnostic Workflow.

Author: Schmidt AY, Hansen TVO, Ahlborn LB, Jønson L, Yde CW, and Nielsen FC
Subjects: Breast Neoplasms diagnosis, Breast Neoplasms pathology, Carcinoma, Ovarian Epithelial, Computational Biology, DNA Copy Number Variations genetics, Female, Genetic Predisposition to Disease, Genetic Testing, Germ-Line Mutation genetics, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Glandular and Epithelial diagnosis, Neoplasms, Glandular and Epithelial pathology, Ovarian Neoplasms diagnosis, Ovarian Neoplasms pathology, BRCA1 Protein genetics, BRCA2 Protein genetics, Breast Neoplasms genetics, Neoplasms, Glandular and Epithelial genetics, Ovarian Neoplasms genetics
Abstract: Genetic testing of BRCA1/2 includes screening for single nucleotide variants and small insertions/deletions and for larger copy number variations (CNVs), primarily by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). With the advent of next-generation sequencing (NGS), it has become feasible to provide CNV information and sequence data using a single platform. We report the use of NGS gene panel sequencing on the Illumina MiSeq platform and JSI SeqPilot SeqNext software to call germline CNVs in BRCA1 and BRCA2. For validation 18 different BRCA1/BRCA2 CNVs previously identified by MLPA in 48 Danish breast and/or ovarian cancer families were analyzed. Moreover, 120 patient samples previously determined as negative for BRCA1/BRCA2 CNVs by MLPA were included in the analysis. Comparison of the NGS data with the data from MLPA revealed that the sensitivity was 100%, whereas the specificity was 95%. Taken together, this study validates a one-step bioinformatics work-flow to call germline BRCA1/2 CNVs using data obtained by NGS of a breast cancer gene panel. The work-flow represents a robust and easy-to-use method for full BRCA1/2 screening, which can be easily implemented in routine diagnostic testing and adapted to genes other than BRCA1/2., (Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.)
Published: 2017
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34. Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients.

Author: Urup T, Staunstrup LM, Michaelsen SR, Vitting-Seerup K, Bennedbæk M, Toft A, Olsen LR, Jønson L, Issazadeh-Navikas S, Broholm H, Hamerlik P, Poulsen HS, and Lassen U
Subjects: Adult, Aged, Female, Gene Expression Profiling, Humans, Male, Middle Aged, Neoplasm Recurrence, Local drug therapy, Young Adult, Antineoplastic Agents therapeutic use, Bevacizumab therapeutic use, Brain Neoplasms drug therapy, Glioblastoma drug therapy, Transcription, Genetic drug effects
Abstract: Background: Bevacizumab combined with chemotherapy produces clinical durable response in 25-30% of recurrent glioblastoma patients. This group of patients has shown improved survival and quality of life. The aim of this study was to investigate changes in gene expression associated with response and resistance to bevacizumab combination therapy., Methods: Recurrent glioblastoma patients who had biomarker-accessible tumor tissue surgically removed both before bevacizumab treatment and at time of progression were included. Patients were grouped into responders (n = 7) and non-responders (n = 14). Gene expression profiling of formalin-fixed paraffin-embedded tumor tissue was performed using RNA-sequencing., Results: By comparing pretreatment samples of responders with those of non-responders no significant difference was observed. In a paired comparison analysis of pre- and posttreatment samples of non-responders 1 gene was significantly differentially expressed. In responders, this approach revealed 256 significantly differentially expressed genes (72 down- and 184 up-regulated genes at the time of progression). Genes differentially expressed in responders revealed a shift towards a more proneural and less mesenchymal phenotype at the time of progression., Conclusions: Bevacizumab combination treatment demonstrated a significant impact on the transcriptional changes in responders; but only minimal changes in non-responders. This suggests that non-responding glioblastomas progress chaotically without following distinct gene expression changes while responding tumors adaptively respond or progress by means of the same transcriptional changes. In conclusion, we hypothesize that the identified gene expression changes of responding tumors are associated to bevacizumab response or resistance mechanisms.
Published: 2017
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35. STAT5 induces miR-21 expression in cutaneous T cell lymphoma.

Author: Lindahl LM, Fredholm S, Joseph C, Nielsen BS, Jønson L, Willerslev-Olsen A, Gluud M, Blümel E, Petersen DL, Sibbesen N, Hu T, Nastasi C, Krejsgaard T, Jæhger D, Persson JL, Mongan N, Wasik MA, Litvinov IV, Sasseville D, Koralov SB, Bonefeld CM, Geisler C, Woetmann A, Ralfkiaer E, Iversen L, and Odum N
Subjects: Female, Humans, Lymphoma, T-Cell, Cutaneous genetics, Male, MicroRNAs genetics, STAT5 Transcription Factor genetics, Skin Neoplasms genetics, Gene Expression Regulation, Neoplastic physiology, Lymphoma, T-Cell, Cutaneous metabolism, MicroRNAs biosynthesis, STAT5 Transcription Factor metabolism, Skin Neoplasms metabolism
Abstract: In cutaneous T cell lymphomas (CTCL), miR-21 is aberrantly expressed in skin and peripheral blood and displays anti-apoptotic properties in malignant T cells. It is, however, unclear exactly which cells express miR-21 and what mechanisms regulate miR-21. Here, we demonstrate miR-21 expression in situ in both malignant and reactive lymphocytes as well as stromal cells. qRT-PCR analysis of 47 patients with mycosis fungoides (MF) and Sezary Syndrome (SS) confirmed an increased miR-21 expression that correlated with progressive disease. In cultured malignant T cells miR-21 expression was inhibited by Tofacitinib (CP-690550), a clinical-grade JAK3 inhibitor. Chromatin immunoprecipitation (ChIP) analysis showed direct binding of STAT5 to the miR-21 promoter. Cytokine starvation ex vivo triggered a decrease in miR-21 expression, whereas IL-2 induced an increased miR-21 expression in primary SS T cells and cultured cytokine-dependent SS cells (SeAx). siRNA-mediated depletion of STAT5 inhibited constitutive- and IL-2-induced miR-21 expression in cytokine-independent and dependent T cell lines, respectively. IL-15 and IL-2 were more potent than IL-21 in inducing miR-21 expression in the cytokine-dependent T cells. In conclusion, we provide first evidence that miR-21 is expressed in situ in CTCL skin lesions, induced by IL-2 and IL-15 cytokines, and is regulated by STAT5 in malignant T cells. Thus, our data provide novel evidence for a pathological role of IL-2Rg cytokines in promoting expression of the oncogenic miR-21 in CTCL., Competing Interests: The authors declare no conflicts of interest.
Published: 2016
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36. Whole-exome sequencing of a patient with severe and complex hemostatic abnormalities reveals a possible contributing frameshift mutation in C3AR1.

Author: Leinøe E, Nielsen OJ, Jønson L, and Rossing M
Abstract: The increasing availability of genome-wide analysis has made it possible to rapidly sequence the exome of patients with undiagnosed or unresolved medical conditions. Here, we present the case of a 64-yr-old male patient with schistocytes in the peripheral blood smear and a complex and life-threatening coagulation disorder causing recurrent venous thromboembolic events, severe thrombocytopenia, and subdural hematomas. Whole-exome sequencing revealed a frameshift mutation (C3AR1 c.355-356dup, p.Asp119Alafs*19) resulting in a premature stop codon in C3AR1 (Complement Component 3a Receptor 1). Based on this finding, atypical hemolytic uremic syndrome was suspected because of a genetic predisposition, and a targeted treatment regime with eculizumab was initiated. Life-threatening hemostatic abnormalities would most likely have persisted had it not been for the implementation of whole-exome sequencing in this particular clinical setting.
Published: 2016
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37. Germline Chromothripsis Driven by L1-Mediated Retrotransposition and Alu/Alu Homologous Recombination.

Author: Nazaryan-Petersen L, Bertelsen B, Bak M, Jønson L, Tommerup N, Hancks DC, and Tümer Z
Subjects: Base Sequence, Chromosome Breakpoints, Chromosomes, Human, Pair 3, Chromosomes, Human, Pair 5, Humans, Minisatellite Repeats, Mutagenesis, Insertional, Retroelements, Sequence Deletion, Alu Elements, Chromothripsis, Germ-Line Mutation, Homologous Recombination, Long Interspersed Nucleotide Elements
Abstract: Chromothripsis (CTH) is a phenomenon where multiple localized double-stranded DNA breaks result in complex genomic rearrangements. Although the DNA-repair mechanisms involved in CTH have been described, the mechanisms driving the localized "shattering" process remain unclear. High-throughput sequence analysis of a familial germline CTH revealed an inserted SVAE retrotransposon associated with a 110-kb deletion displaying hallmarks of L1-mediated retrotransposition. Our analysis suggests that the SVAE insertion did not occur prior to or after, but concurrent with the CTH event. We also observed L1-endonuclease potential target sites in other breakpoints. In addition, we found four Alu elements flanking the 110-kb deletion and associated with an inversion. We suggest that chromatin looping mediated by homologous Alu elements may have brought distal DNA regions into close proximity facilitating DNA cleavage by catalytically active L1-endonuclease. Our data provide the first evidence that active and inactive human retrotransposons can serve as endogenous mutagens driving CTH in the germline., (© 2016 WILEY PERIODICALS, INC.)
Published: 2016
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38. Identification of six pathogenic RAD51C mutations via mutational screening of 1228 Danish individuals with increased risk of hereditary breast and/or ovarian cancer.

Author: Jønson L, Ahlborn LB, Steffensen AY, Djursby M, Ejlertsen B, Timshel S, Nielsen FC, Gerdes AM, and Hansen TV
Subjects: Adult, Aged, Denmark, Exome genetics, Female, Genetic Testing methods, Humans, Introns genetics, Middle Aged, Risk, Breast Neoplasms genetics, DNA-Binding Proteins genetics, Genetic Predisposition to Disease genetics, Mutation genetics, Ovarian Neoplasms genetics
Abstract: Germ-line mutations in the RAD51C gene have recently been identified in families with breast and ovarian cancer and have been associated with an increased risk of ovarian cancer. In this study, we describe the frequency of pathogenic RAD51C mutations identified in Danish breast and/or ovarian cancer families. We screened the RAD51C gene in 1228 Danish hereditary breast and/or ovarian cancer families by next-generation sequencing analysis. The frequency of the identified variants was examined in the exome sequencing project database and in data from 2000 Danish exomes and the presumed significance of missense and intronic variants was predicted by in silico analysis. We identified six families with a pathogenic mutation in RAD51C, including three frameshift mutations, one nonsense mutation, and 2 missense mutations. Overall, pathogenic RAD51C mutations were identified in 0.5 % of Danish families with increased risk of hereditary breast and/or ovarian cancer. Moreover, we identified 24 additional RAD51C variants of which 14 have not been previously reported in the literature. In this study, we determine the prevalence of RAD51C mutations in Danish breast and/or ovarian cancer families. We identified six pathogenic RAD51C mutations as well as 23 variants of uncertain clinical significance and one benign variant. Together, the study extends our knowledge of the RAD51C mutation spectrum and supports that RAD51C should be included in gene panel testing of individuals with high risk of breast and ovarian cancer.
Published: 2016
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39. Whole-exome sequencing and genome-wide methylation analyses identify novel disease associated mutations and methylation patterns in idiopathic hypereosinophilic syndrome.

Author: Andersen CL, Nielsen HM, Kristensen LS, Søgaard A, Vikeså J, Jønson L, Nielsen FC, Hasselbalch H, Bjerrum OW, Punj V, and Grønbæk K
Subjects: Cell Differentiation, Female, Genome-Wide Association Study, Humans, Hypereosinophilic Syndrome pathology, Male, RNA, Messenger genetics, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Biomarkers metabolism, DNA Methylation, Exome genetics, Genome, Human, High-Throughput Nucleotide Sequencing methods, Hypereosinophilic Syndrome genetics, Mutation genetics
Abstract: A thorough understanding of the idiopathic hypereosinophilic syndrome (IHES) and further optimization of diagnostic work-up procedures are warranted. We analyzed purified eosinophils from patients with IHES by next-generation whole-exome sequencing and compared DNA methylation profiles from reactive eosinophilic conditions to known clonal and suspected clonal eosinophilia. Somatic missense mutations in cancer-related genes were detected in three IHES patients. These included the spliceosome gene PUF60 and the cadherin gene CDH17. Furthermore, reactive eosinophilia samples could be differentiated from known- and suspected clonal eosinophilia samples based on 285 differentially methylated CpG sites corresponding to 128 differentially methylated genes. Using Ingenuity pathway analysis, we found that differentially methylated genes were highly enriched in functional pathways such as cancer, cell death and survival, and hematological disease. Our data show that a subset of IHES may be of clonal origin not related to the classical molecular aberrations of FGFR, PDGFRA/B, or T-cells, and that the initiating hits could be point mutations in a variety of genes, including spliceosome mutations or hypermethylated tumor suppressor genes. In addition, we identified a DNA methylation signature that is relevant for distinguishing clonal and suspected clonal eosinophilia from reactive eosinophilia per se, which may be useful in daily clinical work.
Published: 2015
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40. Jak3, STAT3, and STAT5 inhibit expression of miR-22, a novel tumor suppressor microRNA, in cutaneous T-Cell lymphoma.

Author: Sibbesen NA, Kopp KL, Litvinov IV, Jønson L, Willerslev-Olsen A, Fredholm S, Petersen DL, Nastasi C, Krejsgaard T, Lindahl LM, Gniadecki R, Mongan NP, Sasseville D, Wasik MA, Iversen L, Bonefeld CM, Geisler C, Woetmann A, and Odum N
Subjects: Cell Line, Tumor, Genes, Tumor Suppressor, Humans, Janus Kinase 3 antagonists & inhibitors, Janus Kinase 3 genetics, Lymphoma, T-Cell, Cutaneous metabolism, Lymphoma, T-Cell, Cutaneous pathology, MicroRNAs administration & dosage, MicroRNAs biosynthesis, MicroRNAs genetics, Piperidines pharmacology, Protein Kinase Inhibitors pharmacology, Pyrimidines pharmacology, Pyrroles pharmacology, STAT3 Transcription Factor genetics, STAT5 Transcription Factor genetics, Signal Transduction, Skin Neoplasms metabolism, Skin Neoplasms pathology, Transfection, Janus Kinase 3 metabolism, Lymphoma, T-Cell, Cutaneous genetics, MicroRNAs antagonists & inhibitors, STAT3 Transcription Factor metabolism, STAT5 Transcription Factor metabolism, Skin Neoplasms genetics
Abstract: Aberrant activation of Janus kinase-3 (Jak3) and its key down-stream effectors, Signal Transducer and Activator of Transcription-3 (STAT3) and STAT5, is a key feature of malignant transformation in cutaneous T-cell lymphoma (CTCL). However, it remains only partially understood how Jak3/STAT activation promotes lymphomagenesis. Recently, non-coding microRNAs (miRNAs) have been implicated in the pathogenesis of this malignancy. Here, we show that (i) malignant T cells display a decreased expression of a tumor suppressor miRNA, miR-22, when compared to non-malignant T cells, (ii) STAT5 binds the promoter of the miR-22 host gene, and (iii) inhibition of Jak3, STAT3, and STAT5 triggers increased expression of pri-miR-22 and miR-22. Curcumin, a nutrient with anti-Jak3 activity and histone deacetylase inhibitors (HDACi) also trigger increased expression of pri-miR-22 and miR-22. Transfection of malignant T cells with recombinant miR-22 inhibits the expression of validated miR-22 targets including NCoA1, a transcriptional co-activator in others cancers, as well as HDAC6, MAX, MYCBP, PTEN, and CDK2, which have all been implicated in CTCL pathogenesis. In conclusion, we provide the first evidence that de-regulated Jak3/STAT3/STAT5 signalling in CTCL cells represses the expression of the gene encoding miR-22, a novel tumor suppressor miRNA.
Published: 2015
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41. Malignant T cells express lymphotoxin α and drive endothelial activation in cutaneous T cell lymphoma.

Author: Lauenborg B, Christensen L, Ralfkiaer U, Kopp KL, Jønson L, Dabelsteen S, Bonefeld CM, Geisler C, Gjerdrum LM, Zhang Q, Wasik MA, Ralfkiaer E, Ødum N, and Woetmann A
Subjects: Adult, Aged, Aged, 80 and over, Binding Sites genetics, DNA-Binding Proteins metabolism, Endothelial Cells metabolism, Female, Human Umbilical Vein Endothelial Cells, Humans, Janus Kinase 3 genetics, Janus Kinase 3 metabolism, Lymphatic Metastasis pathology, Male, Middle Aged, NF-kappa B metabolism, Neovascularization, Pathologic pathology, Promoter Regions, Genetic genetics, RNA Interference, RNA, Small Interfering, Receptors, Tumor Necrosis Factor, Type II metabolism, STAT5 Transcription Factor genetics, STAT5 Transcription Factor metabolism, T-Lymphocytes pathology, Tumor Cells, Cultured, Tumor Suppressor Proteins genetics, Tumor Suppressor Proteins metabolism, Interleukin-6 metabolism, Lymphoma, T-Cell, Cutaneous pathology, Lymphotoxin-alpha metabolism, Skin Neoplasms pathology, Vascular Endothelial Growth Factor A metabolism
Abstract: Lymphotoxin α (LTα) plays a key role in the formation of lymphatic vasculature and secondary lymphoid structures. Cutaneous T cell lymphoma (CTCL) is the most common primary lymphoma of the skin and in advanced stages, malignant T cells spreads through the lymphatic to regional lymph nodes to internal organs and blood. Yet, little is known about the mechanism of the CTCL dissemination. Here, we show that CTCL cells express LTα in situ and that LTα expression is driven by aberrantly activated JAK3/STAT5 pathway. Importantly, via TNF receptor 2, LTα functions as an autocrine factor by stimulating expression of IL-6 in the malignant cells. LTα and IL-6, together with VEGF promote angiogenesis by inducing endothelial cell sprouting and tube formation. Thus, we propose that LTα plays a role in malignant angiogenesis and disease progression in CTCL and may serve as a therapeutic target in this disease.
Published: 2015
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42. Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers.

Author: Blanco I, Kuchenbaecker K, Cuadras D, Wang X, Barrowdale D, de Garibay GR, Librado P, Sánchez-Gracia A, Rozas J, Bonifaci N, McGuffog L, Pankratz VS, Islam A, Mateo F, Berenguer A, Petit A, Català I, Brunet J, Feliubadaló L, Tornero E, Benítez J, Osorio A, Ramón y Cajal T, Nevanlinna H, Aittomäki K, Arun BK, Toland AE, Karlan BY, Walsh C, Lester J, Greene MH, Mai PL, Nussbaum RL, Andrulis IL, Domchek SM, Nathanson KL, Rebbeck TR, Barkardottir RB, Jakubowska A, Lubinski J, Durda K, Jaworska-Bieniek K, Claes K, Van Maerken T, Díez O, Hansen TV, Jønson L, Gerdes AM, Ejlertsen B, de la Hoya M, Caldés T, Dunning AM, Oliver C, Fineberg E, Cook M, Peock S, McCann E, Murray A, Jacobs C, Pichert G, Lalloo F, Chu C, Dorkins H, Paterson J, Ong KR, Teixeira MR, Hogervorst FB, van der Hout AH, Seynaeve C, van der Luijt RB, Ligtenberg MJ, Devilee P, Wijnen JT, Rookus MA, Meijers-Heijboer HE, Blok MJ, van den Ouweland AM, Aalfs CM, Rodriguez GC, Phillips KA, Piedmonte M, Nerenstone SR, Bae-Jump VL, O'Malley DM, Ratner ES, Schmutzler RK, Wappenschmidt B, Rhiem K, Engel C, Meindl A, Ditsch N, Arnold N, Plendl HJ, Niederacher D, Sutter C, Wang-Gohrke S, Steinemann D, Preisler-Adams S, Kast K, Varon-Mateeva R, Gehrig A, Bojesen A, Pedersen IS, Sunde L, Jensen UB, Thomassen M, Kruse TA, Foretova L, Peterlongo P, Bernard L, Peissel B, Scuvera G, Manoukian S, Radice P, Ottini L, Montagna M, Agata S, Maugard C, Simard J, Soucy P, Berger A, Fink-Retter A, Singer CF, Rappaport C, Geschwantler-Kaulich D, Tea MK, Pfeiler G, John EM, Miron A, Neuhausen SL, Terry MB, Chung WK, Daly MB, Goldgar DE, Janavicius R, Dorfling CM, van Rensburg EJ, Fostira F, Konstantopoulou I, Garber J, Godwin AK, Olah E, Narod SA, Rennert G, Paluch SS, Laitman Y, Friedman E, Liljegren A, Rantala J, Stenmark-Askmalm M, Loman N, Imyanitov EN, Hamann U, Spurdle AB, Healey S, Weitzel JN, Herzog J, Margileth D, Gorrini C, Esteller M, Gómez A, Sayols S, Vidal E, Heyn H, Stoppa-Lyonnet D, Léoné M, Barjhoux L, Fassy-Colcombet M, de Pauw A, Lasset C, Ferrer SF, Castera L, Berthet P, Cornelis F, Bignon YJ, Damiola F, Mazoyer S, Sinilnikova OM, Maxwell CA, Vijai J, Robson M, Kauff N, Corines MJ, Villano D, Cunningham J, Lee A, Lindor N, Lázaro C, Easton DF, Offit K, Chenevix-Trench G, Couch FJ, Antoniou AC, and Pujana MA
Subjects: Aurora Kinase A genetics, Breast Neoplasms enzymology, Breast Neoplasms pathology, Carcinogenesis genetics, Cell Cycle Proteins genetics, Estrogen Receptor alpha metabolism, Evolution, Molecular, Extracellular Matrix Proteins genetics, Female, Genetic Loci genetics, Humans, Hyaluronan Receptors genetics, Likelihood Functions, Mammary Glands, Human metabolism, Microtubule-Associated Proteins genetics, Nuclear Proteins genetics, Polymorphism, Single Nucleotide, Retrospective Studies, Tubulin genetics, Breast Neoplasms genetics, Genes, BRCA1, Genes, BRCA2, Genetic Predisposition to Disease genetics, Mutation
Abstract: While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04-1.15, p = 1.9 x 10(-4) (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03-1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteraction values > 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers.
Published: 2015
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43. Splicing analysis of 14 BRCA1 missense variants classifies nine variants as pathogenic.

Author: Ahlborn LB, Dandanell M, Steffensen AY, Jønson L, Nielsen FC, and Hansen TV
Subjects: Base Sequence, Breast Neoplasms, DNA Mutational Analysis, Female, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Testing, Germ-Line Mutation, Humans, BRCA1 Protein genetics, Mutation, Missense, RNA Splicing
Abstract: Pathogenic germline mutations in the BRCA1 gene predispose carriers to early onset breast and ovarian cancer. Clinical genetic screening of BRCA1 often reveals variants with uncertain clinical significance, complicating patient and family management. Therefore, functional examinations are urgently needed to classify whether these uncertain variants are pathogenic or benign. In this study, we investigated 14 BRCA1 variants by in silico splicing analysis and mini-gene splicing assay. All 14 alterations were missense variants located within the BRCT domain of BRCA1 and had previously been examined by functional analysis at the protein level. Results from a validated mini-gene splicing assay indicated that nine BRCA1 variants resulted in splicing aberrations leading to truncated transcripts and thus can be considered pathogenic (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5072C>T/p.Thr1691Ile, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala), whereas five BRCA1 variants had no effect on splicing (c.4985T>C/p.Phe1662Ser, c.5072C>A/p.Thr1691Lys, c.5153G>C/p.Trp1718Ser, c.5154G>T/p.Trp1718Cys, and c.5333A>G/p.Asp1778Gly). Eight of the variants having an effect on splicing (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala) were previously determined to have no or an uncertain effect on the protein level, whereas one variant (c.5072C>T/p.Thr1691Ile) were shown to have a strong effect on the protein level as well. In conclusion, our study emphasizes that in silico splicing prediction and mini-gene splicing analysis are important for the classification of BRCA1 missense variants located close to exon/intron boundaries.
Published: 2015
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44. Identification of a breast cancer family double heterozygote for RAD51C and BRCA2 gene mutations.

Author: Ahlborn LB, Steffensen AY, Jønson L, Djursby M, Nielsen FC, Gerdes AM, and Hansen TV
Subjects: Adult, Breast Neoplasms genetics, DNA Mutational Analysis, Female, Heterozygote, High-Throughput Nucleotide Sequencing, Humans, Pedigree, DNA-Binding Proteins genetics, Genes, BRCA2, Genetic Predisposition to Disease genetics, Mutation
Abstract: Next-generation sequencing has entered routine genetic testing of hereditary breast cancer. It has provided the opportunity to screen multiple genes simultaneously, and consequently has identified new complex genotypes. Here we report the first identification of a woman double heterozygote for mutations in the RAD51C and BRCA2 genes. The RAD51C missense mutation p.Arg258His has previously been identified in a homozygous state in a patient with Fanconi anemia. This mutation is known to affect the DNA repair function of the RAD51C protein. The BRCA2 p.Leu3216Leu synonymous mutation has not been described before and mini-gene splicing experiments revealed that the mutation results in skipping of exon 26 containing a part of the DNA-binding domain. We conclude that the woman has two potential disease-causing mutations and that predictive testing of family members should include both the RAD51C and BRCA2 mutation. This study illustrates the advantage of sequencing gene panels using next-generation sequencing in terms of genetic testing.
Published: 2015
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45. Mutations in COA3 cause isolated complex IV deficiency associated with neuropathy, exercise intolerance, obesity, and short stature.

Author: Ostergaard E, Weraarpachai W, Ravn K, Born AP, Jønson L, Duno M, Wibrand F, Shoubridge EA, and Vissing J
Subjects: Adult, Child, Preschool, Cyclooxygenase 1 biosynthesis, Cyclooxygenase 1 genetics, Cytochrome-c Oxidase Deficiency pathology, Dwarfism genetics, Dwarfism pathology, Electron Transport Complex IV genetics, Exercise physiology, Exome, Female, Fibroblasts, Gene Expression Regulation, Enzymologic, Humans, Membrane Proteins biosynthesis, Mitochondrial Proteins biosynthesis, Obesity pathology, Cytochrome-c Oxidase Deficiency genetics, Membrane Proteins genetics, Mitochondrial Proteins genetics, Obesity genetics
Abstract: Background: We investigated a subject with an isolated cytochrome c oxidase (COX) deficiency presenting with an unusual phenotype characterised by neuropathy, exercise intolerance, obesity, and short stature., Methods and Results: Blue-native polyacrylamide gel electrophoresis (BN-PAGE) analysis showed an almost complete lack of COX assembly in subject fibroblasts, consistent with the very low enzymatic activity, and pulse-labelling mitochondrial translation experiments showed a specific decrease in synthesis of the COX1 subunit, the core catalytic subunit that nucleates assembly of the holoenzyme. Whole exome sequencing identified compound heterozygous mutations (c.199dupC, c.215A>G) in COA3, a small inner membrane COX assembly factor, resulting in a pronounced decrease in the steady-state levels of COA3 protein. Retroviral expression of a wild-type COA3 cDNA completely rescued the COX assembly and mitochondrial translation defects, confirming the pathogenicity of the mutations, and resulted in increased steady-state levels of COX1 in control cells, demonstrating a role for COA3 in the stabilisation of this subunit. COA3 exists in an early COX assembly complex that contains COX1 and other COX assembly factors including COX14 (C12orf62), another single pass transmembrane protein that also plays a role in coupling COX1 synthesis with holoenzyme assembly. Immunoblot analysis showed that COX14 was undetectable in COA3 subject fibroblasts, and that COA3 was undetectable in fibroblasts from a COX14 subject, demonstrating the interdependence of these two COX assembly factors., Conclusions: The mild clinical course in this patient contrasts with nearly all other cases of severe COX assembly defects that are usually fatal early in life, and underscores the marked tissue-specific involvement in mitochondrial diseases., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.)
Published: 2015
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46. Identification of six new susceptibility loci for invasive epithelial ovarian cancer.

Author: Kuchenbaecker KB, Ramus SJ, Tyrer J, Lee A, Shen HC, Beesley J, Lawrenson K, McGuffog L, Healey S, Lee JM, Spindler TJ, Lin YG, Pejovic T, Bean Y, Li Q, Coetzee S, Hazelett D, Miron A, Southey M, Terry MB, Goldgar DE, Buys SS, Janavicius R, Dorfling CM, van Rensburg EJ, Neuhausen SL, Ding YC, Hansen TV, Jønson L, Gerdes AM, Ejlertsen B, Barrowdale D, Dennis J, Benitez J, Osorio A, Garcia MJ, Komenaka I, Weitzel JN, Ganschow P, Peterlongo P, Bernard L, Viel A, Bonanni B, Peissel B, Manoukian S, Radice P, Papi L, Ottini L, Fostira F, Konstantopoulou I, Garber J, Frost D, Perkins J, Platte R, Ellis S, Godwin AK, Schmutzler RK, Meindl A, Engel C, Sutter C, Sinilnikova OM, Damiola F, Mazoyer S, Stoppa-Lyonnet D, Claes K, De Leeneer K, Kirk J, Rodriguez GC, Piedmonte M, O'Malley DM, de la Hoya M, Caldes T, Aittomäki K, Nevanlinna H, Collée JM, Rookus MA, Oosterwijk JC, Tihomirova L, Tung N, Hamann U, Isaccs C, Tischkowitz M, Imyanitov EN, Caligo MA, Campbell IG, Hogervorst FB, Olah E, Diez O, Blanco I, Brunet J, Lazaro C, Pujana MA, Jakubowska A, Gronwald J, Lubinski J, Sukiennicki G, Barkardottir RB, Plante M, Simard J, Soucy P, Montagna M, Tognazzo S, Teixeira MR, Pankratz VS, Wang X, Lindor N, Szabo CI, Kauff N, Vijai J, Aghajanian CA, Pfeiler G, Berger A, Singer CF, Tea MK, Phelan CM, Greene MH, Mai PL, Rennert G, Mulligan AM, Tchatchou S, Andrulis IL, Glendon G, Toland AE, Jensen UB, Kruse TA, Thomassen M, Bojesen A, Zidan J, Friedman E, Laitman Y, Soller M, Liljegren A, Arver B, Einbeigi Z, Stenmark-Askmalm M, Olopade OI, Nussbaum RL, Rebbeck TR, Nathanson KL, Domchek SM, Lu KH, Karlan BY, Walsh C, Lester J, Hein A, Ekici AB, Beckmann MW, Fasching PA, Lambrechts D, Van Nieuwenhuysen E, Vergote I, Lambrechts S, Dicks E, Doherty JA, Wicklund KG, Rossing MA, Rudolph A, Chang-Claude J, Wang-Gohrke S, Eilber U, Moysich KB, Odunsi K, Sucheston L, Lele S, Wilkens LR, Goodman MT, Thompson PJ, Shvetsov YB, Runnebaum IB, Dürst M, Hillemanns P, Dörk T, Antonenkova N, Bogdanova N, Leminen A, Pelttari LM, Butzow R, Modugno F, Kelley JL, Edwards RP, Ness RB, du Bois A, Heitz F, Schwaab I, Harter P, Matsuo K, Hosono S, Orsulic S, Jensen A, Kjaer SK, Hogdall E, Hasmad HN, Azmi MA, Teo SH, Woo YL, Fridley BL, Goode EL, Cunningham JM, Vierkant RA, Bruinsma F, Giles GG, Liang D, Hildebrandt MA, Wu X, Levine DA, Bisogna M, Berchuck A, Iversen ES, Schildkraut JM, Concannon P, Weber RP, Cramer DW, Terry KL, Poole EM, Tworoger SS, Bandera EV, Orlow I, Olson SH, Krakstad C, Salvesen HB, Tangen IL, Bjorge L, van Altena AM, Aben KK, Kiemeney LA, Massuger LF, Kellar M, Brooks-Wilson A, Kelemen LE, Cook LS, Le ND, Cybulski C, Yang H, Lissowska J, Brinton LA, Wentzensen N, Hogdall C, Lundvall L, Nedergaard L, Baker H, Song H, Eccles D, McNeish I, Paul J, Carty K, Siddiqui N, Glasspool R, Whittemore AS, Rothstein JH, McGuire V, Sieh W, Ji BT, Zheng W, Shu XO, Gao YT, Rosen B, Risch HA, McLaughlin JR, Narod SA, Monteiro AN, Chen A, Lin HY, Permuth-Wey J, Sellers TA, Tsai YY, Chen Z, Ziogas A, Anton-Culver H, Gentry-Maharaj A, Menon U, Harrington P, Lee AW, Wu AH, Pearce CL, Coetzee G, Pike MC, Dansonka-Mieszkowska A, Timorek A, Rzepecka IK, Kupryjanczyk J, Freedman M, Noushmehr H, Easton DF, Offit K, Couch FJ, Gayther S, Pharoah PP, Antoniou AC, and Chenevix-Trench G
Subjects: Adolescent, Adult, Alleles, Carcinoma, Ovarian Epithelial, Female, Genes, Reporter, Genotype, Heterozygote, Humans, Mutation, Quantitative Trait Loci, Risk, Young Adult, BRCA1 Protein genetics, BRCA2 Protein genetics, Genetic Predisposition to Disease, Genome-Wide Association Study methods, Neoplasms, Glandular and Epithelial genetics, Ovarian Neoplasms genetics, Polymorphism, Single Nucleotide
Abstract: Genome-wide association studies (GWAS) have identified 12 epithelial ovarian cancer (EOC) susceptibility alleles. The pattern of association at these loci is consistent in BRCA1 and BRCA2 mutation carriers who are at high risk of EOC. After imputation to 1000 Genomes Project data, we assessed associations of 11 million genetic variants with EOC risk from 15,437 cases unselected for family history and 30,845 controls and from 15,252 BRCA1 mutation carriers and 8,211 BRCA2 mutation carriers (3,096 with ovarian cancer), and we combined the results in a meta-analysis. This new study design yielded increased statistical power, leading to the discovery of six new EOC susceptibility loci. Variants at 1p36 (nearest gene, WNT4), 4q26 (SYNPO2), 9q34.2 (ABO) and 17q11.2 (ATAD5) were associated with EOC risk, and at 1p34.3 (RSPO1) and 6p22.1 (GPX6) variants were specifically associated with the serous EOC subtype, all with P < 5 × 10(-8). Incorporating these variants into risk assessment tools will improve clinical risk predictions for BRCA1 and BRCA2 mutation carriers.
Published: 2015
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47. Candidate genetic modifiers for breast and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers.

Author: Peterlongo P, Chang-Claude J, Moysich KB, Rudolph A, Schmutzler RK, Simard J, Soucy P, Eeles RA, Easton DF, Hamann U, Wilkening S, Chen B, Rookus MA, Schmidt MK, van der Baan FH, Spurdle AB, Walker LC, Lose F, Maia AT, Montagna M, Matricardi L, Lubinski J, Jakubowska A, Gómez Garcia EB, Olopade OI, Nussbaum RL, Nathanson KL, Domchek SM, Rebbeck TR, Arun BK, Karlan BY, Orsulic S, Lester J, Chung WK, Miron A, Southey MC, Goldgar DE, Buys SS, Janavicius R, Dorfling CM, van Rensburg EJ, Ding YC, Neuhausen SL, Hansen TV, Gerdes AM, Ejlertsen B, Jønson L, Osorio A, Martínez-Bouzas C, Benitez J, Conway EE, Blazer KR, Weitzel JN, Manoukian S, Peissel B, Zaffaroni D, Scuvera G, Barile M, Ficarazzi F, Mariette F, Fortuzzi S, Viel A, Giannini G, Papi L, Martayan A, Tibiletti MG, Radice P, Vratimos A, Fostira F, Garber JE, Donaldson A, Brewer C, Foo C, Evans DG, Frost D, Eccles D, Brady A, Cook J, Tischkowitz M, Adlard J, Barwell J, Walker L, Izatt L, Side LE, Kennedy MJ, Rogers MT, Porteous ME, Morrison PJ, Platte R, Davidson R, Hodgson SV, Ellis S, Cole T, Godwin AK, Claes K, Van Maerken T, Meindl A, Gehrig A, Sutter C, Engel C, Niederacher D, Steinemann D, Plendl H, Kast K, Rhiem K, Ditsch N, Arnold N, Varon-Mateeva R, Wappenschmidt B, Wang-Gohrke S, Bressac-de Paillerets B, Buecher B, Delnatte C, Houdayer C, Stoppa-Lyonnet D, Damiola F, Coupier I, Barjhoux L, Venat-Bouvet L, Golmard L, Boutry-Kryza N, Sinilnikova OM, Caron O, Pujol P, Mazoyer S, Belotti M, Piedmonte M, Friedlander ML, Rodriguez GC, Copeland LJ, de la Hoya M, Segura PP, Nevanlinna H, Aittomäki K, van Os TA, Meijers-Heijboer HE, van der Hout AH, Vreeswijk MP, Hoogerbrugge N, Ausems MG, van Doorn HC, Collée JM, Olah E, Diez O, Blanco I, Lazaro C, Brunet J, Feliubadalo L, Cybulski C, Gronwald J, Durda K, Jaworska-Bieniek K, Sukiennicki G, Arason A, Chiquette J, Teixeira MR, Olswold C, Couch FJ, Lindor NM, Wang X, Szabo CI, Offit K, Corines M, Jacobs L, Robson ME, Zhang L, Joseph V, Berger A, Singer CF, Rappaport C, Kaulich DG, Pfeiler G, Tea MK, Phelan CM, Greene MH, Mai PL, Rennert G, Mulligan AM, Glendon G, Tchatchou S, Andrulis IL, Toland AE, Bojesen A, Pedersen IS, Thomassen M, Jensen UB, Laitman Y, Rantala J, von Wachenfeldt A, Ehrencrona H, Askmalm MS, Borg Å, Kuchenbaecker KB, McGuffog L, Barrowdale D, Healey S, Lee A, Pharoah PD, Chenevix-Trench G, Antoniou AC, and Friedman E
Subjects: Adult, Cohort Studies, Female, Humans, Mutation, Polymorphism, Single Nucleotide, Retrospective Studies, Young Adult, Breast Neoplasms genetics, Genes, BRCA1 physiology, Genes, BRCA2 physiology, Ovarian Neoplasms genetics
Abstract: Background: BRCA1 and BRCA2 mutation carriers are at substantially increased risk for developing breast and ovarian cancer. The incomplete penetrance coupled with the variable age at diagnosis in carriers of the same mutation suggests the existence of genetic and nongenetic modifying factors. In this study, we evaluated the putative role of variants in many candidate modifier genes., Methods: Genotyping data from 15,252 BRCA1 and 8,211 BRCA2 mutation carriers, for known variants (n = 3,248) located within or around 445 candidate genes, were available through the iCOGS custom-designed array. Breast and ovarian cancer association analysis was performed within a retrospective cohort approach., Results: The observed P values of association ranged between 0.005 and 1.000. None of the variants was significantly associated with breast or ovarian cancer risk in either BRCA1 or BRCA2 mutation carriers, after multiple testing adjustments., Conclusion: There is little evidence that any of the evaluated candidate variants act as modifiers of breast and/or ovarian cancer risk in BRCA1 or BRCA2 mutation carriers., Impact: Genome-wide association studies have been more successful at identifying genetic modifiers of BRCA1/2 penetrance than candidate gene studies., (©2014 American Association for Cancer Research.)
Published: 2015
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48. Functional characterization of BRCA1 gene variants by mini-gene splicing assay.

Author: Steffensen AY, Dandanell M, Jønson L, Ejlertsen B, Gerdes AM, Nielsen FC, and Hansen Tv
Subjects: Animals, BRCA2 Protein genetics, Breast Neoplasms genetics, COS Cells, Chlorocebus aethiops, Exons, Female, Genetic Counseling, Genetic Predisposition to Disease, Genome, Human, Humans, Molecular Sequence Data, Reproducibility of Results, Sequence Analysis, DNA, BRCA1 Protein genetics, Genetic Variation, RNA Splicing
Abstract: Mutational screening of the breast cancer susceptibility gene BRCA1 leads to the identification of numerous pathogenic variants such as frameshift and nonsense variants, as well as large genomic rearrangements. The screening moreover identifies a large number of variants, for example, missense, silent, and intron variants, which are classified as variants of unknown clinical significance owing to the lack of causal evidence. Variants of unknown clinical significance can potentially have an impact on splicing and therefore functional examinations are warranted to classify whether these variants are pathogenic or benign. Here we validate a mini-gene splicing assay by comparing the results of 24 variants with previously published data from RT-PCR analysis on RNA from blood samples/lymphoblastoid cell lines. The analysis showed an overall concordance of 100%. In addition, we investigated 13 BRCA1 variants of unknown clinical significance or putative variants affecting splicing by in silico analysis and mini-gene splicing assay. Both the in silico analysis and mini-gene splicing assay classified six BRCA1 variants as pathogenic (c.80+1G>A, c.132C>T (p.=), c.213-1G>A, c.670+1delG, c.4185+1G>A, and c.5075-1G>C), whereas six BRCA1 variants were classified as neutral (c.-19-22_-19-21dupAT, c.302-15C>G, c.547+14delG, c.4676-20A>G, c.4987-21G>T, and c.5278-14C>G) and one BRCA1 variant remained unclassified (c.670+16G>A). In conclusion, our study emphasizes that in silico analysis and mini-gene splicing assays are important for the classification of variants, especially if no RNA is available from the patient. This knowledge is crucial for proper genetic counseling of patients and their family members.
Published: 2014
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49. Personalized oncology: genomic screening in phase 1.

Author: Tuxen IV, Jønson L, Santoni-Rugiu E, Hasselby JP, Nielsen FC, and Lassen U
Subjects: Biomarkers, Tumor genetics, Chromosome Mapping, DNA Mutational Analysis, Genetic Variation, Humans, Molecular Targeted Therapy, Neoplasms drug therapy, Clinical Trials, Phase I as Topic, Genetic Testing, Genomics, Neoplasms genetics, Neoplasms pathology, Patient Selection, Precision Medicine
Abstract: Improvements in cancer genomics and tumor biology have reinforced the evidence of cancer development driven by numerous genomic alterations. Advanced genomics technology can be used to characterize genomic alterations that potentially drive tumor growth. With the possibility of screening thousands of genes simultaneously, personalized molecular medicine has become an option. New treatments are being investigated in phase 1 trials around the world. Traditionally, the goal of phase 1 studies was to determine the optimal dose and assess dose-limiting toxicity of a potential new experimental drug. Only a limited number of patients will benefit from the treatment. However, introducing genomic mapping to select patients for early clinical trials with targeted molecular therapy according to the genomic findings, may lead to a better outcome for the patient, an enrichment of phase 1 trials, and thereby accelerated drug development. The overall advantage is to determine which mutation profiles correlate with sensitivity or lack of resistance to specific targeted therapies. The utility and current limitations of genomic screening to guide selection to Phase 1 clinical trial will be discussed., (© 2014 APMIS. Published by John Wiley & Sons Ltd.)
Published: 2014
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50. IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development.

Author: Jønson L, Christiansen J, Hansen TVO, Vikeså J, Yamamoto Y, and Nielsen FC
Subjects: Cell Line, Tumor, Cells, Cultured, HMGA2 Protein genetics, Humans, MicroRNAs genetics, Neoplasms metabolism, RNA, Messenger genetics, RNA-Binding Proteins genetics, Gene Expression Regulation, Neoplastic, HMGA2 Protein metabolism, MicroRNAs metabolism, RNA Stability, RNA, Messenger metabolism, RNA-Binding Proteins metabolism
Abstract: The IMP3 RNA-binding protein is associated with metastasis and poor outcome in human cancer. Using solid cancer transcriptome data, we found that IMP3 correlates with HMGA2 mRNA expression. Cytoplasmic IMP3 granules contain HMGA2, and IMP3 dose-dependently increases HMGA2 mRNA. HMGA2 is regulated by let-7, and let-7 antagomiRs make HMGA2 refractory to IMP3. Removal of let-7 target sites eliminates IMP3-dependent stabilization, and IMP3-containing bodies are depleted of Ago1-4 and miRNAs. The relationship between Hmga2 mRNA and IMPs also exists in the developing limb bud, where IMP1-deficient embryos show dose-dependent Hmga2 mRNA downregulation. Finally, IMP3 ribonucleoproteins (RNPs) contain other let-7 target mRNAs, including LIN28B, and a global gene set enrichment analysis demonstrates that miRNA-regulated transcripts in general are upregulated following IMP3 induction. We conclude that IMP3 RNPs may function as cytoplasmic safe houses and prevent miRNA-directed mRNA decay of oncogenes during tumor progression., (Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.)
Published: 2014
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