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1. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2

Author: O’Mahony, Denise G, Ramus, Susan J, Southey, Melissa C, Meagher, Nicola S, Hadjisavvas, Andreas, John, Esther M, Hamann, Ute, Imyanitov, Evgeny N, Andrulis, Irene L, Sharma, Priyanka, Daly, Mary B, Hake, Christopher R, Weitzel, Jeffrey N, Jakubowska, Anna, Godwin, Andrew K, Arason, Adalgeir, Bane, Anita, Simard, Jacques, Soucy, Penny, Caligo, Maria A, Mai, Phuong L, Claes, Kathleen BM, Teixeira, Manuel R, Chung, Wendy K, Lazaro, Conxi, Hulick, Peter J, Toland, Amanda E, Pedersen, Inge Sokilde, Neuhausen, Susan L, Vega, Ana, de la Hoya, Miguel, Nevanlinna, Heli, Dhawan, Mallika, Zampiga, Valentina, Danesi, Rita, Varesco, Liliana, Gismondi, Viviana, Vellone, Valerio Gaetano, James, Paul A, Janavicius, Ramunas, Nikitina-Zake, Liene, Nielsen, Finn Cilius, van Overeem Hansen, Thomas, Pejovic, Tanja, Borg, Ake, Rantala, Johanna, Offit, Kenneth, Montagna, Marco, Nathanson, Katherine L, Domchek, Susan M, Osorio, Ana, García, María J, Karlan, Beth Y, De Fazio, Anna, Bowtell, David, McGuffog, Lesley, Leslie, Goska, Parsons, Michael T, Dörk, Thilo, Speith, Lisa-Marie, dos Santos, Elizabeth Santana, da Costa, Alexandre André BA, Radice, Paolo, Peterlongo, Paolo, Papi, Laura, Engel, Christoph, Hahnen, Eric, Schmutzler, Rita K, Wappenschmidt, Barbara, Easton, Douglas F, Tischkowitz, Marc, Singer, Christian F, Tan, Yen Yen, Whittemore, Alice S, Sieh, Weiva, Brenton, James D, Yannoukakos, Drakoulis, Fostira, Florentia, Konstantopoulou, Irene, Soukupova, Jana, Vocka, Michal, Chenevix-Trench, Georgia, Pharoah, Paul DP, Antoniou, Antonis C, Goldgar, David E, Spurdle, Amanda B, and Michailidou, Kyriaki
Subjects: Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Rare Diseases, Cancer, Breast Cancer, Genetics, Ovarian Cancer, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Humans, Female, Virulence, BRCA1 Protein, BRCA2 Protein, Ovarian Neoplasms, Genetic Predisposition to Disease, Breast Neoplasms, HEBON Investigators, GEMO Study Collaborators, AOCS Group, CZECANCA Consortium, Consortium of Investigators of Modifiers of BRCA1/2, Evidence-based Network for the Interpretation of Germline Mutant Alleles Consortium, Public Health and Health Services, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract: BackgroundThe distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system.MethodsData for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong).ResultsNo histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis.ConclusionsWe provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.
Published: 2023

2. Distinct Reproductive Risk Profiles for Intrinsic-Like Breast Cancer Subtypes: Pooled Analysis of Population-Based Studies

Author: Jung, Audrey Y, Ahearn, Thomas U, Behrens, Sabine, Middha, Pooja, Bolla, Manjeet K, Wang, Qin, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Freeman, Laura E Beane, Becher, Heiko, Brenner, Hermann, Canzian, Federico, Carey, Lisa A, Consortium, CTS, Czene, Kamila, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Figueroa, Jonine D, Fritschi, Lin, Gabrielson, Marike, Giles, Graham G, Guénel, Pascal, Hadjisavvas, Andreas, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hoppe, Reiner, Hopper, John L, Howell, Anthony, Hunter, David J, Hüsing, Anika, Kaaks, Rudolf, Kosma, Veli-Matti, Koutros, Stella, Kraft, Peter, Lacey, James V, Le Marchand, Loic, Lissowska, Jolanta, Loizidou, Maria A, Mannermaa, Arto, Maurer, Tabea, Murphy, Rachel A, Olshan, Andrew F, Olsson, Håkan, Patel, Alpa V, Perou, Charles M, Rennert, Gad, Shibli, Rana, Shu, Xiao-Ou, Southey, Melissa C, Stone, Jennifer, Tamimi, Rulla M, Teras, Lauren R, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Wang, Sophia S, Wolk, Alicja, Wu, Anna H, Yang, Xiaohong R, Zheng, Wei, Dunning, Alison M, Pharoah, Paul DP, Easton, Douglas F, Milne, Roger L, Chatterjee, Nilanjan, Schmidt, Marjanka K, García-Closas, Montserrat, and Chang-Claude, Jenny
Subjects: Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Breast Cancer, Aging, Reproductive health and childbirth, Female, Humans, Breast Neoplasms, Receptor, ErbB-2, Receptors, Progesterone, Receptors, Estrogen, Triple Negative Breast Neoplasms, Case-Control Studies, Risk Factors, Biomarkers, Tumor, CTS Consortium, Receptor, erbB-2, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract: BackgroundReproductive factors have been shown to be differentially associated with risk of estrogen receptor (ER)-positive and ER-negative breast cancer. However, their associations with intrinsic-like subtypes are less clear.MethodsAnalyses included up to 23 353 cases and 71 072 controls pooled from 31 population-based case-control or cohort studies in the Breast Cancer Association Consortium across 16 countries on 4 continents. Polytomous logistic regression was used to estimate the association between reproductive factors and risk of breast cancer by intrinsic-like subtypes (luminal A-like, luminal B-like, luminal B-HER2-like, HER2-enriched-like, and triple-negative breast cancer) and by invasiveness. All statistical tests were 2-sided.ResultsCompared with nulliparous women, parous women had a lower risk of luminal A-like, luminal B-like, luminal B-HER2-like, and HER2-enriched-like disease. This association was apparent only after approximately 10 years since last birth and became stronger with increasing time (odds ratio [OR] = 0.59, 95% confidence interval [CI] = 0.49 to 0.71; and OR = 0.36, 95% CI = 0.28 to 0.46 for multiparous women with luminal A-like tumors 20 to less than 25 years after last birth and 45 to less than 50 years after last birth, respectively). In contrast, parous women had a higher risk of triple-negative breast cancer right after their last birth (for multiparous women: OR = 3.12, 95% CI = 2.02 to 4.83) that was attenuated with time but persisted for decades (OR = 1.03, 95% CI = 0.79 to 1.34, for multiparous women 25 to less than 30 years after last birth). Older age at first birth (Pheterogeneity < .001 for triple-negative compared with luminal A-like breast cancer) and breastfeeding (Pheterogeneity < .001 for triple-negative compared with luminal A-like breast cancer) were associated with lower risk of triple-negative breast cancer but not with other disease subtypes. Younger age at menarche was associated with higher risk of all subtypes; older age at menopause was associated with higher risk of luminal A-like but not triple-negative breast cancer. Associations for in situ tumors were similar to luminal A-like.ConclusionsThis large and comprehensive study demonstrates a distinct reproductive risk factor profile for triple-negative breast cancer compared with other subtypes, with implications for the understanding of disease etiology and risk prediction.
Published: 2022

3. Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk

Author: Wilcox, Naomi, Dumont, Martine, González-Neira, Anna, Carvalho, Sara, Joly Beauparlant, Charles, Crotti, Marco, Luccarini, Craig, Soucy, Penny, Dubois, Stéphane, Nuñez-Torres, Rocio, Pita, Guillermo, Gardner, Eugene J., Dennis, Joe, Alonso, M. Rosario, Álvarez, Nuria, Baynes, Caroline, Collin-Deschesnes, Annie Claude, Desjardins, Sylvie, Becher, Heiko, Behrens, Sabine, Bolla, Manjeet K., Castelao, Jose E., Chang-Claude, Jenny, Cornelissen, Sten, Dörk, Thilo, Engel, Christoph, Gago-Dominguez, Manuela, Guénel, Pascal, Hadjisavvas, Andreas, Hahnen, Eric, Hartman, Mikael, Herráez, Belén, Jung, Audrey, Keeman, Renske, Kiechle, Marion, Li, Jingmei, Loizidou, Maria A., Lush, Michael, Michailidou, Kyriaki, Panayiotidis, Mihalis I., Sim, Xueling, Teo, Soo Hwang, Tyrer, Jonathan P., van der Kolk, Lizet E., Wahlström, Cecilia, Wang, Qin, Perry, John R. B., Benitez, Javier, Schmidt, Marjanka K., Schmutzler, Rita K., Pharoah, Paul D. P., Droit, Arnaud, Dunning, Alison M., Kvist, Anders, Devilee, Peter, Easton, Douglas F., and Simard, Jacques
Published: 2023
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4. FANCM missense variants and breast cancer risk: a case-control association study of 75,156 European women

Author: Figlioli, Gisella, Billaud, Amandine, Ahearn, Thomas U., Antonenkova, Natalia N., Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blok, Marinus J., Bogdanova, Natalia V., Bonanni, Bernardo, Burwinkel, Barbara, Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Cessna, Melissa H., Chanock, Stephen J., Czene, Kamila, Devilee, Peter, Dörk, Thilo, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A., Figueroa, Jonine D., Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, González-Neira, Anna, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Harrington, Patricia A., He, Wei, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J., Hoppe, Reiner, Howell, Anthony, Humphreys, Keith, Jager, Agnes, Jakubowska, Anna, Khusnutdinova, Elza K., Ko, Yon-Dschun, Kristensen, Vessela N., Lindblom, Annika, Lissowska, Jolanta, Lubiński, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Mavroudis, Dimitrios, Newman, William G., Obi, Nadia, Panayiotidis, Mihalis I., Rashid, Muhammad U., Rhenius, Valerie, Rookus, Matti A., Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Shah, Mitul, Sironen, Reijo, Southey, Melissa C., Suvanto, Maija, Tollenaar, Rob A. E. M., Tomlinson, Ian, Truong, Thérèse, van der Kolk, Lizet E., van Veen, Elke M., Wappenschmidt, Barbara, Yang, Xiaohong R., Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Easton, Douglas F., Lush, Michael, Michailidou, Kyriaki, Pharoah, Paul D. P., Wang, Qin, Adank, Muriel A., Schmidt, Marjanka K., Andrulis, Irene L., Chang-Claude, Jenny, Nevanlinna, Heli, Chenevix-Trench, Georgia, Evans, D. Gareth, Milne, Roger L., Radice, Paolo, and Peterlongo, Paolo
Published: 2023
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5. Breast Cancer Risk Genes — Association Analysis in More than 113,000 Women

Author: Dorling, Leila, Carvalho, Sara, Allen, Jamie, González-Neira, Anna, Luccarini, Craig, Wahlström, Cecilia, Pooley, Karen A, Parsons, Michael T, Fortuno, Cristina, Wang, Qin, Bolla, Manjeet K, Dennis, Joe, Keeman, Renske, Alonso, M Rosario, Álvarez, Nuria, Herraez, Belen, Fernandez, Victoria, Núñez-Torres, Rocio, Osorio, Ana, Valcich, Jeanette, Li, Minerva, Törngren, Therese, Harrington, Patricia A, Baynes, Caroline, Conroy, Don M, Decker, Brennan, Fachal, Laura, Mavaddat, Nasim, Ahearn, Thomas, Aittomäki, Kristiina, Antonenkova, Natalia N, Arnold, Norbert, Arveux, Patrick, Ausems, Margreet GEM, Auvinen, Päivi, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Białkowska, Katarzyna, Blomqvist, Carl, Bogdanova, Natalia V, Bogdanova-Markov, Nadja, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Bremer, Michael, Briceno, Ignacio, Brüning, Thomas, Burwinkel, Barbara, Cameron, David A, Camp, Nicola J, Campbell, Archie, Carracedo, Angel, Castelao, Jose E, Cessna, Melissa H, Chanock, Stephen J, Christiansen, Hans, Collée, J Margriet, Cordina-Duverger, Emilie, Cornelissen, Sten, Czene, Kamila, Dörk, Thilo, Ekici, Arif B, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Försti, Asta, Gabrielson, Marike, Gago-Dominguez, Manuela, Georgoulias, Vassilios, Gil, Fabian, Giles, Graham G, Glendon, Gord, Garcia, Encarna B Gómez, Alnæs, Grethe I Grenaker, Guénel, Pascal, Hadjisavvas, Andreas, Haeberle, Lothar, Hahnen, Eric, Hall, Per, Hamann, Ute, Harkness, Elaine F, Hartikainen, Jaana M, Hartman, Mikael, He, Wei, Heemskerk-Gerritsen, Bernadette AM, Hillemanns, Peter, Hogervorst, Frans BL, Hollestelle, Antoinette, Ho, Weang Kee, Hooning, Maartje J, Howell, Anthony, Humphreys, Keith, Idris, Faiza, Jakubowska, Anna, and Jung, Audrey
Subjects: Breast Cancer, Cancer, Genetics, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Age Factors, Aged, Aged, 80 and over, Breast Neoplasms, Female, Genetic Predisposition to Disease, Genetic Variation, Humans, Logistic Models, Middle Aged, Mutation, Missense, Odds Ratio, Risk, Sequence Analysis, DNA, Young Adult, Breast Cancer Association Consortium, Medical and Health Sciences, General & Internal Medicine
Abstract: BackgroundGenetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking.MethodsWe used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity.ResultsProtein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants.ConclusionsThe results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.).
Published: 2021

6. Author Correction: Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk

Author: Wilcox, Naomi, Dumont, Martine, González-Neira, Anna, Carvalho, Sara, Joly Beauparlant, Charles, Crotti, Marco, Luccarini, Craig, Soucy, Penny, Dubois, Stéphane, Nuñez-Torres, Rocio, Pita, Guillermo, Gardner, Eugene J., Dennis, Joe, Alonso, M. Rosario, Álvarez, Nuria, Baynes, Caroline, Collin-Deschesnes, Annie Claude, Desjardins, Sylvie, Becher, Heiko, Behrens, Sabine, Bolla, Manjeet K., Castelao, Jose E., Chang-Claude, Jenny, Cornelissen, Sten, Dörk, Thilo, Engel, Christoph, Gago-Dominguez, Manuela, Guénel, Pascal, Hadjisavvas, Andreas, Hahnen, Eric, Hartman, Mikael, Herráez, Belén, Jung, Audrey, Keeman, Renske, Kiechle, Marion, Li, Jingmei, Loizidou, Maria A., Lush, Michael, Michailidou, Kyriaki, Panayiotidis, Mihalis I., Sim, Xueling, Teo, Soo Hwang, Tyrer, Jonathan P., van der Kolk, Lizet E., Wahlström, Cecilia, Wang, Qin, Perry, John R. B., Benitez, Javier, Schmidt, Marjanka K., Schmutzler, Rita K., Pharoah, Paul D. P., Droit, Arnaud, Dunning, Alison M., Kvist, Anders, Devilee, Peter, Easton, Douglas F., and Simard, Jacques
Published: 2023
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7. Breast cancer risks associated with missense variants in breast cancer susceptibility genes

Author: Dorling, Leila, Carvalho, Sara, Allen, Jamie, Parsons, Michael T., Fortuno, Cristina, González-Neira, Anna, Heijl, Stephan M., Adank, Muriel A., Ahearn, Thomas U., Andrulis, Irene L., Auvinen, Päivi, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bermisheva, Marina, Bogdanova, Natalia V., Bojesen, Stig E., Bolla, Manjeet K., Bremer, Michael, Briceno, Ignacio, Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Collée, J. Margriet, Czene, Kamila, Dennis, Joe, Dörk, Thilo, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, Giles, Graham G., Glendon, Gord, Guénel, Pascal, Gündert, Melanie, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Harkness, Elaine F., Hartman, Mikael, Hogervorst, Frans B. L., Hollestelle, Antoinette, Hoppe, Reiner, Howell, Anthony, Jakubowska, Anna, Jung, Audrey, Khusnutdinova, Elza, Kim, Sung-Won, Ko, Yon-Dschun, Kristensen, Vessela N., Lakeman, Inge M. M., Li, Jingmei, Lindblom, Annika, Loizidou, Maria A., Lophatananon, Artitaya, Lubiński, Jan, Luccarini, Craig, Madsen, Michael J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Milne, Roger L., Mohd Taib, Nur Aishah, Muir, Kenneth, Nevanlinna, Heli, Newman, William G., Oosterwijk, Jan C., Park, Sue K., Peterlongo, Paolo, Radice, Paolo, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Shah, Mitul, Sim, Xueling, Southey, Melissa C., Surowy, Harald, Suvanto, Maija, Tomlinson, Ian, Torres, Diana, Truong, Thérèse, van Asperen, Christi J., Waltes, Regina, Wang, Qin, Yang, Xiaohong R., Pharoah, Paul D. P., Schmidt, Marjanka K., Benitez, Javier, Vroling, Bas, Dunning, Alison M., Teo, Soo Hwang, Kvist, Anders, de la Hoya, Miguel, Devilee, Peter, Spurdle, Amanda B., Vreeswijk, Maaike P. G., and Easton, Douglas F.
Published: 2022
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8. Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Christodoulou, Kyproula, Spyrou, George M., Kyriacou, Kyriacos, and Hadjisavvas, Andreas
Published: 2021
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9. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility

Author: Landi, Maria Teresa, Bishop, D. Timothy, MacGregor, Stuart, Machiela, Mitchell J., Stratigos, Alexander J., Ghiorzo, Paola, Brossard, Myriam, Calista, Donato, Choi, Jiyeon, Fargnoli, Maria Concetta, Zhang, Tongwu, Rodolfo, Monica, Trower, Adam J., Menin, Chiara, Martinez, Jacobo, Hadjisavvas, Andreas, Song, Lei, Stefanaki, Irene, Scolyer, Richard, Yang, Rose, Goldstein, Alisa M., Potrony, Miriam, Kypreou, Katerina P., Pastorino, Lorenza, Queirolo, Paola, Pellegrini, Cristina, Cattaneo, Laura, Zawistowski, Matthew, Gimenez-Xavier, Pol, Rodriguez, Arantxa, Elefanti, Lisa, Manoukian, Siranoush, Rivoltini, Licia, Smith, Blair H., Loizidou, Maria A., Del Regno, Laura, Massi, Daniela, Mandala, Mario, Khosrotehrani, Kiarash, Akslen, Lars A., Amos, Christopher I., Andresen, Per A., Avril, Marie-Françoise, Azizi, Esther, Soyer, H. Peter, Bataille, Veronique, Dalmasso, Bruna, Bowdler, Lisa M., Burdon, Kathryn P., Chen, Wei V., Codd, Veryan, Craig, Jamie E., Dębniak, Tadeusz, Falchi, Mario, Fang, Shenying, Friedman, Eitan, Simi, Sarah, Galan, Pilar, Garcia-Casado, Zaida, Gillanders, Elizabeth M., Gordon, Scott, Green, Adele, Gruis, Nelleke A., Hansson, Johan, Harland, Mark, Harris, Jessica, Helsing, Per, Henders, Anjali, Hočevar, Marko, Höiom, Veronica, Hunter, David, Ingvar, Christian, Kumar, Rajiv, Lang, Julie, Lathrop, G. Mark, Lee, Jeffrey E., Li, Xin, Lubiński, Jan, Mackie, Rona M., Malt, Maryrose, Malvehy, Josep, McAloney, Kerrie, Mohamdi, Hamida, Molven, Anders, Moses, Eric K., Neale, Rachel E., Novaković, Srdjan, Nyholt, Dale R., Olsson, Håkan, Orr, Nicholas, Fritsche, Lars G., Puig-Butille, Joan Anton, Qureshi, Abrar A., Radford-Smith, Graham L., Randerson-Moor, Juliette, Requena, Celia, Rowe, Casey, Samani, Nilesh J., Sanna, Marianna, Schadendorf, Dirk, Schulze, Hans-Joachim, Simms, Lisa A., Smithers, Mark, Song, Fengju, Swerdlow, Anthony J., van der Stoep, Nienke, Kukutsch, Nicole A., Visconti, Alessia, Wallace, Leanne, Ward, Sarah V., Wheeler, Lawrie, Sturm, Richard A., Hutchinson, Amy, Jones, Kristine, Malasky, Michael, Vogt, Aurelie, Zhou, Weiyin, Pooley, Karen A., Elder, David E., Han, Jiali, Hicks, Belynda, Hayward, Nicholas K., Kanetsky, Peter A., Brummett, Chad, Montgomery, Grant W., Olsen, Catherine M., Hayward, Caroline, Dunning, Alison M., Martin, Nicholas G., Evangelou, Evangelos, Mann, Graham J., Long, Georgina, Pharoah, Paul D. P., Easton, Douglas F., Barrett, Jennifer H., Cust, Anne E., Abecasis, Goncalo, Duffy, David L., Whiteman, David C., Gogas, Helen, De Nicolo, Arcangela, Tucker, Margaret A., Newton-Bishop, Julia A., Peris, Ketty, Chanock, Stephen J., Demenais, Florence, Brown, Kevin M., Puig, Susana, Nagore, Eduardo, Shi, Jianxin, Iles, Mark M., and Law, Matthew H.
Published: 2020
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10. Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset

Author: Sahlberg, Kristine K., Børresen-Dale, Anne-Lise, Gram, Inger Torhild, Olsen, Karina Standahl, Engebråten, Olav, Naume, Bjørn, Geisler, Jürgen, OSBREAC, Grenaker Alnæs, Grethe I., Amor, David, Andrews, Lesley, Antill, Yoland, Balleine, Rosemary, Beesley, Jonathan, Bennett, Ian, Bogwitz, Michael, Bodek, Simon, Botes, Leon, Brennan, Meagan, Brown, Melissa, Buckley, Michael, Burke, Jo, Butow, Phyllis, Caldon, Liz, Campbell, Ian, Cao, Michelle, Chakrabarti, Anannya, Chauhan, Deepa, Chauhan, Manisha, Christian, Alice, Cohen, Paul, Colley, Alison, Crook, Ashley, Cui, James, Courtney, Eliza, Cummings, Margaret, Dawson, Sarah-Jane, deFazio, Anna, Delatycki, Martin, Dickson, Rebecca, Dixon, Joanne, Edwards, Stacey, Farshid, Gelareh, Fellows, Andrew, Fenton, Georgina, Field, Michael, Flanagan, James, Fong, Peter, Forrest, Laura, Fox, Stephen, French, Juliet, Friedlander, Michael, Gaff, Clara, Gattas, Mike, George, Peter, Greening, Sian, Harris, Marion, Hart, Stewart, Harraka, Philip, Hayward, Nick, Hopper, John, Hoskins, Cass, Hunt, Clare, Jenkins, Mark, Kidd, Alexa, Kirk, Judy, Koehler, Jessica, Kollias, James, Lakhani, Sunil, Lawrence, Mitchell, Lee, Jason, Li, Shuai, Lindeman, Geoff, Lippey, Jocelyn, Lipton, Lara, Lobb, Liz, Loi, Sherene, Mann, Graham, Marsh, Deborah, McLachlan, Sue Anne, Meiser, Bettina, Nightingale, Sophie, O'Connell, Shona, O'Sullivan, Sarah, Ortega, David Gallego, Pachter, Nick, Pang, Jia-Min, Pathak, Gargi, Patterson, Briony, Pearn, Amy, Phillips, Kelly, Pieper, Ellen, Ramus, Susan, Rickard, Edwina, Ragunathan, Abi, Robinson, Bridget, Saleh, Mona, Skandarajah, Anita, Salisbury, Elizabeth, Saunders, Christobel, Saunus, Jodi, Savas, Peter, Scott, Rodney, Scott, Clare, Sexton, Adrienne, Shaw, Joanne, Shelling, Andrew, Srinivasa, Shweta, Simpson, Peter, Taylor, Jessica, Taylor, Renea, Thorne, Heather, Trainer, Alison, Tucker, Kathy, Visvader, Jane, Walker, Logan, Williams, Rachael, Winship, Ingrid, Young, Mary Ann, Zaheed, Milita, Davidson, Aimee L., Michailidou, Kyriaki, Parsons, Michael T., Fortuno, Cristina, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Naven, Marc, Abubakar, Mustapha, Ahearn, Thomas U., Alonso, M. Rosario, Andrulis, Irene L., Antoniou, Antonis C., Auvinen, Päivi, Behrens, Sabine, Bermisheva, Marina A., Bogdanova, Natalia V., Bojesen, Stig E., Brüning, Thomas, Byers, Helen J., Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Cessna, Melissa H., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Collée, J. Margriet, Czene, Kamila, Dörk, Thilo, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine D., Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, Glendon, Gord, González-Neira, Anna, Grassmann, Felix, Gronwald, Jacek, Guénel, Pascal, Hadjisavvas, Andreas, Haeberle, Lothar, Hall, Per, Hamann, Ute, Hartman, Mikael, Ho, Peh Joo, Hooning, Maartje J., Hoppe, Reiner, Howell, Anthony, Jakubowska, Anna, Khusnutdinova, Elza K., Kristensen, Vessela N., Li, Jingmei, Lim, Joanna, Lindblom, Annika, Liu, Jenny, Lophatananon, Artitaya, Mannermaa, Arto, Mavroudis, Dimitrios A., Mensenkamp, Arjen R., Milne, Roger L., Muir, Kenneth R., Newman, William G., Obi, Nadia, Panayiotidis, Mihalis I., Park, Sue K., Park-Simon, Tjoung-Won, Peterlongo, Paolo, Radice, Paolo, Rashid, Muhammad U., Rhenius, Valerie, Saloustros, Emmanouil, Sawyer, Elinor J., Schmidt, Marjanka K., Seibold, Petra, Shah, Mitul, Southey, Melissa C., Teo, Soo Hwang, Tomlinson, Ian, Torres, Diana, Truong, Thérèse, van de Beek, Irma, van der Hout, Annemieke H., Wendt, Camilla C., Dunning, Alison M., Pharoah, Paul D.P., Devilee, Peter, Easton, Douglas F., James, Paul A., and Spurdle, Amanda B.
Published: 2024
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11. Improved cellular uptake of perfluorocarbon nanoparticles for in vivo murine cardiac 19F MRS/MRI and temporal tracking of progenitor cells

Author: Constantinides, Christakis, McNeill, Eileen, Carnicer, Ricardo, Al Haj Zen, Ayman, Sainz-Urruela, Raquel, Shaw, Andrew, Patel, Jyoti, Swider, Edyta, Alonaizan, Rita, Potamiti, Louiza, Hadjisavvas, Andreas, Padilla-Parra, Sergi, Kyriacou, Kyriacos, Srinivas, Mangala, and Carr, Carolyn A.
Published: 2019
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12. Multi-gene panel testing and association analysis in Cypriot breast cancer cases and controls

Author: Zanti, Maria, primary, Loizidou, Maria A., additional, O’Mahony, Denise G., additional, Dorling, Leila, additional, Dennis, Joe, additional, Devilee, Peter, additional, Easton, Douglas F., additional, Panayiotidis, Mihalis I., additional, Hadjisavvas, Andreas, additional, and Michailidou, Kyriaki, additional
Published: 2023
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13. The Mediterranean diet and breast cancer risk

Author: Demetriou, Christiana A., primary, Kakkoura, Maria G., additional, Hadjisavvas, Andreas, additional, Loizidou, Maria A., additional, Sacerdote, Carlotta, additional, Vineis, Paolo, additional, and Kyriacou, Kyriacos, additional
Published: 2020
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14. Contributors

Author: Abete, Itziar, primary, Aboussaleh, Youssef, additional, Accardi, Giulia, additional, Aiello, Anna, additional, Alkhatib, Ahmad, additional, Alves Castro, Inar, additional, Andújar, Isabel, additional, Antonopoulou, Smaragdi, additional, Arsic, Aleksandra, additional, Arvanitidou, Eirini-Iro, additional, Assaf-Balut, Carla, additional, Barabash, Ana, additional, Barbagallo, Mario, additional, Bastida, Sara, additional, Beccari, Giovanni, additional, Benedí, Juana, additional, Bentrad, Najla, additional, Bernal-Lopez, M. Rosa, additional, Bonaccio, Marialaura, additional, Bonanni, Americo, additional, Bordiú, Elena, additional, Bottalico, Francesco, additional, Boutopoulou, Barbara, additional, Buscemi, Silvio, additional, Calle-Pascual, Alfonso Luis, additional, Cámara, Montaña, additional, Candore, Giuseppina, additional, Capone, Roberto, additional, Caputo, Marina, additional, Cardone, Gianluigi, additional, Caruso, Calogero, additional, Caso, Giulia, additional, Castro-Quezada, Itandehui, additional, Cebadera-Miranda, Laura, additional, Cerezo, Ana B., additional, Corleo, Davide, additional, Corrêa, Rúbia C.G., additional, Covarelli, Lorenzo, additional, Czarczyńska-Goślińska, Beata, additional, Davinelli, Sergio, additional, del Valle, Laura, additional, Delgado-Andrade, Cristina, additional, Demetriou, Christiana A., additional, Detopoulou, Paraskevi, additional, Di Gioia, Francesco, additional, Diamantopoulos, E.J., additional, Dominguez, Ligia J., additional, Donati, Maria Benedetta, additional, Douros, Konstantinos, additional, Durán, Alejandra, additional, El Bilali, Hamid, additional, El Kinany, Khaoula, additional, El Rhazi, Karima, additional, Ergoren, Mahmut Cerkez, additional, De Feo, Vincenzo, additional, Ferreira, Isabel C.F.R., additional, Formica, Melissa, additional, Fragopoulou, Elizabeth, additional, Fratianni, Florinda, additional, de Gaetano, Giovanni, additional, Gaforio, José J., additional, Galarregui, Cristina, additional, Gallardo-Escribano, Cristina, additional, Galozzi, Paola, additional, Galvano, Fabio, additional, Garces-Martin, Maria, additional, Garcia-Larsen, Vanessa, additional, Garcia-Parrilla, M. Carmen, additional, Garcimartín, Alba, additional, Geliebter, Jan, additional, George, Elena S., additional, Georgousopoulou, Ekavi N., additional, Gesteiro, E., additional, Gkiouras, Konstantinos, additional, Gómez-Pérez, Ana María, additional, Goulis, Dimitrios G., additional, Gouveri, E., additional, Grammatikopoulou, Maria G., additional, Hadjisavvas, Andreas, additional, Hamida-Ferhat, Asma, additional, Hardman, Roy J., additional, Hornedo-Ortega, Ruth, additional, Iacoviello, Licia, additional, Iriti, Marcello, additional, Jeszka-Skowron, Magdalena, additional, Kakkoura, Maria G., additional, Karras, Spyridon N., additional, Knox, E., additional, Kotsa, Kalliopi, additional, Koufakis, Theocharis, additional, Koumpagioti, Despina, additional, Kyriacou, Kyriacos, additional, de la Torre, Nuria García, additional, Lampropoulou, Maria, additional, Loizidou, Maria A., additional, De Lorenzo, Antonino, additional, Macho-González, Adrián, additional, Magriplis, Emmanuella, additional, Marakomichelakis, G., additional, Martínez, J. Alfredo, additional, De Martino, Laura, additional, Medina, F. Xavier, additional, Mellor, Duane D., additional, Menotti, Alessandro, additional, Mesías, Marta, additional, Molina-Vega, María, additional, Morales, Patricia, additional, Moreno, Juan A., additional, Muros, J.J., additional, Nazzaro, Filomena, additional, Nomikos, Tzortzis, additional, Oliviero, Francesca, additional, Ottomano Palmisano, Giovanni, additional, de Pablos, Rocío M., additional, Panagiotakos, Demosthenes B., additional, Papandreou, Christopher, additional, Petropoulos, Spyridon A., additional, Prodam, Flavia, additional, Puddu, Paolo Emilio, additional, Punzi, Leonardo, additional, Quiles, José L., additional, Ramirez-Perez, Cristina, additional, Ramirez-Tortosa, Cesar L., additional, Ramírez-Tortosa, MCarmen, additional, Richard, Tristan, additional, Ricotti, Roberta, additional, Ríos, José-Luis, additional, Rodríguez-García, Carmen, additional, Román-Viñas, Blanca, additional, Ros, Emilio, additional, Rubio, Miguel Angel, additional, Ruiz-Moreno, M. Isabel, additional, Sacerdote, Carlotta, additional, Salas-Salvadó, Jordi, additional, Sánchez-Muniz, Francisco J., additional, Sánchez-Quesada, Cristina, additional, Scapagnini, Giovanni, additional, Scolaro, Bianca, additional, Seiquer, Isabel, additional, Serra-Majem, Lluís, additional, Sfriso, Paolo, additional, Spinella, Paolo, additional, Theodoridis, Xenophon, additional, Tinahones, Francisco J., additional, Tini, Francesco, additional, Tiwari, Raj, additional, Tranidou, Antigoni, additional, Troncoso, Ana M., additional, Tsofliou, Fotini, additional, Tuncel, Gulten, additional, Valerio, Johanna, additional, Varoni, Elena Maria, additional, Vilches-Perez, Alberto, additional, Vineis, Paolo, additional, Vitalini, Sara, additional, Zalvan, Craig H., additional, Zampelas, Antonis, additional, Zebekakis, Pantelis, additional, and Zulet, M. Angeles, additional
Published: 2020
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15. The effect of l-Arginine on Ciliary Beat Frequency in PCD patients, non-PCD respiratory patients and healthy controls

Author: Kouis, Panayiotis, Hadjisavvas, Andreas, Middleton, Nicos, Papatheodorou, Stefania I., Kyriacou, Kyriacos, and Yiallouros, Panayiotis K.
Published: 2018
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16. Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis

Author: Nicolaou, Orthodoxia, Sokratous, Kleitos, Makowska, Zuzanna, Morell, María, De Groof, Aurélie, Montigny, Pauline, Hadjisavvas, Andreas, Michailidou, Kyriaki, Oulas, Anastasis, Spyrou, George M., Demetriou, Christiana, Alarcón-Riquelme, Marta E., Psarellis, Savvas, Kousios, Andreas, Lauwerys, Bernard, and Kyriacou, Kyriacos
Published: 2020
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17. BRCA1, BRCA2 molecular study of Cypriot breast cancer patients

Author: Hadjisavvas, Andreas
Subjects: 616, Genetics
Published: 2001

18. Gene variants of adhesion molecules predispose to MS: A case-control study

Author: Dardiotis, Efthimios, Panayiotou, Elena, Siokas, Vasileios, Aloizou, Athina-Maria, Christodoulou, Kyproula, Hadjisavvas, Andreas, Pantzaris, Marios, Grigoriadis, Nikolaos, Hadjigeorgiou, Georgios M., and Kyriakides, Theodoros
Published: 2019
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19. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2.

Author: O'Mahony, Denise G, O'Mahony, Denise G, Ramus, Susan J, Southey, Melissa C, Meagher, Nicola S, Hadjisavvas, Andreas, John, Esther M, Hamann, Ute, Imyanitov, Evgeny N, Andrulis, Irene L, Sharma, Priyanka, Daly, Mary B, Hake, Christopher R, Weitzel, Jeffrey N, Jakubowska, Anna, Godwin, Andrew K, Arason, Adalgeir, Bane, Anita, Simard, Jacques, Soucy, Penny, Caligo, Maria A, Mai, Phuong L, Claes, Kathleen BM, Teixeira, Manuel R, Chung, Wendy K, Lazaro, Conxi, Hulick, Peter J, Toland, Amanda E, Pedersen, Inge Sokilde, HEBON Investigators, Neuhausen, Susan L, Vega, Ana, de la Hoya, Miguel, Nevanlinna, Heli, Dhawan, Mallika, Zampiga, Valentina, Danesi, Rita, Varesco, Liliana, Gismondi, Viviana, Vellone, Valerio Gaetano, James, Paul A, Janavicius, Ramunas, Nikitina-Zake, Liene, Nielsen, Finn Cilius, van Overeem Hansen, Thomas, Pejovic, Tanja, Borg, Ake, Rantala, Johanna, Offit, Kenneth, Montagna, Marco, Nathanson, Katherine L, Domchek, Susan M, Osorio, Ana, García, María J, Karlan, Beth Y, GEMO Study Collaborators, De Fazio, Anna, Bowtell, David, AOCS Group, McGuffog, Lesley, Leslie, Goska, Parsons, Michael T, Dörk, Thilo, Speith, Lisa-Marie, Dos Santos, Elizabeth Santana, da Costa, Alexandre André BA, Radice, Paolo, Peterlongo, Paolo, Papi, Laura, Engel, Christoph, Hahnen, Eric, Schmutzler, Rita K, Wappenschmidt, Barbara, Easton, Douglas F, Tischkowitz, Marc, Singer, Christian F, Tan, Yen Yen, Whittemore, Alice S, Sieh, Weiva, Brenton, James D, Yannoukakos, Drakoulis, Fostira, Florentia, Konstantopoulou, Irene, Soukupova, Jana, Vocka, Michal, CZECANCA Consortium, Chenevix-Trench, Georgia, Pharoah, Paul DP, Antoniou, Antonis C, Goldgar, David E, Spurdle, Amanda B, Michailidou, Kyriaki, Consortium of Investigators of Modifiers of BRCA1/2, Evidence-based Network for the Interpretation of Germline Mutant Alleles Consortium, O'Mahony, Denise G, O'Mahony, Denise G, Ramus, Susan J, Southey, Melissa C, Meagher, Nicola S, Hadjisavvas, Andreas, John, Esther M, Hamann, Ute, Imyanitov, Evgeny N, Andrulis, Irene L, Sharma, Priyanka, Daly, Mary B, Hake, Christopher R, Weitzel, Jeffrey N, Jakubowska, Anna, Godwin, Andrew K, Arason, Adalgeir, Bane, Anita, Simard, Jacques, Soucy, Penny, Caligo, Maria A, Mai, Phuong L, Claes, Kathleen BM, Teixeira, Manuel R, Chung, Wendy K, Lazaro, Conxi, Hulick, Peter J, Toland, Amanda E, Pedersen, Inge Sokilde, HEBON Investigators, Neuhausen, Susan L, Vega, Ana, de la Hoya, Miguel, Nevanlinna, Heli, Dhawan, Mallika, Zampiga, Valentina, Danesi, Rita, Varesco, Liliana, Gismondi, Viviana, Vellone, Valerio Gaetano, James, Paul A, Janavicius, Ramunas, Nikitina-Zake, Liene, Nielsen, Finn Cilius, van Overeem Hansen, Thomas, Pejovic, Tanja, Borg, Ake, Rantala, Johanna, Offit, Kenneth, Montagna, Marco, Nathanson, Katherine L, Domchek, Susan M, Osorio, Ana, García, María J, Karlan, Beth Y, GEMO Study Collaborators, De Fazio, Anna, Bowtell, David, AOCS Group, McGuffog, Lesley, Leslie, Goska, Parsons, Michael T, Dörk, Thilo, Speith, Lisa-Marie, Dos Santos, Elizabeth Santana, da Costa, Alexandre André BA, Radice, Paolo, Peterlongo, Paolo, Papi, Laura, Engel, Christoph, Hahnen, Eric, Schmutzler, Rita K, Wappenschmidt, Barbara, Easton, Douglas F, Tischkowitz, Marc, Singer, Christian F, Tan, Yen Yen, Whittemore, Alice S, Sieh, Weiva, Brenton, James D, Yannoukakos, Drakoulis, Fostira, Florentia, Konstantopoulou, Irene, Soukupova, Jana, Vocka, Michal, CZECANCA Consortium, Chenevix-Trench, Georgia, Pharoah, Paul DP, Antoniou, Antonis C, Goldgar, David E, Spurdle, Amanda B, Michailidou, Kyriaki, Consortium of Investigators of Modifiers of BRCA1/2, and Evidence-based Network for the Interpretation of Germline Mutant Alleles Consortium
Abstract: BackgroundThe distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system.MethodsData for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong).ResultsNo histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis.ConclusionsWe provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.
Published: 2023

20. FANCM missense variants and breast cancer risk:a case-control association study of 75,156 European women

Author: Billaud, Amandine, Figlioli, Gisella, Ahearn, Thomas U, Antonenkova, Natalia N, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blok, Marinus J, Bogdanova, Natalia V, Bonanni, Bernardo, Burwinkel, Barbara, Camp, Nicola J, Campbell, Archie, Castelao, Jose E, Cessna, Melissa H, Chanock, Stephen J, Czene, Kamila, Devilee, Peter, Dörk, Thilo, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine D, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, González-Neira, Anna, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Harrington, Patricia A, He, Wei, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J, Hoppe, Reiner, Howell, Anthony, Humphreys, Keith, Jager, Agnes, Jakubowska, Anna, Khusnutdinova, Elza K, Ko, Yon-Dschun, Kristensen, Vessela N, Lindblom, Annika, Billaud, Amandine, Figlioli, Gisella, Ahearn, Thomas U, Antonenkova, Natalia N, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blok, Marinus J, Bogdanova, Natalia V, Bonanni, Bernardo, Burwinkel, Barbara, Camp, Nicola J, Campbell, Archie, Castelao, Jose E, Cessna, Melissa H, Chanock, Stephen J, Czene, Kamila, Devilee, Peter, Dörk, Thilo, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine D, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, González-Neira, Anna, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Harrington, Patricia A, He, Wei, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J, Hoppe, Reiner, Howell, Anthony, Humphreys, Keith, Jager, Agnes, Jakubowska, Anna, Khusnutdinova, Elza K, Ko, Yon-Dschun, Kristensen, Vessela N, and Lindblom, Annika
Abstract: Evidence from literature, including the BRIDGES study, indicates that germline protein truncating variants (PTVs) in FANCM confer moderately increased risk of ER-negative and triple-negative breast cancer (TNBC), especially for women with a family history of the disease. Association between FANCM missense variants (MVs) and breast cancer risk has been postulated. In this study, we further used the BRIDGES study to test 689 FANCM MVs for association with breast cancer risk, overall and in ER-negative and TNBC subtypes, in 39,885 cases (7566 selected for family history) and 35,271 controls of European ancestry. Sixteen common MVs were tested individually; the remaining rare 673 MVs were tested by burden analyses considering their position and pathogenicity score. We also conducted a meta-analysis of our results and those from published studies. We did not find evidence for association for any of the 16 variants individually tested. The rare MVs were significantly associated with increased risk of ER-negative breast cancer by burden analysis comparing familial cases to controls (OR = 1.48; 95% CI 1.07-2.04; P = 0.017). Higher ORs were found for the subgroup of MVs located in functional domains or predicted to be pathogenic. The meta-analysis indicated that FANCM MVs overall are associated with breast cancer risk (OR = 1.22; 95% CI 1.08-1.38; P = 0.002). Our results support the definition from previous analyses of FANCM as a moderate-risk breast cancer gene and provide evidence that FANCM MVs could be low/moderate risk factors for ER-negative and TNBC subtypes. Further genetic and functional analyses are necessary to clarify better the increased risks due to FANCM MVs.
Published: 2023

21. Clinical features of primary ciliary dyskinesia in Cyprus with emphasis on lobectomized patients

Author: Yiallouros, Panayiotis K., Kouis, Panayiotis, Middleton, Nicos, Nearchou, Marianna, Adamidi, Tonia, Georgiou, Andreas, Eleftheriou, Adonis, Ioannou, Phivos, Hadjisavvas, Andreas, and Kyriacou, Kyriacos
Published: 2015
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22. Observational study of health utilities in adult primary ciliary dyskinesia patients: preliminary data on associations with molecular diagnosis, clinical phenotype and HRQOL measures

Author: Kouis, Panayiotis, primary, Kakkoura, Maria G., additional, Elia, Stavria Artemis, additional, Ioannou, Phivos, additional, Anagnostopoulou, Pinelopi, additional, Potamiti, Louiza, additional, Loizidou, Maria A., additional, Panayiotidis, Mihalis I., additional, Kyriacou, Kyriacos, additional, Hadjisavvas, Andreas, additional, and Yiallouros, Panayiotis K., additional
Published: 2022
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23. Genetic Study of Early Onset Parkinson’s Disease in Cyprus

Author: Abu Manneh, Rana, primary, Chairta, Paraskevi P., additional, Mitsi, Ellie, additional, Loizidou, Maria A., additional, Georgiou, Andrea N., additional, Christou, Yiolanda P., additional, Pantzaris, Marios, additional, Zamba-Papanicolaou, Eleni, additional, and Hadjisavvas, Andreas, additional
Published: 2022
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24. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2

Author: O’Mahony, Denise G., Ramus, Susan J., Southey, Melissa C., Meagher, Nicola S., Hadjisavvas, Andreas, John, Esther M., Hamann, Ute, Imyanitov, Evgeny N., Andrulis, Irene L., Sharma, Priyanka, Daly, Mary B., Hake, Christopher R., Weitzel, Jeffrey N., Jakubowska, Anna, Godwin, Andrew K., Arason, Adalgeir, Bane, Anita, Simard, Jacques, Soucy, Penny, Caligo, Maria A., Mai, Phuong L., Claes, Kathleen B. M., Teixeira, Manuel R., Chung, Wendy K., Lazaro, Conxi, Hulick, Peter J., Toland, Amanda E., Pedersen, Inge Sokilde, Mourits, Marian J. E., Neuhausen, Susan L., Vega, Ana, de la Hoya, Miguel, Nevanlinna, Heli, Dhawan, Mallika, Zampiga, Valentina, Danesi, Rita, Varesco, Liliana, Gismondi, Viviana, Vellone, Valerio Gaetano, James, Paul A., Janavičius, Ramūnas, Nikitina-Zake, Liene, Nielsen, Finn Cilius, van Overeem Hansen, Thomas, Pejovic, Tanja, Borg, Ake, Rantala, Johanna, Offit, Kenneth, Montagna, Marco, Nathanson, Katherine L., Domchek, Susan M., Osorio, Ana, García, María J., Karlan, Beth Y., Lesueur, Fabienne, De Fazio, Anna, Bowtell, David, McGuffog, Lesley, Leslie, Goska, Parsons, Michael T., Dörk, Thilo, Speith, Lisa-Marie, dos Santos, Elizabeth Santana, da Costa, Alexandre André B. A., Radice, Paolo, Peterlongo, Paolo, Papi, Laura, Engel, Christoph, Hahnen, Eric, Schmutzler, Rita K., Wappenschmidt, Barbara, Easton, Douglas F., Tischkowitz, Marc, Singer, Christian F., Tan, Yen Yen, Whittemore, Alice S., Sieh, Weiva, Brenton, James D., Yannoukakos, Drakoulis, Fostira, Florentia, Konstantopoulou, Irene, Soukupova, Jana, Vocka, Michal, Chenevix-Trench, Georgia, Pharoah, Paul D. P., Antoniou, Antonis C., Goldgar, David E., Spurdle, Amanda B., and Michailidou, Kyriaki
Abstract: Background: The distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system. Methods: Data for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong). Results: No histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis. Conclusions: We provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management.
Published: 2023

25. The synergistic effect between the Mediterranean diet and GSTP1 or NAT2 SNPs decreases breast cancer risk in Greek-Cypriot women

Author: Kakkoura, Maria G., Loizidou, Maria A., Demetriou, Christiana A., Loucaides, Giorgos, Daniel, Maria, Kyriacou, Kyriacos, and Hadjisavvas, Andreas
Published: 2017
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26. FANCM missense variants and breast cancer risk: a case-control association study of 75,156 European women

Author: Figlioli, Gisella, Billaud, Amandine, Ahearn, Thomas U, Antonenkova, Natalia N, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blok, Marinus J, Bogdanova, Natalia V, Bonanni, Bernardo, Burwinkel, Barbara, Camp, Nicola J, Campbell, Archie, Castelao, Jose E, Cessna, Melissa H, Chanock, Stephen J, NBCS Collaborators, Czene, Kamila, Devilee, Peter, Dörk, Thilo, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine D, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, González-Neira, Anna, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Harrington, Patricia A, He, Wei, Hillemanns, Peter, Hollestelle, Antoinette, Hooning, Maartje J, Hoppe, Reiner, Howell, Anthony, Humphreys, Keith, KConFab Investigators, Jager, Agnes, Jakubowska, Anna, Khusnutdinova, Elza K, Ko, Yon-Dschun, Kristensen, Vessela N, Lindblom, Annika, Lissowska, Jolanta, Lubiński, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Mavroudis, Dimitrios, Newman, William G, Obi, Nadia, Panayiotidis, Mihalis I, Rashid, Muhammad U, Rhenius, Valerie, Rookus, Matti A, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Shah, Mitul, Sironen, Reijo, Southey, Melissa C, Suvanto, Maija, Tollenaar, Rob AEM, Tomlinson, Ian, Truong, Thérèse, Van Der Kolk, Lizet E, Van Veen, Elke M, Wappenschmidt, Barbara, Yang, Xiaohong R, Bolla, Manjeet K, Dennis, Joe, Dunning, Alison M, Easton, Douglas F, Lush, Michael, Michailidou, Kyriaki, Pharoah, Paul DP, Wang, Qin, Adank, Muriel A, Schmidt, Marjanka K, Andrulis, Irene L, Chang-Claude, Jenny, Nevanlinna, Heli, Chenevix-Trench, Georgia, Evans, D Gareth, Milne, Roger L, Radice, Paolo, Peterlongo, Paolo, Figlioli, Gisella [0000-0002-0740-1363], Becher, Heiko [0000-0002-8808-6667], Behrens, Sabine [0000-0002-9714-104X], Blok, Marinus J [0000-0002-7935-5933], Bonanni, Bernardo [0000-0003-3589-2128], Chanock, Stephen J [0000-0002-2324-3393], Devilee, Peter [0000-0002-8023-2009], Dörk, Thilo [0000-0002-9458-0282], Fasching, Peter A [0000-0003-4885-8471], Grassmann, Felix [0000-0003-1390-7528], Hollestelle, Antoinette [0000-0003-1166-1966], Jakubowska, Anna [0000-0002-5650-0501], Lissowska, Jolanta [0000-0003-2695-5799], Newman, William G [0000-0002-6382-4678], Panayiotidis, Mihalis I [0000-0002-1450-3552], Rashid, Muhammad U [0000-0002-7684-3122], Saloustros, Emmanouil [0000-0002-0485-0120], Yang, Xiaohong R [0000-0003-4451-8664], Dennis, Joe [0000-0003-4591-1214], Easton, Douglas F [0000-0003-2444-3247], Michailidou, Kyriaki [0000-0001-7065-1237], Pharoah, Paul DP [0000-0001-8494-732X], Schmidt, Marjanka K [0000-0002-2228-429X], Andrulis, Irene L [0000-0002-4226-6435], Nevanlinna, Heli [0000-0002-0916-2976], Milne, Roger L [0000-0001-5764-7268], Radice, Paolo [0000-0001-6298-4111], Peterlongo, Paolo [0000-0001-6951-6855], and Apollo - University of Cambridge Repository
Subjects: DNA Helicases, Humans, Female, Breast Neoplasms, Triple Negative Breast Neoplasms, Genetic Predisposition to Disease, KConFab Investigators, NBCS Collaborators
Abstract: Evidence from literature, including the BRIDGES study, indicates that germline protein truncating variants (PTVs) in FANCM confer moderately increased risk of ER-negative and triple-negative breast cancer (TNBC), especially for women with a family history of the disease. Association between FANCM missense variants (MVs) and breast cancer risk has been postulated. In this study, we further used the BRIDGES study to test 689 FANCM MVs for association with breast cancer risk, overall and in ER-negative and TNBC subtypes, in 39,885 cases (7566 selected for family history) and 35,271 controls of European ancestry. Sixteen common MVs were tested individually; the remaining rare 673 MVs were tested by burden analyses considering their position and pathogenicity score. We also conducted a meta-analysis of our results and those from published studies. We did not find evidence for association for any of the 16 variants individually tested. The rare MVs were significantly associated with increased risk of ER-negative breast cancer by burden analysis comparing familial cases to controls (OR = 1.48; 95% CI 1.07-2.04; P = 0.017). Higher ORs were found for the subgroup of MVs located in functional domains or predicted to be pathogenic. The meta-analysis indicated that FANCM MVs overall are associated with breast cancer risk (OR = 1.22; 95% CI 1.08-1.38; P = 0.002). Our results support the definition from previous analyses of FANCM as a moderate-risk breast cancer gene and provide evidence that FANCM MVs could be low/moderate risk factors for ER-negative and TNBC subtypes. Further genetic and functional analyses are necessary to clarify better the increased risks due to FANCM MVs.
Published: 2022
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27. Ovarian cancer pathology characteristics as predictors of variant pathogenicity in BRCA1 and BRCA2.

Author: O'Mahony, Denise G., Ramus, Susan J., Southey, Melissa C., Meagher, Nicola S., Hadjisavvas, Andreas, John, Esther M., Hamann, Ute, Imyanitov, Evgeny N., Andrulis, Irene L., Sharma, Priyanka, Daly, Mary B., Hake, Christopher R., Weitzel, Jeffrey N., Jakubowska, Anna, Godwin, Andrew K., Arason, Adalgeir, Bane, Anita, Simard, Jacques, Soucy, Penny, and Caligo, Maria A.
Abstract: Background: The distribution of ovarian tumour characteristics differs between germline BRCA1 and BRCA2 pathogenic variant carriers and non-carriers. In this study, we assessed the utility of ovarian tumour characteristics as predictors of BRCA1 and BRCA2 variant pathogenicity, for application using the American College of Medical Genetics and the Association for Molecular Pathology (ACMG/AMP) variant classification system. Methods: Data for 10,373 ovarian cancer cases, including carriers and non-carriers of BRCA1 or BRCA2 pathogenic variants, were collected from unpublished international cohorts and consortia and published studies. Likelihood ratios (LR) were calculated for the association of ovarian cancer histology and other characteristics, with BRCA1 and BRCA2 variant pathogenicity. Estimates were aligned to ACMG/AMP code strengths (supporting, moderate, strong). Results: No histological subtype provided informative ACMG/AMP evidence in favour of BRCA1 and BRCA2 variant pathogenicity. Evidence against variant pathogenicity was estimated for the mucinous and clear cell histologies (supporting) and borderline cases (moderate). Refined associations are provided according to tumour grade, invasion and age at diagnosis. Conclusions: We provide detailed estimates for predicting BRCA1 and BRCA2 variant pathogenicity based on ovarian tumour characteristics. This evidence can be combined with other variant information under the ACMG/AMP classification system, to improve classification and carrier clinical management. [ABSTRACT FROM AUTHOR]
Published: 2023
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28. MnSOD and CAT polymorphisms modulate the effect of the Mediterranean diet on breast cancer risk among Greek-Cypriot women

Author: Kakkoura, Maria G., Demetriou, Christiana A., Loizidou, Maria A., Loucaides, Giorgos, Neophytou, Ioanna, Malas, Simon, Kyriacou, Kyriacos, and Hadjisavvas, Andreas
Published: 2016
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29. Relative validity and reproducibility of the CyFFQ semiquantitative food frequency questionnaire for assessing dietary intake in Cypriot adults

Author: Philippou, Elena, primary, Demetriou, Christiana A., additional, Loucaides, George, additional, Solomonidou, Nastazia, additional, Critselis, Elena, additional, Polykarpou, Maria, additional, Sioulis, Spyros, additional, Hadjisavvas, Andreas, additional, and Kyriacou, Kyriacos, additional
Published: 2022
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30. Exome sequencing identifies novel susceptibility genes and defines the contribution of coding variants to breast cancer risk.

Author: Wilcox, Naomi, primary, Dumont, Martine, additional, González-Neira, Anna, additional, Carvalho, Sara, additional, Beauparlant, Charles Joly, additional, Crotti, Marco, additional, Luccarini, Craig, additional, Soucy, Penny, additional, Dubois, Stéphane, additional, Nuñez-Torres, Rocio, additional, Pita, Guillermo, additional, Alonso, M. Rosario, additional, Álvarez, Nuria, additional, Baynes, Caroline, additional, Becker, Heiko, additional, Behrens, Sabine, additional, Bolla, Manjeet K., additional, Castelao, Jose E., additional, Chang-Claude, Jenny, additional, Cornelissen, Sten, additional, Dennis, Joe, additional, Dörk, Thilo, additional, Engel, Christoph, additional, Gago-Dominguez, Manuela, additional, Guenel, Pascal, additional, Hadjisavvas, Andreas, additional, Hahnen, Eric, additional, Hartman, Mikael, additional, Herráez, Belén, additional, Investigators, SGBCC, additional, Jung, Audrey, additional, Keeman, Renske, additional, Kiechle, Marion, additional, Li, Jingmei, additional, Loizidou, Maria A., additional, Lush, Michael, additional, Michailidou, Kyriaki, additional, Panayiotidis, Mihalis I., additional, Sim, Xueling, additional, Teo, Soo Hwang, additional, Tyrer, Jonathan P., additional, van der Kolk, Lizet E., additional, Wahlstrom, Cecilia, additional, Wang, Qin, additional, Benitez, Javier, additional, Schmidt, Marjanka K., additional, Schmutzler, Rita K., additional, Pharoah, Paul, additional, Droit, Arnaud, additional, Dunning, Alison M, additional, Kvist, Anders, additional, Devilee, Peter, additional, Easton, Douglas F., additional, and Simard, Jacques, additional
Published: 2022
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31. Pathology of Tumors Associated With Pathogenic Germline Variants in 9 Breast Cancer Susceptibility Genes

Author: Breast Cancer Association Consortium, Mavaddat, Nasim, Dorling, Leila, Carvalho, Sara, Allen, Jamie, González-Neira, Anna, Keeman, Renske, Bolla, Manjeet K, Dennis, Joe, Wang, Qin, Ahearn, Thomas U, Andrulis, Irene L, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Briceno, Ignacio, Brüning, Thomas, Camp, Nicola J, Campbell, Archie, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Chenevix-Trench, Georgia, Christiansen, Hans, Czene, Kamila, Dörk, Thilo, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine D, Flyger, Henrik, Gabrielson, Marike, Gago-Dominguez, Manuela, Geisler, Jürgen, Giles, Graham G, Guénel, Pascal, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Hartikainen, Jaana M, Hartman, Mikael, Hoppe, Reiner, Howell, Anthony, Jakubowska, Anna, Jung, Audrey, Khusnutdinova, Elza K, Kristensen, Vessela N, Li, Jingmei, Lim, Swee Ho, Lindblom, Annika, Loizidou, Maria A, Lophatananon, Artitaya, Lubinski, Jan, Madsen, Michael J, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Milne, Roger L, Mohd Taib, Nur Aishah, Morra, Anna, Muir, Kenneth, Obi, Nadia, Osorio, Ana, Park-Simon, Tjoung-Won, Peterlongo, Paolo, Radice, Paolo, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Shah, Mitul, Sim, Xueling, Southey, Melissa C, Thorne, Heather, Tomlinson, Ian, Torres, Diana, Truong, Thérèse, Yip, Cheng Har, Spurdle, Amanda B, Vreeswijk, Maaike PG, Dunning, Alison M, García-Closas, Montserrat, Pharoah, Paul DP, Kvist, Anders, Muranen, Taru A, Nevanlinna, Heli, Teo, Soo Hwang, Devilee, Peter, Schmidt, Marjanka K, Easton, Douglas F, Mavaddat, Nasim [0000-0003-0307-055X], Wilson, Leila [0000-0003-1214-8080], Dennis, Joe [0000-0003-4591-1214], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Medicum, Clinicum, Department of Oncology, HUS Comprehensive Cancer Center, Research Program in Systems Oncology, HUS Gynecology and Obstetrics, Department of Obstetrics and Gynecology, and Biosciences
Subjects: EXPRESSION, Adult, Cancer Research, Adolescent, CHK2, 3122 Cancers, Genes, BRCA2, Breast Neoplasms, SUBTYPES, ACTIVATION, SUBCLASSES, Young Adult, BRCA2 MUTATION CARRIERS, PRIMARY THERAPY, Online First, Humans, Genetic Predisposition to Disease, Germ-Line Mutation, Original Investigation, Aged, MOLECULAR PORTRAITS, Research, INTERNATIONAL EXPERT CONSENSUS, Middle Aged, Germ Cells, Oncology, Case-Control Studies, PALB2, Female, Comments
Abstract: Key Points Question What breast tumor characteristics are associated with rare pathogenic protein truncating or missense variants in breast cancer susceptibility genes? Findings In this case-control study involving 46 387 control participants and 42 680 women with a diagnosis of breast cancer, pathology features (eg, tumor subtype, morphology, size, TNM stage, and lymph node involvement) associated with rare germline (likely) pathogenic variants in 9 different breast cancer susceptibility genes were studied. Substantial differences in tumor subtype distribution by gene were found. Meaning The results of this study suggest that tumor subtypes differ by gene; these findings can potentially inform guidelines for gene panel testing, risk prediction in unaffected individuals, variant classification, and understanding of breast cancer etiology., Importance Rare germline genetic variants in several genes are associated with increased breast cancer (BC) risk, but their precise contributions to different disease subtypes are unclear. This information is relevant to guidelines for gene panel testing and risk prediction. Objective To characterize tumors associated with BC susceptibility genes in large-scale population- or hospital-based studies. Design, Setting, and Participants The multicenter, international case-control analysis of the BRIDGES study included 42 680 patients and 46 387 control participants, comprising women aged 18 to 79 years who were sampled independently of family history from 38 studies. Studies were conducted between 1991 and 2016. Sequencing and analysis took place between 2016 and 2021. Exposures Protein-truncating variants and likely pathogenic missense variants in ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53. Main Outcomes and Measures The intrinsic-like BC subtypes as defined by estrogen receptor, progesterone receptor, and ERBB2 (formerly known as HER2) status, and tumor grade; morphology; size; stage; lymph node involvement; subtype-specific odds ratios (ORs) for carrying protein-truncating variants and pathogenic missense variants in the 9 BC susceptibility genes. Results The mean (SD) ages at interview (control participants) and diagnosis (cases) were 55.1 (11.9) and 55.8 (10.6) years, respectively; all participants were of European or East Asian ethnicity. There was substantial heterogeneity in the distribution of intrinsic subtypes by gene. RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (OR, 6.19 [95% CI, 3.17-12.12]; OR, 6.19 [95% CI, 2.99-12.79]; and OR, 10.05 [95% CI, 5.27-19.19], respectively). CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease. For ATM variants, the association was strongest for the hormone receptor (HR)+ERBB2− high-grade subtype (OR, 4.99; 95% CI, 3.68-6.76). BRCA1 was associated with increased risk of all subtypes, but the ORs varied widely, being highest for triple-negative disease (OR, 55.32; 95% CI, 40.51-75.55). BRCA2 and PALB2 variants were also associated with triple-negative disease. TP53 variants were most strongly associated with HR+ERBB2+ and HR–ERBB2+ subtypes. Tumors occurring in pathogenic variant carriers were of higher grade. For most genes and subtypes, a decline in ORs was observed with increasing age. Together, the 9 genes were associated with 27.3% of all triple-negative tumors in women 40 years or younger. Conclusions and Relevance The results of this case-control study suggest that variants in the 9 BC risk genes differ substantially in their associated pathology but are generally associated with triple-negative and/or high-grade disease. Knowing the age and tumor subtype distributions associated with individual BC genes can potentially aid guidelines for gene panel testing, risk prediction, and variant classification and guide targeted screening strategies., This case-control study examines tumors associated with breast cancer susceptibility genes in large-scale population- or hospital-based studies.
Published: 2022

32. Pathology of Tumors Associated With Pathogenic Germline Variants in 9 Breast Cancer Susceptibility Genes

Author: Mavaddat, Nasim, Dorling, Leila, Carvalho, Sara, Allen, Jamie, Gonzalez-Neira, Anna, Keeman, Renske, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Ahearn, Thomas U., Andrulis, Irene L., Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Briceno, Ignacio, Bruning, Thomas, Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Christiansen, Hans, Czene, Kamila, Dork, Thilo, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine D., Flyger, Henrik, Gabrielson, Marike, Gago-Dominguez, Manuela, Geisler, Jurgen, Giles, Graham G., Guenel, Pascal, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Hartikainen, Jaana M., Hartman, Mikael, Hoppe, Reiner, Howell, Anthony, Jakubowska, Anna, Jung, Audrey, Khusnutdinova, Elza K., Kristensen, Vessela N., Li, Jingmei, Lim, Swee Ho, Lindblom, Annika, Loizidou, Maria A., Lophatananon, Artitaya, Lubinski, Jan, Madsen, Michael J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Milne, Roger L., Taib, Nur Aishah Mohd, Morra, Anna, Muir, Kenneth, Obi, Nadia, Osorio, Ana, Park-Simon, Tjoung-Won, Peterlongo, Paolo, Radice, Paolo, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Shah, Mitul, Sim, Xueling, Southey, Melissa C., Thorne, Heather, Tomlinson, Ian, Torres, Diana, Truong, Therese, Yip, Cheng Har, Spurdle, Amanda B., Vreeswijk, Maaike P. G., Dunning, Alison M., Garcia-Closas, Montserrat, Pharoah, Paul D. P., Kvist, Anders, Muranen, Taru A., Nevanlinna, Heli, Teo, Soo Hwang, Devilee, Peter, Schmidt, Marjanka K., Easton, Douglas F., Mavaddat, Nasim, Dorling, Leila, Carvalho, Sara, Allen, Jamie, Gonzalez-Neira, Anna, Keeman, Renske, Bolla, Manjeet K., Dennis, Joe, Wang, Qin, Ahearn, Thomas U., Andrulis, Irene L., Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia, V, Bojesen, Stig E., Briceno, Ignacio, Bruning, Thomas, Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Christiansen, Hans, Czene, Kamila, Dork, Thilo, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine D., Flyger, Henrik, Gabrielson, Marike, Gago-Dominguez, Manuela, Geisler, Jurgen, Giles, Graham G., Guenel, Pascal, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Hartikainen, Jaana M., Hartman, Mikael, Hoppe, Reiner, Howell, Anthony, Jakubowska, Anna, Jung, Audrey, Khusnutdinova, Elza K., Kristensen, Vessela N., Li, Jingmei, Lim, Swee Ho, Lindblom, Annika, Loizidou, Maria A., Lophatananon, Artitaya, Lubinski, Jan, Madsen, Michael J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Milne, Roger L., Taib, Nur Aishah Mohd, Morra, Anna, Muir, Kenneth, Obi, Nadia, Osorio, Ana, Park-Simon, Tjoung-Won, Peterlongo, Paolo, Radice, Paolo, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Shah, Mitul, Sim, Xueling, Southey, Melissa C., Thorne, Heather, Tomlinson, Ian, Torres, Diana, Truong, Therese, Yip, Cheng Har, Spurdle, Amanda B., Vreeswijk, Maaike P. G., Dunning, Alison M., Garcia-Closas, Montserrat, Pharoah, Paul D. P., Kvist, Anders, Muranen, Taru A., Nevanlinna, Heli, Teo, Soo Hwang, Devilee, Peter, Schmidt, Marjanka K., and Easton, Douglas F.
Abstract: IMPORTANCE Rare germline genetic variants in several genes are associated with increased breast cancer (BC) risk, but their precise contributions to different disease subtypes are unclear. This information is relevant to guidelines for gene panel testing and risk prediction. OBJECTIVE To characterize tumors associated with BC susceptibility genes in large-scale population- or hospital-based studies. DESIGN, SETTING, AND PARTICIPANTS The multicenter, international case-control analysis of the BRIDGES study included 42 680 patients and 46 387 control participants, comprising women aged 18 to 79 years who were sampled independently of family history from 38 studies. Studies were conducted between 1991and 2016. Sequencing and analysis took place between 2016 and 2021. EXPOSURES Protein-truncating variants and likely pathogenic missense variants in ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53. MAIN OUTCOMES AND MEASURES The intrinsic-like BC subtypes as defined by estrogen receptor, progesterone receptor, and ERBB2 (formerly known as HER2) status, and tumor grade; morphology; size; stage; lymph node involvement; subtype-specific odds ratios (ORs) for carrying protein-truncating variants and pathogenic missense variants in the 9 BC susceptibility genes. RESULTS The mean (SD) ages at interview (control participants) and diagnosis (cases) were 55.1(11.9) and 55.8 (10.6) years, respectively; all participants were of European or East Asian ethnicity. There was substantial heterogeneity in the distribution of intrinsic subtypes by gene. RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (OR, 6.19 [95% CI, 3.17-12.12]; OR, 6.19 [95% CI, 2.99-12.79]; and OR, 10.05 [95% CI, 5.27-19.19], respectively). CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease. For ATM variants, the association was strongest for the hormone receptor (HR)(+)ERBB2(-) high-grade subtype
Published: 2022

33. Additional file 1 of Breast cancer risks associated with missense variants in breast cancer susceptibility genes

Author: Dorling, Leila, Carvalho, Sara, Allen, Jamie, Parsons, Michael T., Fortuno, Cristina, González-Neira, Anna, Heijl, Stephan M., Adank, Muriel A., Ahearn, Thomas U., Andrulis, Irene L., Auvinen, Päivi, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bermisheva, Marina, Bogdanova, Natalia V., Bojesen, Stig E., Bolla, Manjeet K., Bremer, Michael, Briceno, Ignacio, Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Collée, J. Margriet, Czene, Kamila, Dennis, Joe, Dörk, Thilo, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, Giles, Graham G., Glendon, Gord, Guénel, Pascal, Gündert, Melanie, Hadjisavvas, Andreas, Hahnen, Eric, Hall, Per, Hamann, Ute, Harkness, Elaine F., Hartman, Mikael, Hogervorst, Frans B. L., Hollestelle, Antoinette, Hoppe, Reiner, Howell, Anthony, Jakubowska, Anna, Jung, Audrey, Khusnutdinova, Elza, Kim, Sung-Won, Ko, Yon-Dschun, Kristensen, Vessela N., Lakeman, Inge M. M., Li, Jingmei, Lindblom, Annika, Loizidou, Maria A., Lophatananon, Artitaya, Lubiński, Jan, Luccarini, Craig, Madsen, Michael J., Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Milne, Roger L., Mohd Taib, Nur Aishah, Muir, Kenneth, Nevanlinna, Heli, Newman, William G., Oosterwijk, Jan C., Park, Sue K., Peterlongo, Paolo, Radice, Paolo, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Shah, Mitul, Sim, Xueling, Southey, Melissa C., Surowy, Harald, Suvanto, Maija, Tomlinson, Ian, Torres, Diana, Truong, Thérèse, van Asperen, Christi J., Waltes, Regina, Wang, Qin, Yang, Xiaohong R., Pharoah, Paul D. P., Schmidt, Marjanka K., Benitez, Javier, Vroling, Bas, Dunning, Alison M., Teo, Soo Hwang, Kvist, Anders, de la Hoya, Miguel, Devilee, Peter, Spurdle, Amanda B., Vreeswijk, Maaike P. G., and Easton, Douglas F.
Subjects: Data_FILES
Abstract: Additional file 1.
Published: 2022
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34. Characterization of IgG Antibody Response against SARS-CoV-2 (COVID-19) in the Cypriot Population

Author: Krashias, George, primary, Deeba, Elie, additional, Constantinou, Astero, additional, Hadjiagapiou, Maria, additional, Koptides, Dana, additional, Richter, Jan, additional, Tryfonos, Christina, additional, Bashiardes, Stavros, additional, Lambrianides, Anastasia, additional, Loizidou, Maria A., additional, Hadjisavvas, Andreas, additional, Panayiotidis, Mihalis I., additional, and Christodoulou, Christina, additional
Published: 2021
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35. Relative validity and reproducibility of the CyFFQ semiquantitative food frequency questionnaire for assessing dietary intake in Cypriot adults.

Author: Philippou, Elena, Demetriou, Christiana A., Loucaides, George, Solomonidou, Nastazia, Critselis, Elena, Polykarpou, Maria, Sioulis, Spyros, Hadjisavvas, Andreas, and Kyriacou, Kyriacos
Subjects: EXPERIMENTAL design, STATISTICS, NUTRITIONAL assessment, RESEARCH evaluation, RESEARCH methodology, RESEARCH methodology evaluation, NUTRITIONAL requirements, INTERVIEWING, QUESTIONNAIRES, INTRACLASS correlation, MICRONUTRIENTS, DATA analysis
Abstract: Background: Assessment of dietary intake is fundamental for evaluating the interrelationships between diet and disease. The present study aimed to develop and validate the semiquantitative Cypriot food frequency questionnaire (CyFFQ). Methods: A 171‐item paper‐and‐pencil semiquantitative interview‐administered FFQ was developed, including local foods and culturally specific meals commonly consumed among Cypriot adults. FFQ reproducibility was assessed by comparing the energy‐adjusted daily macro‐ and micronutrients intake at baseline (FFQ1) and 1 year later (FFQ2) using a Wilcoxon matched pairs signed rank test and intraclass correlation coefficients (ICCs) in a random sample of Cypriot adults. FFQ relative validity was evaluated by comparing the intake as estimated by FFQ2 with that obtained from the average of three 24‐h recalls taken over the year between FFQ1 and FFQ2. Associations between nutrient intakes estimated using FFQ2 and the 24‐h recalls were assessed using Spearman rank correlation and Bland–Altman plots were used to assess agreement between the FFQ and the 24‐h recalls. Results: Among eligible participants, 68 (78%) completed the study (44.1% males, aged 30.5–47.5 years). The energy‐adjusted intakes of macro‐ and micronutrients did not significantly differ between the two FFQs, excluding magnesium. The FFQ2 and the averaged 24‐h recalls were significantly correlated for most macro‐ and micronutrients. The median (interquartile) ICC for all macro‐ and micronutrients was 0.46 (0.38–0.52) (p < 0.05). Agreement was satisfactory (>30%) for most micro‐ and macronutrients. Bland–Altman plots also confirmed good agreement between the two methods. Conclusions: The CyFFQ is a valid and reliable tool for assessing dietary consumption in Cypriot adults. Key points: Culturally applicable dietary intake assessment tools are necessary to evaluate the relationships between diet and health/disease aspects.The present study aimed to develop and validate the semiquantitative Cypriot food frequency questionnaire (CyFFQ).After developing a 171‐paper‐and‐pencil semiquantitative interview‐administered FFQ, including local and culturally specific meals, both reproducibility and relative validity were assessed in a random sample of Cypriot adults.In statistical analysis comparing the FFQ provided to the participants at baseline and 1 year later, energy‐adjusted intakes of macro‐ and micronutrients did not significantly differ between the two FFQs, with the exception of magnesium. A comparison between the energy‐adjusted daily macro‐ and micronutrients intake 1 year later (FFQ2) and the average of three 24‐h recalls provided between baseline and FFQ2 showed significant correlation and agreement, using various methods, for most macro‐ and micronutrients.Our findings indicate that the CyFFQ is a valid and reliable tool for assessing dietary consumption in Cypriot adults and thus can be used in future research. [ABSTRACT FROM AUTHOR]
Published: 2023
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36. Contributors

Author: Agudo, Antonio, primary, Alarcón, Marisa, additional, Aldasoro, Juan José, additional, Antonopoulou, Smaragdi, additional, Arnoni, Yardena, additional, Arranz, Sara, additional, Atteia, Hebatallah Husseini, additional, Azzini, Elena, additional, Badimon, Lina, additional, Bastida, Sara, additional, Beccari, Giovanni, additional, Berry, Elliot M., additional, Biandolino, Francesca, additional, Bonaccio, Marialaura, additional, Bonachela, Santiago, additional, Bonanni, Americo, additional, Bosco, Gerardo, additional, Buckland, Genevieve, additional, Calabriso, Nadia, additional, Caliskan, Oguzhan, additional, Carluccio, Maria Annunziata, additional, Casas, J. Jesús, additional, Casas, Rosa, additional, Castro-Quezada, Itandehui, additional, Chiva-Blanch, Gemma, additional, Conti, Gea Oliveri, additional, Copat, Chiara, additional, Couture, Patrick, additional, Covarelli, Lorenzo, additional, De Caterina, Raffaele, additional, De Feo, Vincenzo, additional, de Gaetano, Giovanni, additional, de Lorgeril, Michel, additional, De Martino, Laura, additional, Demetriou, Christiana A., additional, Detopoulou, Paraskevi, additional, Diamantopoulos, Emmanuel J., additional, Djuric, Zora, additional, Donati, Maria Benedetta, additional, Doreste-Alonso, Jorge, additional, El Rhazi, Karima, additional, El-Swefy, Sahar Elsayed, additional, Rodilla, Manuel Espárrago, additional, Estruch, Ramon, additional, Fallico, Roberto, additional, Farajian, Paul, additional, Fenoy, Encarnación, additional, Fernandez, J.M., additional, Fernandez, Maria Luz, additional, Fernández-Real, José Manuel, additional, Ferrante, Margherita, additional, Fragopoulou, Elizabeth, additional, Fuentes-Jimenez, F., additional, Gaforio, José J., additional, Garaulet, Marta, additional, Garcia-Larsen, Vanessa, additional, Gardener, Hannah, additional, Gesteiro, Eva, additional, Goldstein, Mark R., additional, González, Carlos A., additional, Gouveri, Evanthia, additional, Granados, Sergio, additional, Grimaldi, Keith, additional, Hadjisavvas, Andreas, additional, Henríquez-Sánchez, Patricia, additional, Hernández, Joaquín, additional, Iacoviello, Licia, additional, Iriti, Marcello, additional, Karageorgou, Dimitra, additional, Kontou, Niki, additional, Kyriacou, Kyriacos, additional, La Torre, Giuseppe, additional, Lairon, Denis, additional, Lamarche, Benoît, additional, Lee, Jaime, additional, Loizidou, Maria A., additional, López-Biedma, Alicia, additional, Macpherson, Helen, additional, Maiani, Giuseppe, additional, Mancini, Emilia, additional, Martin, Colin R., additional, Martínez-González, Miguel Ángel, additional, Mascitelli, Luca, additional, Massaro, Marika, additional, Medina, F. Xavier, additional, Mendieta, Guiomar, additional, Mesías, Marta, additional, Micha, Renata, additional, Moreno-Navarrete, José María, additional, Moyano, Francisco J., additional, Navarro, M. Pilar, additional, Nazzaro, Filomena, additional, Nejjari, Chakib, additional, Nilsson, Lena Maria, additional, Nomikos, Tzortzis, additional, Oliviero, Francesca, additional, Erdogan Orhan, Ilkay, additional, Paoli, Antonio, additional, Papandreou, Christopher, additional, Pase, Matthew, additional, Pellegrino, Mariangela, additional, Pipingas, Andrew, additional, Potenza, Concetta, additional, Prato, Ermelinda, additional, Preedy, Victor R., additional, Pulido-Moran, Mario, additional, Punzi, Leonardo, additional, Quiles, José L., additional, Ramírez-Tortose, Ma del Carmen, additional, Richard, Caroline, additional, Rodríguez Bernal, Beatriz, additional, Román-Viñas, Blanca, additional, Ros, Emilio, additional, Rosado-Alvarez, D., additional, Ríos, José-Luis, additional, Ruano, Cristina, additional, Sahingoz, Semra Akar, additional, Salen, Patricia, additional, Sánchez Benito, José L., additional, Soriano, Eva Sánchez, additional, Sánchez-Muniz, Francisco J., additional, Sánchez-Quesada, Cristina, additional, Sánchez-Villegas, Almudena, additional, Saulle, Rosella, additional, Scholey, Andrew, additional, Sciacca, Salvatore, additional, Scoditti, Egeria, additional, Seiquer, Isabel, additional, Semyonov, Leda, additional, Serra-Majem, Lluís, additional, Sewell, Dean A., additional, Sfriso, Paolo, additional, Sheikh, Aziz, additional, Skroza, Nevena, additional, Spinella, Paolo, additional, Tosi, Laura, additional, Tumen, Ibrahim, additional, Valderas-Martinez, Palmira, additional, Varoni, Elena M., additional, Vilahur, Gemma, additional, Villalon, Lorena, additional, Villarroya, Gemma Xifra, additional, Vineis, Paolo, additional, Warleta, Fernando, additional, Wright, Clinton B., additional, Zacharski, Leo R., additional, Zampelas, Antonis, additional, and Zuber, Sara, additional
Published: 2015
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37. The Mediterranean Diet and Breast Cancer Risk

Author: Demetriou, Christiana A., primary, Hadjisavvas, Andreas, additional, Loizidou, Maria A., additional, Vineis, Paolo, additional, and Kyriacou, Kyriacos, additional
Published: 2015
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38. Identification of a mutation in complement factor H-related protein 5 in patients of Cypriot origin with glomerulonephritis

Author: Gale, Daniel P, de Jorge, Elena Goicoechea, Cook, H Terence, Martinez-Barricarte, Rubén, Hadjisavvas, Andreas, McLean, Adam G, Pusey, Charles D, Pierides, Alkis, Kyriacou, Kyriacos, Athanasiou, Yiannis, Voskarides, Konstantinos, Deltas, Constantinos, Palmer, Andrew, Frémeaux-Bacchi, Véronique, de Cordoba, Santiago Rodriguez, Maxwell, Patrick H, and Pickering, Matthew C
Published: 2010
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39. Combination of a 15-SNP Polygenic Risk Score and Classical Risk Factors for the Prediction of Breast Cancer Risk in Cypriot Women

Author: Yiangou, Kristia, primary, Kyriacou, Kyriacos, additional, Kakouri, Eleni, additional, Marcou, Yiola, additional, Panayiotidis, Mihalis I., additional, Loizidou, Maria A., additional, Hadjisavvas, Andreas, additional, and Michailidou, Kyriaki, additional
Published: 2021
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40. Prediction of Parkinson’s Disease Risk Based on Genetic Profile and Established Risk Factors

Author: Chairta, Paraskevi P., primary, Hadjisavvas, Andreas, additional, Georgiou, Andrea N., additional, Loizidou, Maria A., additional, Yiangou, Kristia, additional, Demetriou, Christiana A., additional, Christou, Yiolanda P., additional, Pantziaris, Marios, additional, Michailidou, Kyriaki, additional, and Zamba-Papanicolaou, Eleni, additional
Published: 2021
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41. Molecular epidemiology of SARS-CoV-2 in Cyprus

Author: Richter, Jan, primary, Fanis, Pavlos, additional, Tryfonos, Christina, additional, Koptides, Dana, additional, Krashias, George, additional, Bashiardes, Stavros, additional, Hadjisavvas, Andreas, additional, Loizidou, Maria, additional, Oulas, Anastasis, additional, Alexandrou, Denise, additional, Kalakouta, Olga, additional, Panayiotidis, Mihalis I., additional, Spyrou, George M., additional, and Christodoulou, Christina, additional
Published: 2021
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42. Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women

Author: Breast Cancer Association Consortium, Dorling, Leila, Carvalho, Sara, Allen, Jamie, González-Neira, Anna, Luccarini, Craig, Wahlström, Cecilia, Pooley, Karen A, Parsons, Michael T, Fortuno, Cristina, Wang, Qin, Bolla, Manjeet K, Dennis, Joe, Keeman, Renske, Alonso, M Rosario, Álvarez, Nuria, Herraez, Belen, Fernandez, Victoria, Núñez-Torres, Rocio, Osorio, Ana, Valcich, Jeanette, Li, Minerva, Törngren, Therese, Harrington, Patricia A, Baynes, Caroline, Conroy, Don M, Decker, Brennan, Fachal, Laura, Mavaddat, Nasim, Ahearn, Thomas, Aittomäki, Kristiina, Antonenkova, Natalia N, Arnold, Norbert, Arveux, Patrick, Ausems, Margreet GEM, Auvinen, Päivi, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Białkowska, Katarzyna, Blomqvist, Carl, Bogdanova, Natalia V, Bogdanova-Markov, Nadja, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Bremer, Michael, Briceno, Ignacio, Brüning, Thomas, Burwinkel, Barbara, Cameron, David A, Camp, Nicola J, Campbell, Archie, Carracedo, Angel, Castelao, Jose E, Cessna, Melissa H, Chanock, Stephen J, Christiansen, Hans, Collée, J Margriet, Cordina-Duverger, Emilie, Cornelissen, Sten, Czene, Kamila, Dörk, Thilo, Ekici, Arif B, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Försti, Asta, Gabrielson, Marike, Gago-Dominguez, Manuela, Georgoulias, Vassilios, Gil, Fabian, Giles, Graham G, Glendon, Gord, Garcia, Encarna B Gómez, Alnæs, Grethe I Grenaker, Guénel, Pascal, Hadjisavvas, Andreas, Haeberle, Lothar, Hahnen, Eric, Hall, Per, Hamann, Ute, Harkness, Elaine F, Hartikainen, Jaana M, Hartman, Mikael, He, Wei, Heemskerk-Gerritsen, Bernadette AM, Hillemanns, Peter, Hogervorst, Frans BL, Hollestelle, Antoinette, Ho, Weang Kee, Hooning, Maartje J, Howell, Anthony, Humphreys, Keith, Idris, Faiza, and Jakubowska, Anna
Subjects: Risk, Adult, Adolescent, Breast Neoplasms, Medical and Health Sciences, Young Adult, General & Internal Medicine, Breast Cancer, Odds Ratio, 80 and over, Genetics, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Aetiology, Aged, Cancer, Age Factors, Genetic Variation, DNA, Middle Aged, Logistic Models, Mutation, Breast Cancer Association Consortium, Female, Missense, Sequence Analysis
Abstract: BackgroundGenetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking.MethodsWe used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity.ResultsProtein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants.ConclusionsThe results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.).
Published: 2021

43. Additional file 2 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 2: Table S2. EuroGentest and the European Society of Human Genetics, guidelines for the evaluation and validation of NGS applications.
Published: 2021
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44. Additional file 1 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 1: Table S1. TruSight Cancer (Illumina) target genes in alphabetical order.
Published: 2021
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45. Additional file 3 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 3: Figure S1. Sequencing and Mapping Evaluation. a. Number of reads and clusters generated per run. b Number of unmapped reads per sample and alignment method.
Published: 2021
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46. Additional file 9 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 9. Detailed commands and parameters used for data pre-processing, sequence alignment, post-alignment processing and variant discovery.
Published: 2021
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47. Additional file 7 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 7: Figure S3. Box plot of Matthew Correlation coefficient (MCC) comparisons per alignment, variant calling or padding method. Each dot represents one observation and horizontal bold lines denote median MCC values. Boxes extend from the 25th to the 75th percentile of each group’s distribution of values. Vertical extending lines (whiskers) denote the upper and lower adjacent values. Statistical analyses were performed using the non-parametric Kruskal-Wallis or one-way ANOVA tests.
Published: 2021
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48. Additional file 8 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 8: Figure S4. Box plot comparisons of False Positive Rates (FPR). Only statistically significant differences are shown. Each dot represents one observation and horizontal bold lines denote median FPR values. Boxes extend from the 25th to the 75th percentile of each group’s distribution of values. Vertical extending lines (whiskers) denote the upper and lower adjacent values. Statistical analysis was performed using the non-parametric Kruskal-–Wallis test.
Published: 2021
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49. Additional file 4 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 4: Table S3. Number of reads per sample and mapping tool.
Published: 2021
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50. Additional file 5 of Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels

Author: Zanti, Maria, Michailidou, Kyriaki, Loizidou, Maria A., Machattou, Christina, Pirpa, Panagiota, Kyproula Christodoulou, Spyrou, George M., Kyriacos Kyriacou, and Hadjisavvas, Andreas
Abstract: Additional file 5: Table S4. Minimum, mean and maximum depth of coverage, per gene and alignment algorithm. Depth of coverage results upon NextSeq 500 High-Output kit 2x75 cycles and 2x150 cycles sequencing.
Published: 2021
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