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1. Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach

Author: Gao, Guimin, Zhao, Fangyuan, Ahearn, Thomas U, Lunetta, Kathryn L, Troester, Melissa A, Du, Zhaohui, Ogundiran, Temidayo O, Ojengbede, Oladosu, Blot, William, Nathanson, Katherine L, Domchek, Susan M, Nemesure, Barbara, Hennis, Anselm, Ambs, Stefan, McClellan, Julian, Nie, Mark, Bertrand, Kimberly, Zirpoli, Gary, Yao, Song, Olshan, Andrew F, Bensen, Jeannette T, Bandera, Elisa V, Nyante, Sarah, Conti, David V, Press, Michael F, Ingles, Sue A, John, Esther M, Bernstein, Leslie, Hu, Jennifer J, Deming-Halverson, Sandra L, Chanock, Stephen J, Ziegler, Regina G, Rodriguez-Gil, Jorge L, Sucheston-Campbell, Lara E, Sandler, Dale P, Taylor, Jack A, Kitahara, Cari M, O’Brien, Katie M, Bolla, Manjeet K, Dennis, Joe, Dunning, Alison M, Easton, Douglas F, Michailidou, Kyriaki, Pharoah, Paul D P, Wang, Qin, Figueroa, Jonine, Biritwum, Richard, Adjei, Ernest, Wiafe, Seth, Ambrosone, Christine B, Zheng, Wei, Olopade, Olufunmilayo I, García-Closas, Montserrat, Palmer, Julie R, Haiman, Christopher A, and Huo, Dezheng
Subjects: Multifactorial Inheritance, Receptors, Estrogen/genetics, Breast Neoplasms, General Medicine, Breast Neoplasms/genetics, Receptors, Estrogen, Risk Factors, Genetics, Humans, Original Article, Female, Genetic Predisposition to Disease, Multifactorial Inheritance/genetics, Molecular Biology, Genetics (clinical), Genome-Wide Association Study
Abstract: Polygenic risk scores (PRSs) are useful for predicting breast cancer risk, but the prediction accuracy of existing PRSs in women of African ancestry (AA) remains relatively low. We aim to develop optimal PRSs for the prediction of overall and estrogen receptor (ER) subtype-specific breast cancer risk in AA women. The AA dataset comprised 9235 cases and 10 184 controls from four genome-wide association study (GWAS) consortia and a GWAS study in Ghana. We randomly divided samples into training and validation sets. We built PRSs using individual-level AA data by a forward stepwise logistic regression and then developed joint PRSs that combined (1) the PRSs built in the AA training dataset and (2) a 313-variant PRS previously developed in women of European ancestry. PRSs were evaluated in the AA validation set. For overall breast cancer, the odds ratio per standard deviation of the joint PRS in the validation set was 1.34 [95% confidence interval (CI): 1.27–1.42] with the area under receiver operating characteristic curve (AUC) of 0.581. Compared with women with average risk (40th–60th PRS percentile), women in the top decile of the PRS had a 1.98-fold increased risk (95% CI: 1.63–2.39). For PRSs of ER-positive and ER-negative breast cancer, the AUCs were 0.608 and 0.576, respectively. Compared with existing methods, the proposed joint PRSs can improve prediction of breast cancer risk in AA women.
Published: 2022

2. Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry

Author: Mueller, Stefanie H, Lai, Alvina G, Valkovskaya, Maria, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Lush, Michael, Abu-Ful, Zomoruda, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Baert, Thais, Freeman, Laura E Beane, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Brenner, Hermann, Brucker, Sara Y, Buys, Saundra S, Castelao, Jose E, Chan, Tsun L, Chang-Claude, Jenny, Chanock, Stephen J, Choi, Ji-Yeob, Chung, Wendy K, NBCS Collaborators, Colonna, Sarah V, CTS Consortium, Cornelissen, Sten, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Devilee, Peter, Dörk, Thilo, Dossus, Laure, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Engel, Christoph, Evans, D Gareth, Fasching, Peter A, Fletcher, Olivia, Flyger, Henrik, Gago-Dominguez, Manuela, Gao, Yu-Tang, García-Closas, Montserrat, García-Sáenz, José A, Genkinger, Jeanine, Gentry-Maharaj, Aleksandra, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Harkness, Elaine F, Harrington, Patricia A, Hartikainen, Jaana M, Hartman, Mikael, Hein, Alexander, Ho, Weang-Kee, Hooning, Maartje J, Hoppe, Reiner, Hopper, John L, Houlston, Richard S, Howell, Anthony, Hunter, David J, Huo, Dezheng, ABCTB Investigators, Ito, Hidemi, Iwasaki, Motoki, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jones, Michael E, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Khusnutdinova, Elza K, Kim, Sung-Won, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, Kurian, Allison W, Kwong, Ava, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Linet, Martha, Lo, Wing-Yee, Long, Jirong, Lophatananon, Artitaya, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Matsuo, Keitaro, Mavroudis, Dimitrios, Menon, Usha, Muir, Kenneth, Murphy, Rachel A, Nevanlinna, Heli, Newman, William G, Niederacher, Dieter, O'Brien, Katie M, Obi, Nadia, Offit, Kenneth, Olopade, Olufunmilayo I, Olshan, Andrew F, Olsson, Håkan, Park, Sue K, Patel, Alpa V, Patel, Achal, Perou, Charles M, Peto, Julian, Pharoah, Paul DP, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rack, Brigitte, Radice, Paolo, Ramachandran, Dhanya, Rashid, Muhammad U, Rennert, Gad, Romero, Atocha, Ruddy, Kathryn J, Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schmidt, Marjanka K, Schmutzler, Rita K, Schneider, Michael O, Scott, Christopher, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Surowy, Harald, Tamimi, Rulla M, Tapper, William J, Taylor, Jack A, Teo, Soo Hwang, Teras, Lauren R, Toland, Amanda E, Tollenaar, Rob AEM, Torres, Diana, Torres-Mejía, Gabriela, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Vijai, Joseph, Weinberg, Clarice R, Wendt, Camilla, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Yamaji, Taiki, Yang, Xiaohong R, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, Argyrios, Ziv, Elad, Dunning, Alison M, Easton, Douglas F, Hemingway, Harry, Hamann, Ute, Kuchenbaecker, Karoline B, Kuchenbaecker, Karoline B [0000-0001-9726-603X], and Apollo - University of Cambridge Repository
Subjects: Genome-wide association study, Breast cancer susceptibility, Diverse ancestry, Humans, Black People, Formins, Female, Genetic Predisposition to Disease, Rare variants, Breast Neoplasms, Genetic Testing, Polymorphism, Single Nucleotide, Gene regulation
Abstract: BACKGROUND: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes. METHODS: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry. RESULTS: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10-6) and AC058822.1 (P = 1.47 × 10-4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C. CONCLUSIONS: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10-5), demonstrating the importance of diversifying study cohorts.
Published: 2023
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3. Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry

Author: Mueller, Stefanie H, Lai, Alvina G, Valkovskaya, Maria, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Lush, Michael, Abu-Ful, Zomoruda, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Baert, Thais, Freeman, Laura E Beane, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Brenner, Hermann, Brucker, Sara Y, Buys, Saundra S, Castelao, Jose E, Chan, Tsun L, Chang-Claude, Jenny, Chanock, Stephen J, Choi, Ji-Yeob, Chung, Wendy K, Sahlberg, Kristine K, Børresen-Dale, Anne-Lise, Ottestad, Lars, Kåresen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebråten, Olav, Naume, Bjørn, Fosså, Alexander, Kiserud, Cecile E, Reinertsen, Kristin V, Helland, Åslaug, Riis, Margit, Geisler, Jürgen, Grenaker Alnaes, Grethe I, Colonna, Sarah V, Cornelissen, Sten, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Devilee, Peter, Dörk, Thilo, Dossus, Laure, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Engel, Christoph, Evans, D Gareth, Fasching, Peter A, Fletcher, Olivia, Flyger, Henrik, Gago-Dominguez, Manuela, Gao, Yu-Tang, García-Closas, Montserrat, García-Sáenz, José A, Genkinger, Jeanine, Gentry-Maharaj, Aleksandra, Grassmann, Felix, Guénel, Pascal, Gündert, Melanie, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Harkness, Elaine F, Harrington, Patricia A, Hartikainen, Jaana M, Hartman, Mikael, Hein, Alexander, Ho, Weang-Kee, Hooning, Maartje J, Hoppe, Reiner, Hopper, John L, Houlston, Richard S, Howell, Anthony, Hunter, David J, Huo, Dezheng, Marsh, Deborah, Scott, Rodney, Baxter, Robert, Yip, Desmond, Carpenter, Jane, Davis, Alison, Pathmanathan, Nirmala, Simpson, Peter, Graham, Dinny, Sachchithananthan, Mythily, Ito, Hidemi, Iwasaki, Motoki, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jones, Michael E, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Khusnutdinova, Elza K, Kim, Sung-Won, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kubelka-Sabit, Katerina, Kurian, Allison W, Kwong, Ava, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Linet, Martha, Lo, Wing-Yee, Long, Jirong, Lophatananon, Artitaya, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Matsuo, Keitaro, Mavroudis, Dimitrios, Menon, Usha, Muir, Kenneth, Murphy, Rachel A, Nevanlinna, Heli, Newman, William G, Niederacher, Dieter, O’Brien, Katie M, Obi, Nadia, Offit, Kenneth, Olopade, Olufunmilayo I, Olshan, Andrew F, Olsson, Håkan, Park, Sue K, Patel, Alpa V, Patel, Achal, Perou, Charles M, Peto, Julian, Pharoah, Paul DP, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rack, Brigitte, Radice, Paolo, Ramachandran, Dhanya, Rashid, Muhammad U, Rennert, Gad, Romero, Atocha, Ruddy, Kathryn J, Ruebner, Matthias, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schmidt, Marjanka K, Schmutzler, Rita K, Schneider, Michael O, Scott, Christopher, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Surowy, Harald, Tamimi, Rulla M, Tapper, William J, Taylor, Jack A, Teo, Soo Hwang, Teras, Lauren R, Toland, Amanda E, Tollenaar, Rob AEM, Torres, Diana, Torres-Mejía, Gabriela, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Vijai, Joseph, Weinberg, Clarice R, Wendt, Camilla, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Yamaji, Taiki, Yang, Xiaohong R, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, Argyrios, Ziv, Elad, Dunning, Alison M, Easton, Douglas F, Hemingway, Harry, Hamann, Ute, Kuchenbaecker, Karoline B, HUS Comprehensive Cancer Center, Department of Oncology, Clinicum, Medicum, University of Helsinki, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, Medical Oncology, Kuchenbaecker, Karoline B [0000-0001-9726-603X], and Apollo - University of Cambridge Repository
Subjects: Genome-wide association study, Black People, Breast Neoplasms/genetics, VARIANTS, PHENOTYPE, Polymorphism, Single Nucleotide, SDG 3 - Good Health and Well-being, Genetics, Humans, Genetic Predisposition to Disease, ddc:610, Genetic Testing, GENOME-WIDE ASSOCIATION, Molecular Biology, Genetics (clinical), Medicinsk genetik, Genetics & Heredity, RISK, Science & Technology, Breast cancer susceptibility, Manchester Cancer Research Centre, IDENTIFICATION, HERITABILITY, Diverse ancestry, ResearchInstitutes_Networks_Beacons/mcrc, Research, 1184 Genetics, developmental biology, physiology, PATHWAYS, Rare variants, Formins/genetics, LIGASE CBL-B, Gene regulation, METASTASIS, Genome-Wide Association Study/methods, Molecular Medicine, Female, Medical Genetics, Life Sciences & Biomedicine, FUNCTIONAL ANNOTATION
Abstract: Background Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes. Methods We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes’ coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry. Results In European ancestry samples, 14 genes were significantly associated (q FMNL3 (P = 6.11 × 10−6) and AC058822.1 (P = 1.47 × 10−4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C. Conclusions Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10−5), demonstrating the importance of diversifying study cohorts.
Published: 2023
Full Text: View/download PDF

4. Prenatal organophosphate ester exposure and executive function in Norwegian preschoolers

Author: Hall, Amber M., Keil, Alexander P., Choi, Giehae, Ramos, Amanda M., Richardson, David B., Olshan, Andrew F., Martin, Chantel L., Villanger, Gro Dehli, Reichborn-Kjennerud, Ted, Zeiner, Pål, Øvergaard, Kristin, Sakhi, Amrit Kaur, Thomsen, Cathrine, Aase, Heidi, and Engel, Stephanie M.
Abstract: Background: Organophosphate esters (OPEs) are ubiquitous chemicals, used as flame retardants and plasticizers. OPE usage has increased over time as a substitute for other controlled compounds. This study investigates the impact of prenatal OPE exposure on executive function (EF) in preschoolers. Methods: We selected 340 preschoolers from the Norwegian Mother, Father, and Child Cohort Study. Diphenyl-phosphate (DPhP), di-n-butyl-phosphate (DnBP), bis(2-butoxyethyl) phosphate (BBOEP), and bis(1,3-dichloro-2-propyl) phosphate (BDCIPP) were measured in maternal urine. EF was measured using the Behavior Rating Inventory of Executive Functioning-Preschool (BRIEF-P) and the Stanford-Binet fifth edition (SB-5). EF scores were scaled so a higher score indicated worse performance. We estimated exposure-outcome associations and evaluated modification by child sex using linear regression. Results: Higher DnBP was associated with lower EF scores across multiple rater-based domains. Higher DPhP and BDCIPP were associated with lower SB-5 verbal working memory (β = 0.49, 95% CI = 0.12, 0.87; β = 0.53, 95% CI = 0.08, 1.02), and higher BBOEP was associated with lower teacher-rated inhibition (β = 0.34, 95% CI = 0.01, 0.63). DPhP was associated with lower parent-reported BRIEF-P measures in boys but not girls [inhibition: boys: 0.37 (95% CI = 0.03, 0.93); girls: –0.48 (95% CI = –1.27, 0.19); emotional control: boys: 0.44 (95% CI = –0.13, 1.26); girls: –0.83 (95% CI = –1.73, –0.00); working memory: boys: 0.49 (95% CI = 0.03, 1.08); girls: –0.40 (95% CI = –1.11, 0.36)]. Fewer sex interactions were observed for DnBP, BBOEP, and BDCIPP, with irregular patterns observed across EF domains. Conclusions: We found some evidence prenatal OPE exposure may impact EF in preschoolers and variation in associations by sex.
Published: 2023

5. 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, Beane Freeman, Laura E, Becher, Heiko, Brenner, Hermann, Canzian, Federico, Carey, Lisa A, CTS Consortium, 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, Chang-Claude, Jenny, Jung, Audrey Y [0000-0003-0875-6673], Ahearn, Thomas U [0000-0003-0771-7752], Behrens, Sabine [0000-0002-9714-104X], Middha, Pooja [0000-0001-5503-8215], Wang, Qin [0000-0002-9139-0627], Arndt, Volker [0000-0001-9320-8684], Aronson, Kristan J [0000-0002-7865-7243], Becher, Heiko [0000-0002-8808-6667], Brenner, Hermann [0000-0002-6129-1572], Canzian, Federico [0000-0002-4261-4583], Czene, Kamila [0000-0002-3233-5695], Eliassen, A Heather [0000-0002-3961-6609], Figueroa, Jonine D [0000-0002-5100-623X], Fritschi, Lin [0000-0002-7692-3560], Gabrielson, Marike [0000-0002-3171-1556], Giles, Graham G [0000-0003-4946-9099], Guénel, Pascal [0000-0002-8359-518X], Hadjisavvas, Andreas [0000-0002-5636-0799], Håkansson, Niclas [0000-0001-7673-5554], Hall, Per [0000-0002-5640-9126], Hüsing, Anika [0000-0002-2685-9732], Koutros, Stella [0000-0001-5294-5485], Kraft, Peter [0000-0002-4472-8103], Le Marchand, Loic [0000-0001-5013-980X], Lissowska, Jolanta [0000-0003-2695-5799], Loizidou, Maria A [0000-0003-4503-7758], Mannermaa, Arto [0000-0001-8250-1930], Murphy, Rachel A [0000-0003-4383-5641], Olsson, Håkan [0000-0002-7721-4619], Patel, Alpa V [0000-0001-8834-9896], Perou, Charles M [0000-0001-9827-2247], Shu, Xiao-Ou [0000-0002-0711-8314], Southey, Melissa C [0000-0002-6313-9005], Stone, Jennifer [0000-0001-5077-0124], Tamimi, Rulla M [0000-0003-2306-8668], Vachon, Celine M [0000-0002-1962-9322], Wolk, Alicja [0000-0001-7387-6845], Dunning, Alison M [0000-0001-6651-7166], Pharoah, Paul DP [0000-0001-8494-732X], Easton, Douglas F [0000-0003-2444-3247], Milne, Roger L [0000-0001-5764-7268], Schmidt, Marjanka K [0000-0002-2228-429X], García-Closas, Montserrat [0000-0003-1033-2650], Chang-Claude, Jenny [0000-0001-8919-1971], and Apollo - University of Cambridge Repository
Subjects: Receptors, Estrogen, Receptor, ErbB-2, Risk Factors, Case-Control Studies, Biomarkers, Tumor, Humans, Female, Breast Neoplasms, Triple Negative Breast Neoplasms, Receptors, Progesterone
Abstract: BACKGROUND: Reproductive 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. METHODS: Analyses 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. RESULTS: Compared 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. CONCLUSIONS: This 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

6. Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach

Author: Gao, Guimin, Zhao, Fangyuan, Ahearn, Thomas U, Lunetta, Kathryn L, Troester, Melissa A, Du, Zhaohui, Ogundiran, Temidayo O, Ojengbede, Oladosu, Blot, William, Nathanson, Katherine L, Domchek, Susan M, Nemesure, Barbara, Hennis, Anselm, Ambs, Stefan, McClellan, Julian, Nie, Mark, Bertrand, Kimberly, Zirpoli, Gary, Yao, Song, Olshan, Andrew F, Bensen, Jeannette T, Bandera, Elisa V, Nyante, Sarah, Conti, David V, Press, Michael F, Ingles, Sue A, John, Esther M, Bernstein, Leslie, Hu, Jennifer J, Deming-Halverson, Sandra L, Chanock, Stephen J, Ziegler, Regina G, Rodriguez-Gil, Jorge L, Sucheston-Campbell, Lara E, Sandler, Dale P, Taylor, Jack A, Kitahara, Cari M, O'Brien, Katie M, Bolla, Manjeet K, Dennis, Joe, Dunning, Alison M, Easton, Douglas F, Michailidou, Kyriaki, Pharoah, Paul DP, Wang, Qin, Figueroa, Jonine, Biritwum, Richard, Adjei, Ernest, Wiafe, Seth, GBHS Study Team, Ambrosone, Christine B, Zheng, Wei, Olopade, Olufunmilayo I, García-Closas, Montserrat, Palmer, Julie R, Haiman, Christopher A, Huo, Dezheng, Dunning, Alison M [0000-0001-6651-7166], Huo, Dezheng [0000-0002-4041-1678], and Apollo - University of Cambridge Repository
Subjects: Multifactorial Inheritance, Receptors, Estrogen, Risk Factors, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease, Genome-Wide Association Study
Abstract: Polygenic risk scores (PRSs) are useful for predicting breast cancer risk, but the prediction accuracy of existing PRSs in women of African ancestry (AA) remains relatively low. We aim to develop optimal PRSs for the prediction of overall and estrogen receptor (ER) subtype-specific breast cancer risk in AA women. The AA dataset comprised 9235 cases and 10 184 controls from four genome-wide association study (GWAS) consortia and a GWAS study in Ghana. We randomly divided samples into training and validation sets. We built PRSs using individual-level AA data by a forward stepwise logistic regression and then developed joint PRSs that combined (1) the PRSs built in the AA training dataset and (2) a 313-variant PRS previously developed in women of European ancestry. PRSs were evaluated in the AA validation set. For overall breast cancer, the odds ratio per standard deviation of the joint PRS in the validation set was 1.34 [95% confidence interval (CI): 1.27-1.42] with the area under receiver operating characteristic curve (AUC) of 0.581. Compared with women with average risk (40th-60th PRS percentile), women in the top decile of the PRS had a 1.98-fold increased risk (95% CI: 1.63-2.39). For PRSs of ER-positive and ER-negative breast cancer, the AUCs were 0.608 and 0.576, respectively. Compared with existing methods, the proposed joint PRSs can improve prediction of breast cancer risk in AA women.
Published: 2022
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7. Lessons learned from the INHANCE consortium: An overview of recent results on head and neck cancer

Author: Bravi, Francesca, Lee, Yuan‐Chin Amy, Hashibe, Mia, Boffetta, Paolo, Conway, David I., Ferraroni, Monica, La Vecchia, Carlo, Edefonti, Valeria, Agudo, Antonio, Ahrens, Wolfgang, Benhamou, Simone, Boccia, Stefania, Brennan, Paul, Brenner, Hermann, Cadoni, Gabriella, Canova, Cristina, Chen, Chu, Chuang, Shu‐Chun, Curado, Maria Paula, Dal Maso, Luigino, Daudt, Alexander W., D'Souza, Gypsyamber, Fabianova, Eleonora, Fernandez, Leticia, Franceschi, Silvia, Garavello, Werner, Gillison, Maura, Gross, Neil D., Hayes, Richard B., Healy, Claire, Herrero, Rolando, Holcatova, Ivana, Kelsey, Karl, Kjaerheim, Kristina, Koifman, Rosalina, Lagiou, Pagona, Lazarus, Philip, Levi, Fabio, Li, Guojun, Lissowska, Jolanta, Luce, Daniele, Macfarlane, Gary J., Mates, Dana, Matsuo, Keitaro, McClean, Michael, Menezes, Ana, Menvielle, Gwenn, Morgenstern, Hal, Moyses, Raquel A., Moysich, Kirsten, Muscat, Joshua, Negri, Eva, Olshan, Andrew F., Pandics, Tamas, Polesel, Jerry, Purdue, Mark P., Radoï, Loredana, Ramroth, Heribert, Richiardi, Lorenzo, Schantz, Stimson, Schwartz, Stephen M., Serraino, Diego, Shangina, Oxana, Smith, Elaine, Sturgis, Erich M., Świątkowska, Beata, Thomson, Peter, Toporcov, Tatiana N., Vaughan, Thomas L., Vilensky, Marta, Winn, Deborah M., Wunsch‐Filho, Victor, Yu, Guo‐Pei, Zevallos, Jose P, Zhang, Zuo‐Feng, Zheng, Tongzhang, Znaor, Ariana, Bravi, F, Lee, Y, Hashibe, M, Boffetta, P, Conway, D, Ferraroni, M, La Vecchia, C, Edefonti, V, Agudo, A, Ahrens, W, Benhamou, S, Boccia, S, Brennan, P, Brenner, H, Cadoni, G, Canova, C, Chen, C, Chuang, S, Curado, M, Dal Maso, L, Daudt, A, D'Souza, G, Fabianova, E, Fernandez, L, Franceschi, S, Garavello, W, Gillison, M, Gross, N, Hayes, R, Healy, C, Herrero, R, Holcatova, I, Kelsey, K, Kjaerheim, K, Koifman, R, Lagiou, P, Lazarus, P, Levi, F, Li, G, Lissowska, J, Luce, D, Macfarlane, G, Mates, D, Matsuo, K, Mcclean, M, Menezes, A, Menvielle, G, Morgenstern, H, Moyses, R, Moysich, K, Muscat, J, Negri, E, Olshan, A, Pandics, T, Polesel, J, Purdue, M, Radoi, L, Ramroth, H, Richiardi, L, Schantz, S, Schwartz, S, Serraino, D, Shangina, O, Smith, E, Sturgis, E, Swiatkowska, B, Thomson, P, Toporcov, T, Vaughan, T, Vilensky, M, Winn, D, Wunsch-Filho, V, Yu, G, Zevallos, J, Zhang, Z, Zheng, T, Znaor, A, Bravi F., Lee Y.-C.A., Hashibe M., Boffetta P., Conway D.I., Ferraroni M., La Vecchia C., Edefonti V., Agudo A., Ahrens W., Benhamou S., Boccia S., Brennan P., Brenner H., Cadoni G., Canova C., Chen C., Chuang S.-C., Curado M.P., Dal Maso L., Daudt A.W., D'Souza G., Fabianova E., Fernandez L., Franceschi S., Garavello W., Gillison M., Gross N.D., Hayes R.B., Healy C., Herrero R., Holcatova I., Kelsey K., Kjaerheim K., Koifman R., Lagiou P., Lazarus P., Levi F., Li G., Lissowska J., Luce D., Macfarlane G.J., Mates D., Matsuo K., McClean M., Menezes A., Menvielle G., Morgenstern H., Moyses R.A., Moysich K., Muscat J., Negri E., Olshan A.F., Pandics T., Polesel J., Purdue M.P., Radoi L., Ramroth H., Richiardi L., Schantz S., Schwartz S.M., Serraino D., Shangina O., Smith E., Sturgis E.M., Swiatkowska B., Thomson P., Toporcov T.N., Vaughan T.L., Vilensky M., Winn D.M., Wunsch-Filho V., Yu G.-P., Zevallos J.P., Zhang Z.-F., Zheng T., and Znaor A.
Subjects: INHANCE, medicine.medical_specialty, Oral health, Cancer recurrence, Article, Tobacco Use, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, Epidemiology, medicine, Humans, pooled analysi, prognostic factor, General Dentistry, Beneficial effects, Head and Neck Neoplasm, business.industry, Incidence (epidemiology), Head and neck cancer, oral cavity cancer, Case-control study, prognostic factors, 030206 dentistry, medicine.disease, risk factor, Otorhinolaryngology, Head and Neck Neoplasms, Case-Control Studies, 030220 oncology & carcinogenesis, Family medicine, Etiology, laryngeal cancer, head and neck cancer, Settore MED/31 - OTORINOLARINGOIATRIA, pooled analysis, Neoplasm Recurrence, Local, Case-Control Studie, business, Human
Abstract: Objective:\ud \ud To summarize the latest evidence on head and neck cancer epidemiology from the International Head and Neck Cancer Epidemiology (INHANCE) consortium.\ud \ud Subjects and Methods:\ud \ud INHANCE was established in 2004 to elucidate the etiology of head and neck cancer through pooled analyses of individual‐level data on a large scale. We summarize results from recent INHANCE‐based publications updating our 2015 overview.\ud \ud Results:\ud \ud Seventeen papers were published between 2015 and May 2020. These studies further define the nature of risks associated with tobacco and alcohol, and occupational exposures on head and neck cancer. The beneficial effects on incidence of head and neck cancer were identified for good oral health, endogenous and exogenous hormonal factors, and selected aspects of diet related to fruit and vegetables. INHANCE has begun to develop risk prediction models and to pool follow‐up data on their studies, finding that ~30% of cases had cancer recurrence and 9% second primary cancers, with overall‐ and disease‐specific 5‐year‐survival of 51% and 57%, respectively.\ud \ud Conclusions:\ud \ud The number and importance of INHANCE scientific findings provides further evidence of the advantages of large‐scale internationally collaborative projects and will support the development of prevention strategies.
Published: 2020

8. Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis

Author: Escala-Garcia, Maria, Canisius, Sander, Keeman, Renske, Beesley, Jonathan, Anton-Culver, Hoda, Arndt, Volker, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dunning, Alison M, Easton, Douglas F, Ekici, Arif B, Eliassen, A Heather, Fasching, Peter A, Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Geisler, Jürgen, Giles, Graham G, Grip, Mervi, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hartikainen, Jaana M, Heemskerk-Gerritsen, Bernadette AM, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Hunter, David J, Jacot, William, Jakubowska, Anna, John, Esther M, Jung, Audrey Y, Kaaks, Rudolf, Khusnutdinova, Elza, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Luben, Robert N, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Muranen, Taru A, Nevanlinna, Heli, Olshan, Andrew F, Olsson, Håkan, Park-Simon, Tjoung-Won, Patel, Alpa V, Peterlongo, Paolo, Pharoah, Paul DP, Punie, Kevin, Radice, Paolo, Rennert, Gad, Rennert, Hedy S, Romero, Atocha, Roylance, Rebecca, Rüdiger, Thomas, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schoemaker, Minouk J, Scott, Christopher, Southey, Melissa C, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Teras, Lauren R, Thomas, Emilie, Tomlinson, Ian, Troester, Melissa A, Vachon, Celine M, Wang, Qin, Winqvist, Robert, and Wolk, Alicja
Subjects: screening and diagnosis, Tumor, Prevention, kConFab/AOCS Investigators, Genetic Variation, Breast Neoplasms, Single Nucleotide, Kaplan-Meier Estimate, 4.1 Discovery and preclinical testing of markers and technologies, Detection, Germ Cells, Cancer Survivors, Breast Cancer, Genetics, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Female, Polymorphism, Aetiology, skin and connective tissue diseases, Germ-Line Mutation, Biomarkers, Cancer
Abstract: Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 × 10-8 and 4.42 × 10-8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations.
Published: 2021

9. Evaluating Polygenic Risk Scores for Breast Cancer in Women of African Ancestry

Author: Du, Zhaohui, Gao, Guimin, Adedokun, Babatunde, Ahearn, Thomas, Lunetta, Kathryn L, Zirpoli, Gary, Troester, Melissa A, Ruiz-Narváez, Edward A, Haddad, Stephen A, PalChoudhury, Parichoy, Figueroa, Jonine, John, Esther M, Bernstein, Leslie, Zheng, Wei, Hu, Jennifer J, Ziegler, Regina G, Nyante, Sarah, Bandera, Elisa V, Ingles, Sue A, Mancuso, Nicholas, Press, Michael F, Deming, Sandra L, Rodriguez-Gil, Jorge L, Yao, Song, Ogundiran, Temidayo O, Ojengbe, Oladosu, Bolla, Manjeet K, Dennis, Joe, Dunning, Alison M, Easton, Douglas F, Michailidou, Kyriaki, Pharoah, Paul DP, Sandler, Dale P, Taylor, Jack A, Wang, Qin, Weinberg, Clarice R, Kitahara, Cari M, Blot, William, Nathanson, Katherine L, Hennis, Anselm, Nemesure, Barbara, Ambs, Stefan, Sucheston-Campbell, Lara E, Bensen, Jeannette T, Chanock, Stephen J, Olshan, Andrew F, Ambrosone, Christine B, Olopade, Olufunmilayo I, Yarney, Joel, Awuah, Baffour, Wiafe-Addai, Beatrice, Conti, David V, GBHS Study Team, Palmer, Julie R, Garcia-Closas, Montserrat, Huo, Dezheng, Haiman, Christopher A, Ahearn, Thomas [0000-0003-0771-7752], Lunetta, Kathryn L [0000-0002-9268-810X], Zirpoli, Gary [0000-0003-1417-5349], Figueroa, Jonine [0000-0002-5100-623X], Bernstein, Leslie [0000-0002-7692-6518], Hu, Jennifer J [0000-0002-0021-5699], Ziegler, Regina G [0000-0002-5100-9852], Nyante, Sarah [0000-0002-1770-5993], Ingles, Sue A [0000-0001-9181-8745], Press, Michael F [0000-0003-3400-6614], Rodriguez-Gil, Jorge L [0000-0002-1125-1281], Yao, Song [0000-0001-9442-1313], Ogundiran, Temidayo O [0000-0001-6405-2131], Dennis, Joe [0000-0003-4591-1214], Dunning, Alison M [0000-0001-6651-7166], Easton, Douglas F [0000-0003-2444-3247], Michailidou, Kyriaki [0000-0001-7065-1237], Pharoah, Paul DP [0000-0001-8494-732X], Sandler, Dale P [0000-0002-6776-0018], Taylor, Jack A [0000-0001-5303-6398], Wang, Qin [0000-0002-9139-0627], Kitahara, Cari M [0000-0001-6416-4432], Nathanson, Katherine L [0000-0002-6740-0901], Ambs, Stefan [0000-0001-7651-9309], Ambrosone, Christine B [0000-0003-1717-9943], Palmer, Julie R [0000-0002-6534-335X], Garcia-Closas, Montserrat [0000-0003-1033-2650], Huo, Dezheng [0000-0002-4041-1678], and Apollo - University of Cambridge Repository
Subjects: Aged, 80 and over, Asian People, Risk Factors, Black People, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease
Abstract: BACKGROUND: Polygenic risk scores (PRSs) have been demonstrated to identify women of European, Asian, and Latino ancestry at elevated risk of developing breast cancer (BC). We evaluated the performance of existing PRSs trained in European ancestry populations among women of African ancestry. METHODS: We assembled genotype data for women of African ancestry, including 9241 case subjects and 10 193 control subjects. We evaluated associations of 179- and 313-variant PRSs with overall and subtype-specific BC risk. PRS discriminatory accuracy was assessed using area under the receiver operating characteristic curve. We also evaluated a recalibrated PRS, replacing the index variant with variants in each region that better captured risk in women of African ancestry and estimated lifetime absolute risk of BC in African Americans by PRS category. RESULTS: For overall BC, the odds ratio per SD of the 313-variant PRS (PRS313) was 1.27 (95% confidence interval [CI] = 1.23 to 1.31), with an area under the receiver operating characteristic curve of 0.571 (95% CI = 0.562 to 0.579). Compared with women with average risk (40th-60th PRS percentile), women in the top decile of PRS313 had a 1.54-fold increased risk (95% CI = 1.38-fold to 1.72-fold). By age 85 years, the absolute risk of overall BC was 19.6% for African American women in the top 1% of PRS313 and 6.7% for those in the lowest 1%. The recalibrated PRS did not improve BC risk prediction. CONCLUSION: The PRSs stratify BC risk in women of African ancestry, with attenuated performance compared with that reported in European, Asian, and Latina populations. Future work is needed to improve BC risk stratification for women of African ancestry.
Published: 2021
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10. Combined Associations of a Polygenic Risk Score and Classical Risk Factors With Breast Cancer Risk

Author: Kapoor, Pooja Middha, Mavaddat, Nasim, Choudhury, Parichoy Pal, Wilcox, Amber N, Lindström, Sara, Behrens, Sabine, Michailidou, Kyriaki, Dennis, Joe, Bolla, Manjeet K, Wang, Qin, Jung, Audrey, Abu-Ful, Zomoroda, Ahearn, Thomas, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Auer, Paul L, Freeman, Laura E Beane, Becher, Heiko, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Benitez, Javier, Bernstein, Leslie, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Cai, Qiuyin, Campa, Daniele, Canzian, Federico, Carracedo, Angel, Carter, Brian D, Castelao, Jose E, Chanock, Stephen J, Chatterjee, Nilanjan, Chenevix-Trench, Georgia, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Dai, James Y, Earp, H Shelton, Ekici, Arif B, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M, Gaudet, Mia M, Giles, Graham G, González-Neira, Anna, Guénel, Pascal, Haeberle, Lothar, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hatse, Sigrid, Heyworth, Jane, Holleczek, Bernd, Hoover, Robert N, Hopper, John L, Howell, Anthony, Hunter, David J, ABCTB Investigators, kConFab/AOCS Investigators, John, Esther M, Jones, Michael E, Kaaks, Rudolf, Keeman, Renske, Kitahara, Cari M, Ko, Yon-Dschun, Koutros, Stella, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, MacInnis, Robert J, Martinez, Maria Elena, Maurer, Tabea, McLean, Catriona, Neuhausen, Susan L, Newman, William G, Norman, Aaron, O'Brien, Katie M, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, and Orr, Nick
Subjects: Aging, kConFab/AOCS Investigators, Oncology and Carcinogenesis, ABCTB Investigators, Breast Neoplasms, White People, Body Mass Index, Risk Factors, Clinical Research, Receptors, Breast Cancer, 80 and over, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Oncology & Carcinogenesis, Polymorphism, Aetiology, Medical History Taking, Aged, Cancer, Prevention, Single Nucleotide, Middle Aged, Estrogen, Logistic Models, Case-Control Studies, Female
Abstract: We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.
Published: 2021

11. Combined Associations of a Polygenic Risk Score and Classical Risk Factors With Breast Cancer Risk

Author: Kapoor, Pooja Middha, Mavaddat, Nasim, Choudhury, Parichoy Pal, Wilcox, Amber N, Lindström, Sara, Behrens, Sabine, Michailidou, Kyriaki, Dennis, Joe, Bolla, Manjeet K, Wang, Qin, Jung, Audrey, Abu-Ful, Zomoroda, Ahearn, Thomas, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Auer, Paul L, Freeman, Laura E Beane, Becher, Heiko, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Benitez, Javier, Bernstein, Leslie, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Cai, Qiuyin, Campa, Daniele, Canzian, Federico, Carracedo, Angel, Carter, Brian D, Castelao, Jose E, Chanock, Stephen J, Chatterjee, Nilanjan, Chenevix-Trench, Georgia, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Dai, James Y, Earp, H Shelton, Ekici, Arif B, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M, Gaudet, Mia M, Giles, Graham G, González-Neira, Anna, Guénel, Pascal, Haeberle, Lothar, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hatse, Sigrid, Heyworth, Jane, Holleczek, Bernd, Hoover, Robert N, Hopper, John L, Howell, Anthony, Hunter, David J, ABCTB Investigators, kConFab/AOCS Investigators, John, Esther M, Jones, Michael E, Kaaks, Rudolf, Keeman, Renske, Kitahara, Cari M, Ko, Yon-Dschun, Koutros, Stella, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, MacInnis, Robert J, Martinez, Maria Elena, Maurer, Tabea, McLean, Catriona, Neuhausen, Susan L, Newman, William G, Norman, Aaron, O'Brien, Katie M, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Orr, Nick, Perou, Charles M, Pita, Guillermo, Polley, Eric C, Prentice, Ross L, Rennert, Gad, Rennert, Hedy S, Ruddy, Kathryn J, Sandler, Dale P, Saunders, Christobel, Schoemaker, Minouk J, Schöttker, Ben, Schumacher, Fredrick, Scott, Christopher, Scott, Rodney J, Shu, Xiao-Ou, Smeets, Ann, Southey, Melissa C, Spinelli, John J, Stone, Jennifer, Swerdlow, Anthony J, Tamimi, Rulla M, Taylor, Jack A, Troester, Melissa A, Vachon, Celine M, van Veen, Elke M, Wang, Xiaoliang, Weinberg, Clarice R, Weltens, Caroline, Willett, Walter, Winham, Stacey J, Wolk, Alicja, Yang, Xiaohong R, Zheng, Wei, Ziogas, Argyrios, Dunning, Alison M, Pharoah, Paul DP, Schmidt, Marjanka K, Kraft, Peter, Easton, Douglas F, Milne, Roger L, García-Closas, Montserrat, Chang-Claude, Jenny, Mavaddat, Nasim [0000-0003-0307-055X], Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Dunning, Alison [0000-0001-6651-7166], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository
Subjects: Aged, 80 and over, Breast Neoplasms, Middle Aged, Polymorphism, Single Nucleotide, White People, Body Mass Index, Logistic Models, Receptors, Estrogen, Risk Factors, Case-Control Studies, Humans, Female, Genetic Predisposition to Disease, Medical History Taking, Aged
Abstract: We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.
Published: 2021

12. Breast Cancer Risk Factors and Survival by Tumor Subtype: Pooled Analyses from the Breast Cancer Association Consortium

Author: Morra, Anna, Jung, Audrey Y, Behrens, Sabine, Keeman, Renske, Ahearn, Thomas U, Anton-Culver, Hoda, Arndt, Volker, Augustinsson, Annelie, Auvinen, Päivi K, Beane Freeman, Laura E, Becher, Heiko, Beckmann, Matthias W, Blomqvist, Carl, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Briceno, Ignacio, Brucker, Sara Y, Camp, Nicola J, Campa, Daniele, Canzian, Federico, Castelao, Jose E, Chanock, Stephen J, Choi, Ji-Yeob, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Dörk, Thilo, Dunning, Alison M, Dwek, Miriam, Easton, Douglas F, Eccles, Diana M, Egan, Kathleen M, Evans, D Gareth, Fasching, Peter A, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Sáenz, José A, Gaudet, Mia M, Giles, Graham G, Grip, Mervi, Guénel, Pascal, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Han, Sileny N, Hart, Steven N, Hartman, Mikael, Heyworth, Jane S, Hoppe, Reiner, Hopper, John L, Hunter, David J, Ito, Hidemi, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, Janni, Wolfgang, Kaaks, Rudolf, Kang, Daehee, Kapoor, Pooja Middha, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Lacey, James V, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Lindblom, Annika, Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mariapun, Shivaani, Matsuo, Keitaro, Mavroudis, Dimitrios, Milne, Roger L, Muranen, Taru A, Newman, William G, Noh, Dong-Young, Nordestgaard, Børge G, Obi, Nadia, Olshan, Andrew F, Olsson, Håkan, Park-Simon, Tjoung-Won, Petridis, Christos, Pharoah, Paul DP, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rashid, Muhammad U, Rennert, Gad, Rennert, Hedy S, Rhenius, Valerie, Romero, Atocha, Saloustros, Emmanouil, Sawyer, Elinor J, Schneeweiss, Andreas, Schwentner, Lukas, Scott, Christopher, Shah, Mitul, Shen, Chen-Yang, Shu, Xiao-Ou, Southey, Melissa C, Stram, Daniel O, Tamimi, Rulla M, Tapper, William, Tollenaar, Rob AEM, Tomlinson, Ian, Torres, Diana, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Wang, Qin, Wang, Sophia S, Williams, Justin A, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Yoo, Keun-Young, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, Argyrios, Yang, Xiaohong R, Eliassen, A Heather, Holmes, Michelle D, García-Closas, Montserrat, Teo, Soo Hwang, Schmidt, Marjanka K, Chang-Claude, Jenny, ABCTB Investigators, NBCS Collaborators, Behrens, Sabine [0000-0002-9714-104X], Keeman, Renske [0000-0002-5452-9933], Ahearn, Thomas U [0000-0003-0771-7752], Arndt, Volker [0000-0001-9320-8684], Augustinsson, Annelie [0000-0003-3415-0536], Brenner, Hermann [0000-0002-6129-1572], Camp, Nicola J [0000-0002-4788-1998], Canzian, Federico [0000-0002-4261-4583], Cox, Angela [0000-0002-5138-1099], Dunning, Alison M [0000-0001-6651-7166], Evans, D Gareth [0000-0002-8482-5784], Fasching, Peter A [0000-0003-4885-8471], Gago-Dominguez, Manuela [0000-0001-6713-4351], García-Sáenz, José A [0000-0001-6880-0301], Gaudet, Mia M [0000-0002-6429-4007], Giles, Graham G [0000-0003-4946-9099], Guénel, Pascal [0000-0002-8359-518X], Hall, Per [0000-0002-5640-9126], Hart, Steven N [0000-0001-7714-2734], Hartman, Mikael [0000-0001-5726-9965], Ito, Hidemi [0000-0002-8023-4581], Jager, Agnes [0000-0002-7713-1450], Jakubowska, Anna [0000-0002-5650-0501], Janni, Wolfgang [0000-0001-5911-2400], Kaaks, Rudolf [0000-0003-3751-3929], Kapoor, Pooja Middha [0000-0001-5503-8215], Koutros, Stella [0000-0001-5294-5485], Lambrechts, Diether [0000-0002-3429-302X], Li, Jingmei [0000-0001-8587-7511], Matsuo, Keitaro [0000-0003-1761-6314], Milne, Roger L [0000-0001-5764-7268], Muranen, Taru A [0000-0002-5895-1808], Newman, William G [0000-0002-6382-4678], Park-Simon, Tjoung-Won [0000-0002-2863-3040], Pharoah, Paul DP [0000-0001-8494-732X], Rennert, Gad [0000-0002-8512-068X], Rennert, Hedy S [0000-0001-5772-2977], Rhenius, Valerie [0000-0003-4215-3235], Romero, Atocha [0000-0002-1634-7397], Saloustros, Emmanouil [0000-0002-0485-0120], Schneeweiss, Andreas [0000-0002-2429-4512], Scott, Christopher [0000-0003-1340-0647], Southey, Melissa C [0000-0002-6313-9005], Stram, Daniel O [0000-0001-7099-9022], Tamimi, Rulla M [0000-0003-2306-8668], Tomlinson, Ian [0000-0003-3037-1470], Torres, Diana [0000-0002-9879-9775], Vachon, Celine M [0000-0002-1962-9322], Wolk, Alicja [0000-0001-7387-6845], Ziogas, Argyrios [0000-0003-4529-3727], Holmes, Michelle D [0000-0002-8664-2172], García-Closas, Montserrat [0000-0003-1033-2650], Teo, Soo Hwang [0000-0002-0444-590X], Schmidt, Marjanka K [0000-0002-2228-429X], Chang-Claude, Jenny [0000-0001-8919-1971], and Apollo - University of Cambridge Repository
Subjects: Adult, Risk Factors, Cause of Death, Humans, Breast Neoplasms, Female, Neoplasm Invasiveness, Prospective Studies, Middle Aged, Life Style, Survival Analysis, Aged, Neoplasm Staging
Abstract: BACKGROUND: It is not known whether modifiable lifestyle factors that predict survival after invasive breast cancer differ by subtype. METHODS: We analyzed data for 121,435 women diagnosed with breast cancer from 67 studies in the Breast Cancer Association Consortium with 16,890 deaths (8,554 breast cancer specific) over 10 years. Cox regression was used to estimate associations between risk factors and 10-year all-cause mortality and breast cancer-specific mortality overall, by estrogen receptor (ER) status, and by intrinsic-like subtype. RESULTS: There was no evidence of heterogeneous associations between risk factors and mortality by subtype (P adj > 0.30). The strongest associations were between all-cause mortality and BMI ≥30 versus 18.5-25 kg/m2 [HR (95% confidence interval (CI), 1.19 (1.06-1.34)]; current versus never smoking [1.37 (1.27-1.47)], high versus low physical activity [0.43 (0.21-0.86)], age ≥30 years versus 0
Published: 2021
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13. A framework for transcriptome-wide association studies in breast cancer in diverse study populations

Author: Bhattacharya, Arjun, García-Closas, Montserrat, Olshan, Andrew F., Perou, Charles M., Troester, Melissa A., and Love, Michael I.
Subjects: Survival, lcsh:QH426-470, Quantitative Trait Loci, Population, Breast Neoplasms, Genome-wide association study, Computational biology, Biology, Expression quantitative trait loci (eQTL), 03 medical and health sciences, Breast cancer, 0302 clinical medicine, Genotype, Genetic variation, medicine, Humans, education, Transcriptome-wide analysis (TWAS), lcsh:QH301-705.5, 030304 developmental biology, Genetic association, 0303 health sciences, education.field_of_study, Polymorphism, Genetic, Research, Reproducibility of Results, medicine.disease, Human genetics, Black or African American, lcsh:Genetics, Polygenic traits, lcsh:Biology (General), Polygene, 030220 oncology & carcinogenesis, Cohort, Expression quantitative trait loci, Female, Transcriptome, Genome-Wide Association Study
Abstract: BackgroundThe relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studies (GWAS) have interrogated breast cancer survival but often are underpowered due to subtype heterogeneity and clinical covariates and detect loci in non-coding regions that are difficult to interpret. Transcriptome-wide association studies (TWAS) show increased power in detecting functionally relevant loci by leveraging expression quantitative trait loci (eQTLs) from external reference panels in relevant tissues. However, ancestry- or race-specific reference panels may be needed to draw correct inference in ancestrally diverse cohorts. Such panels for breast cancer are lacking.ResultsWe provide a framework for TWAS for breast cancer in diverse populations, using data from the Carolina Breast Cancer Study (CBCS), a population-based cohort that oversampled black women. We perform eQTL analysis for 406 breast cancer-related genes to train race-stratified predictive models of tumor expression from germline genotypes. Using these models, we impute expression in independent data from CBCS and TCGA, accounting for sampling variability in assessing performance. These models are not applicable across race, and their predictive performance varies across tumor subtype. Within CBCS (N = 3,828), at a false discovery-adjusted significance of 0.10 and stratifying for race, we identify associations in black women nearAURKA,CAPN13,PIK3CA, andSERPINB5via TWAS that are underpowered in GWAS.ConclusionsWe show that carefully implemented and thoroughly validated TWAS is an efficient approach for understanding the genetics underpinning breast cancer outcomes in diverse populations.
Published: 2020

14. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Author: Escala-Garcia, Maria, Abraham, Jean, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Ashworth, Alan, Auer, Paul L, Auvinen, Päivi, Beckmann, Matthias W, Beesley, Jonathan, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Blot, William, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brucker, Sara Y, Burwinkel, Barbara, Caldas, Carlos, Canzian, Federico, Chang-Claude, Jenny, Chanock, Stephen J, Chin, Suet-Feung, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dunn, Janet A, Dunning, Alison M, Dwek, Miriam, Earl, Helena M, Eccles, Diana M, Eliassen, A Heather, Ellberg, Carolina, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, George, Angela, Giles, Graham G, Goldgar, David E, González-Neira, Anna, Grip, Mervi, Guénel, Pascal, Guo, Qi, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Harrington, Patricia A, Hiller, Louise, Hooning, Maartje J, Hopper, John L, Howell, Anthony, Huang, Chiun-Sheng, Huang, Guanmengqian, Hunter, David J, Jakubowska, Anna, John, Esther M, Kaaks, Rudolf, Kapoor, Pooja Middha, Keeman, Renske, Kitahara, Cari M, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Lambrechts, Diether, Le Marchand, Loic, Lejbkowicz, Flavio, Lindblom, Annika, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Maurer, Tabea, Mavroudis, Dimitrios, Meindl, Alfons, Milne, Roger L, Mulligan, Anna Marie, Neuhausen, Susan L, Nevanlinna, Heli, Newman, William G, Olshan, Andrew F, Olson, Janet E, and Olsson, Håkan
Subjects: Gq-G11, screening and diagnosis, Genotype, Computational Biology, Genetic Variation, Breast Neoplasms, Apoptosis, Prognosis, Estrogen, GTP-Binding Protein alpha Subunits, 4.1 Discovery and preclinical testing of markers and technologies, Detection, Germ Cells, Circadian Clocks, Receptors, Breast Cancer, Genetics, Humans, 2.1 Biological and endogenous factors, Female, Gene Regulatory Networks, Aetiology, Signal Transduction, Genome-Wide Association Study, Cancer
Abstract: Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.
Published: 2020

15. Centered Partition Process: Informative Priors for Clustering

Author: Paganin, Sally, Herring, Amy H., Olshan, Andrew F., and Dunson, David B.
Subjects: Methodology (stat.ME), FOS: Computer and information sciences, Applications (stat.AP), Statistics - Applications, Statistics - Methodology
Abstract: There is a very rich literature proposing Bayesian approaches for clustering starting with a prior probability distribution on partitions. Most approaches assume exchangeability, leading to simple representations in terms of Exchangeable Partition Probability Functions (EPPF). Gibbs-type priors encompass a broad class of such cases, including Dirichlet and Pitman-Yor processes. Even though there have been some proposals to relax the exchangeability assumption, allowing covariate-dependence and partial exchangeability, limited consideration has been given on how to include concrete prior knowledge on the partition. For example, we are motivated by an epidemiological application, in which we wish to cluster birth defects into groups and we have prior knowledge of an initial clustering provided by experts. As a general approach for including such prior knowledge, we propose a Centered Partition (CP) process that modifies the EPPF to favor partitions close to an initial one. Some properties of the CP prior are described, a general algorithm for posterior computation is developed, and we illustrate the methodology through simulation examples and an application to the motivating epidemiology study of birth defects.
Published: 2019
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16. AUT753563_Lay_Abstract – Supplemental material for Associations between parental broader autism phenotype and child autism spectrum disorder phenotype in the Study to Explore Early Development

Author: Rubenstein, Eric, Wiggins, Lisa D, Schieve, Laura A, Chyrise Bradley, DiGuiseppi, Carolyn, Moody, Eric, Pandey, Juhi, Pretzel, Rebecca Edmondson, Howard, Annie Green, Olshan, Andrew F, Pence, Brian W, and Daniels, Julie
Subjects: FOS: Psychology, FOS: Clinical medicine, 170199 Psychology not elsewhere classified, 111799 Public Health and Health Services not elsewhere classified, FOS: Educational sciences, 110319 Psychiatry (incl. Psychotherapy), FOS: Health sciences, 130312 Special Education and Disability, Education
Abstract: Supplemental material, AUT753563_Lay_Abstract for Associations between parental broader autism phenotype and child autism spectrum disorder phenotype in the Study to Explore Early Development by Eric Rubenstein, Lisa D Wiggins, Laura A Schieve, Chyrise Bradley, Carolyn DiGuiseppi, Eric Moody, Juhi Pandey, Rebecca Edmondson Pretzel, Annie Green Howard, Andrew F Olshan, Brian W Pence and Julie Daniels in Autism
Published: 2018
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17. AUT753563_Supplementary_material – Supplemental material for Associations between parental broader autism phenotype and child autism spectrum disorder phenotype in the Study to Explore Early Development

Author: Rubenstein, Eric, Wiggins, Lisa D, Schieve, Laura A, Chyrise Bradley, DiGuiseppi, Carolyn, Moody, Eric, Pandey, Juhi, Pretzel, Rebecca Edmondson, Howard, Annie Green, Olshan, Andrew F, Pence, Brian W, and Daniels, Julie
Subjects: FOS: Psychology, FOS: Clinical medicine, 170199 Psychology not elsewhere classified, 111799 Public Health and Health Services not elsewhere classified, FOS: Educational sciences, 110319 Psychiatry (incl. Psychotherapy), FOS: Health sciences, 130312 Special Education and Disability, Education
Abstract: Supplemental material, AUT753563_Supplementary_material for Associations between parental broader autism phenotype and child autism spectrum disorder phenotype in the Study to Explore Early Development by Eric Rubenstein, Lisa D Wiggins, Laura A Schieve, Chyrise Bradley, Carolyn DiGuiseppi, Eric Moody, Juhi Pandey, Rebecca Edmondson Pretzel, Annie Green Howard, Andrew F Olshan, Brian W Pence and Julie Daniels in Autism
Published: 2018
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18. Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer

Author: Lesseur, Corina, Diergaarde, Brenda, Olshan, Andrew F, Wünsch-Filho, Victor, Ness, Andrew R, Liu, Geoffrey, Lacko, Martin, Eluf-Neto, José, Franceschi, Silvia, Lagiou, Pagona, Macfarlane, Gary J, Richiardi, Lorenzo, Boccia, Stefania, Polesel, Jerry, Kjaerheim, Kristina, Zaridze, David, Johansson, Mattias, Menezes, Ana M, Curado, Maria Paula, Robinson, Max, Ahrens, Wolfgang, Canova, Cristina, Znaor, Ariana, Castellsagué, Xavier, Conway, David I, Holcátová, Ivana, Mates, Dana, Vilensky, Marta, Healy, Claire M, Szeszenia-Dąbrowska, Neonila, Fabiánová, Eleonóra, Lissowska, Jolanta, Grandis, Jennifer R, Weissler, Mark C, Tajara, Eloiza H, Nunes, Fabio D, de Carvalho, Marcos B, Thomas, Steve, Hung, Rayjean J, Peters, Wilbert HM, Herrero, Rolando, Cadoni, Gabriella, Bueno-de-Mesquita, H Bas, Steffen, Annika, Agudo, Antonio, Shangina, Oxana, Xiao, Xiangjun, Gaborieau, Valérie, Chabrier, Amélie, Anantharaman, Devasena, Boffetta, Paolo, Amos, Christopher I, McKay, James D, and Brennan, Paul
Subjects: Genetic Markers, Male, Medical and Health Sciences, Clinical Research, HLA Antigens, Genetics, 2.1 Biological and endogenous factors, Humans, Genetic Predisposition to Disease, Dental/Oral and Craniofacial Disease, Aetiology, Papillomaviridae, Cancer, Aged, Mouth, Human Genome, Papillomavirus Infections, Genetic Variation, Pharyngeal Neoplasms, Middle Aged, Biological Sciences, Haplotypes, Case-Control Studies, Mouth Neoplasms, Female, Digestive Diseases, Genome-Wide Association Study, Developmental Biology
Abstract: We conducted a genome-wide association study of oral cavity and pharyngeal cancer in 6,034 cases and 6,585 controls from Europe, North America and South America. We detected eight significantly associated loci (P < 5 × 10-8), seven of which are new for these cancer sites. Oral and pharyngeal cancers combined were associated with loci at 6p21.32 (rs3828805, HLA-DQB1), 10q26.13 (rs201982221, LHPP) and 11p15.4 (rs1453414, OR52N2-TRIM5). Oral cancer was associated with two new regions, 2p23.3 (rs6547741, GPN1) and 9q34.12 (rs928674, LAMC3), and with known cancer-related loci-9p21.3 (rs8181047, CDKN2B-AS1) and 5p15.33 (rs10462706, CLPTM1L). Oropharyngeal cancer associations were limited to the human leukocyte antigen (HLA) region, and classical HLA allele imputation showed a protective association with the class II haplotype HLA-DRB1*1301-HLA-DQA1*0103-HLA-DQB1*0603 (odds ratio (OR) = 0.59, P = 2.7 × 10-9). Stratified analyses on a subgroup of oropharyngeal cases with information available on human papillomavirus (HPV) status indicated that this association was considerably stronger in HPV-positive (OR = 0.23, P = 1.6 × 10-6) than in HPV-negative (OR = 0.75, P = 0.16) cancers.
Published: 2016

19. A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci

Author: Rand, Kristin A, Song, Chi, Dean, Eric, Serie, Daniel J, Curtin, Karen, Sheng, Xin, Hu, Donglei, Huff, Carol Ann, Bernal-Mizrachi, Leon, Tomasson, Michael H, Ailawadhi, Sikander, Singhal, Seema, Pawlish, Karen, Peters, Edward S, Bock, Cathryn H, Stram, Alex, Van Den Berg, David J, Edlund, Christopher K, Conti, David V, Zimmerman, Todd, Hwang, Amie E, Huntsman, Scott, Graff, John, Nooka, Ajay, Kong, Yinfei, Pregja, Silvana L, Berndt, Sonja I, Blot, William J, Carpten, John, Casey, Graham, Chu, Lisa, Diver, W Ryan, Stevens, Victoria L, Lieber, Michael R, Goodman, Phyllis J, Hennis, Anselm JM, Hsing, Ann W, Mehta, Jayesh, Kittles, Rick A, Kolb, Suzanne, Klein, Eric A, Leske, Cristina, Murphy, Adam B, Nemesure, Barbara, Neslund-Dudas, Christine, Strom, Sara S, Vij, Ravi, Rybicki, Benjamin A, Stanford, Janet L, Signorello, Lisa B, Witte, John S, Ambrosone, Christine B, Bhatti, Parveen, John, Esther M, Bernstein, Leslie, Zheng, Wei, Olshan, Andrew F, Hu, Jennifer J, Ziegler, Regina G, Nyante, Sarah J, Bandera, Elisa V, Birmann, Brenda M, Ingles, Sue A, Press, Michael F, Atanackovic, Djordje, Glenn, Martha J, Cannon-Albright, Lisa A, Jones, Brandt, Tricot, Guido, Martin, Thomas G, Kumar, Shaji K, Wolf, Jeffrey L, Deming Halverson, Sandra L, Rothman, Nathaniel, Brooks-Wilson, Angela R, Rajkumar, S Vincent, Kolonel, Laurence N, Chanock, Stephen J, Slager, Susan L, Severson, Richard K, Janakiraman, Nalini, Terebelo, Howard R, Brown, Elizabeth E, De Roos, Anneclaire J, Mohrbacher, Ann F, Colditz, Graham A, Giles, Graham G, Spinelli, John J, Chiu, Brian C, Munshi, Nikhil C, Anderson, Kenneth C, Levy, Joan, Zonder, Jeffrey A, Orlowski, Robert Z, Lonial, Sagar, Camp, Nicola J, Vachon, Celine M, Ziv, Elad, Stram, Daniel O, and Hazelett, Dennis J
Subjects: Adult, Male, Epidemiology, Transmembrane Activator and CAML Interactor Protein, Black People, Protein Serine-Threonine Kinases, Medical and Health Sciences, White People, Rare Diseases, Clinical Research, Genetics, Humans, 2.1 Biological and endogenous factors, Genetic Predisposition to Disease, Polymorphism, Aetiology, Aged, Cancer, Polycomb Repressive Complex 1, Human Genome, Single Nucleotide, Hematology, Middle Aged, Repressor Proteins, Genetic Loci, Female, Multiple Myeloma, Genome-Wide Association Study
Abstract: BackgroundGenome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma.MethodsWe performed association testing of common variation in eight regions in 1,318 patients with multiple myeloma and 1,480 controls of European ancestry and 1,305 patients with multiple myeloma and 7,078 controls of African ancestry and conducted a meta-analysis to localize the signals, with epigenetic annotation used to predict functionality.ResultsWe found that variants in 7p15.3, 17p11.2, 22q13.1 were statistically significantly (P < 0.05) associated with multiple myeloma risk in persons of African ancestry and persons of European ancestry, and the variant in 3p22.1 was associated in European ancestry only. In a combined African ancestry-European ancestry meta-analysis, variation in five regions (2p23.3, 3p22.1, 7p15.3, 17p11.2, 22q13.1) was statistically significantly associated with multiple myeloma risk. In 3p22.1, the correlated variants clustered within the gene body of ULK4 Correlated variants in 7p15.3 clustered around an enhancer at the 3' end of the CDCA7L transcription termination site. A missense variant at 17p11.2 (rs34562254, Pro251Leu, OR, 1.32; P = 2.93 × 10-7) in TNFRSF13B encodes a lymphocyte-specific protein in the TNF receptor family that interacts with the NF-κB pathway. SNPs correlated with the index signal in 22q13.1 cluster around the promoter and enhancer regions of CBX7 CONCLUSIONS: We found that reported multiple myeloma susceptibility regions contain risk variants important across populations, supporting the use of multiple racial/ethnic groups with different underlying genetic architecture to enhance the localization and identification of putatively functional alleles.ImpactA subset of reported risk loci for multiple myeloma has consistent effects across populations and is likely to be functional. Cancer Epidemiol Biomarkers Prev; 25(12); 1609-18. ©2016 AACR.
Published: 2016

20. Geographic heterogeneity in the prevalence of human papillomavirus in head and neck cancer

Author: Anantharaman, Devasena, Abedi Ardekani, Behnoush, Beachler, Daniel C., Gheit, Tarik, Olshan, Andrew F., Wisniewski, Kathy, Wunsch Filho, Victor, Toporcov, Tatiana N., Tajara, Eloiza H., Levi, José Eduardo, Moyses, Raquel A., Boccia, Stefania, Cadoni, Gabriella, Rindi, Guido, Ahrens, Wolfgang, Merletti, Franco, Conway, David I., Wright, Sylvia, Carreira, Christine, Renard, Helene, Chopard, Priscilia, McKay Chopin, Sandrine, Scelo, Ghislaine, Tommasino, Massimo, Brennan, Paul, and D'Souza, Gypsyamber
Subjects: HPV16, Cancer Research, HPV, prevalence, smoking, Article, Biomarkers, Tumor, Humans, Settore MED/42 - IGIENE GENERALE E APPLICATA, Cyclin-Dependent Kinase Inhibitor p16, Neoplastic, Human papillomavirus 16, Tumor, alcohol, Medicine (all), head and neck cancer, oropharynx, Brazil, Europe, Gene Expression Regulation, Neoplastic, Head and Neck Neoplasms, United States, Oncology, Gene Expression Regulation, Settore MED/31 - OTORINOLARINGOIATRIA, Biomarkers
Abstract: Human papillomavirus (HPV) causes oropharyngeal squamous cell carcinoma (OPSCC), although strongly divergent results have been reported regarding the prevalence of HPV16 in different countries, whether this represents important differences in etiology remains unclear. Applying rigorous protocols for sample processing, we centrally evaluated 1,420 head and neck tumors (533 oropharynx, 395 oral cavity and 482 larynx) from studies conducted in the US, Europe and Brazil for mucosal HPV DNA and p16(INK4a) expression to evaluate regional heterogeneity in the proportion of HPV16-associated OPSCC and other head and neck cancer, and to assess covariates associated with the risk of HPV16-positive OPSCC. While majority of OPSCC in the US (60%) were HPV16-positive, this proportion was 31% in Europe and only 4% in Brazil (p < 0.01). Similar differences were observed for other head and neck tumors, ranging from 7% in the US and 5% in Europe, to 0% in South America. The odds of HPV16-positive OPSCC declined with increasing pack years of smoking (OR: 0.75; 95% CI: 0.64–0.87) and drink years of alcohol use (OR: 0.64; 95% CI: 0.54–0.76). These results suggest that while the contribution of HPV16 is substantial for the oropharynx, it remains limited for oral cavity and laryngeal cancers.
Published: 2016

21. IARC monographs: 40 years of evaluating carcinogenic hazards to humans

Author: Pearce, Neil, Blair, Aaron, Vineis, Paolo, Ahrens, Wolfgang, Andersen, Aage, Anto, Josep M, Armstrong, Bruce K, Baccarelli, Andrea A, Beland, Frederick A, Berrington, Amy, Bertazzi, Pier Alberto, Birnbaum, Linda S, Brownson, Ross C, Bucher, John R, Cantor, Kenneth P, Cardis, Elisabeth, Cherrie, John W, Christiani, David C, Cocco, Pierluigi, Coggon, David, Comba, Pietro, Demers, Paul A, Dement, John M, Douwes, Jeroen, Eisen, Ellen A, Engel, Lawrence S, Fenske, Richard A, Fleming, Lora E, Fletcher, Tony, Fontham, Elizabeth, Forastiere, Francesco, Frentzel-Beyme, Rainer, Fritschi, Lin, Gerin, Michel, Goldberg, Marcel, Grandjean, Philippe, Grimsrud, Tom K, Gustavsson, Per, Haines, Andy, Hartge, Patricia, Hansen, Johnni, Hauptmann, Michael, Heederik, Dick, Hemminki, Kari, Hemon, Denis, Hertz-Picciotto, Irva, Hoppin, Jane A, Huff, James, Jarvholm, Bengt, Kang, Daehee, Karagas, Margaret R, Kjaerheim, Kristina, Kjuus, Helge, Kogevinas, Manolis, Kriebel, David, Kristensen, Petter, Kromhout, Hans, Laden, Francine, Lebailly, Pierre, LeMasters, Grace, Lubin, Jay H, Lynch, Charles F, Lynge, Elsebeth, 't Mannetje, Andrea, McMichael, Anthony J, McLaughlin, John R, Marrett, Loraine, Martuzzi, Marco, Merchant, James A, Merler, Enzo, Merletti, Franco, Miller, Anthony, Mirer, Franklin E, Monson, Richard, Nordby, Karl-Cristian, Olshan, Andrew F, Parent, Marie-Elise, Perera, Frederica P, Perry, Melissa J, Pesatori, Angela Cecilia, Pirastu, Roberta, Porta, Miquel, Pukkala, Eero, Rice, Carol, Richardson, David B, Ritter, Leonard, Ritz, Beate, Ronckers, Cecile M, Rushton, Lesley, Rusiecki, Jennifer A, Rusyn, Ivan, Samet, Jonathan M, Sandler, Dale P, de Sanjose, Silvia, Schernhammer, Eva, Costantini, Adele Seniori, Seixas, Noah, Shy, Carl, Siemiatycki, Jack, and Silverman, Debra T
Subjects: Biomedical Research, Neoplasms, Publications, Carcinogens, Humans, International Agencies, Public Health, Toxicology, Medical and Health Sciences, Environmental Sciences, Environmental
Abstract: BackgroundRecently, the International Agency for Research on Cancer (IARC) Programme for the Evaluation of Carcinogenic Risks to Humans has been criticized for several of its evaluations, and also for the approach used to perform these evaluations. Some critics have claimed that failures of IARC Working Groups to recognize study weaknesses and biases of Working Group members have led to inappropriate classification of a number of agents as carcinogenic to humans.ObjectivesThe authors of this Commentary are scientists from various disciplines relevant to the identification and hazard evaluation of human carcinogens. We examined criticisms of the IARC classification process to determine the validity of these concerns. Here, we present the results of that examination, review the history of IARC evaluations, and describe how the IARC evaluations are performed.DiscussionWe concluded that these recent criticisms are unconvincing. The procedures employed by IARC to assemble Working Groups of scientists from the various disciplines and the techniques followed to review the literature and perform hazard assessment of various agents provide a balanced evaluation and an appropriate indication of the weight of the evidence. Some disagreement by individual scientists to some evaluations is not evidence of process failure. The review process has been modified over time and will undoubtedly be altered in the future to improve the process. Any process can in theory be improved, and we would support continued review and improvement of the IARC processes. This does not mean, however, that the current procedures are flawed.ConclusionsThe IARC Monographs have made, and continue to make, major contributions to the scientific underpinning for societal actions to improve the public's health.
Published: 2015

22. Adult height and head and neck cancer: a pooled analysis within the INHANCE Consortium

Author: Leoncini, Emanuele, Ricciardi, Walter, Cadoni, Gabriella, Arzani, Dario, Petrelli, Livia, Paludetti, Gaetano, Brennan, Paul, Luce, Daniele, Stucker, Isabelle, Matsuo, Keitaro, Talamini, Renato, La Vecchia, Carlo, Olshan, Andrew F, Winn, Deborah M, Herrero, Rolando, Franceschi, Silvia, Castellsague, Xavier, Muscat, Joshua, Morgenstern, Hal, Zhang, Zuo-Feng, Levi, Fabio, Dal Maso, Luigino, Kelsey, Karl, McClean, Michael, Vaughan, Thomas L, Lazarus, Philip, Purdue, Mark P, Hayes, Richard B, Chen, Chu, Schwartz, Stephen M, Shangina, Oxana, Koifman, Sergio, Ahrens, Wolfgang, Matos, Elena, Lagiou, Pagona, Lissowska, Jolanta, Szeszenia-Dabrowska, Neonila, Fernandez, Leticia, Menezes, Ana, Agudo, Antonio, Daudt, Alexander W, Richiardi, Lorenzo, Kjaerheim, Kristina, Mates, Dana, Betka, Jaroslav, Yu, Guo-Pei, Schantz, Stimson, Simonato, Lorenzo, Brenner, Hermann, Conway, David I, Macfarlane, Tatiana V, Thomson, Peter, Fabianova, Eleonora, Znaor, Ariana, Rudnai, Peter, Healy, Claire, Boffetta, Paolo, Chuang, Shu-Chun, Lee, Yuan-Chin Amy, Hashibe, Mia, and Boccia, Stefania
Subjects: Adult, Male, Alcohol Drinking, Epidemiology, Head and neck neoplasms, Interviews as Topic, Rare Diseases, Risk Factors, Clinical Research, Tobacco, Odds Ratio, Humans, Dental/Oral and Craniofacial Disease, Aged, Cancer, Tobacco Smoke and Health, Height, Incidence, Prevention, Smoking, Middle Aged, Overweight, Body Height, Logistic Models, Good Health and Well Being, Case-Control Studies, Public Health and Health Services, Educational Status, Female, Consortium
Abstract: Several epidemiological studies have shown a positive association between adult height and cancer incidence. The only study conducted among women on mouth and pharynx cancer risk, however, reported an inverse association. This study aims to investigate the association between height and the risk of head and neck cancer (HNC) within a large international consortium of HNC. We analyzed pooled individual-level data from 24 case-control studies participating in the International Head and Neck Cancer Epidemiology Consortium. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated separately for men and women for associations between height and HNC risk. Educational level, tobacco smoking, and alcohol consumption were included in all regression models. Stratified analyses by HNC subsites were performed. This project included 17,666 cases and 28,198 controls. We found an inverse association between height and HNC (adjusted OR per 10 cm height = 0.91, 95% CI 0.86-0.95 for men; adjusted OR = 0.86, 95% CI 0.79-0.93 for women). In men, the estimated OR did vary by educational level, smoking status, geographic area, and control source. No differences by subsites were detected. Adult height is inversely associated with HNC risk. As height can be considered a marker of childhood illness and low energy intake, the inverse association is consistent with prior studies showing that HNC occur more frequently among deprived individuals. Further studies designed to elucidate the mechanism of such association would be warranted.
Published: 2014

23. Diet and the risk of head and neck cancer: a pooled analysis in the INHANCE consortium

Author: Chuang, Shu-Chun, Jenab, Mazda, Heck, Julia E, Bosetti, Cristina, Talamini, Renato, Matsuo, Keitaro, Castellsague, Xavier, Franceschi, Silvia, Herrero, Rolando, Winn, Deborah M, La Vecchia, Carlo, Morgenstern, Hal, Zhang, Zuo-Feng, Levi, Fabio, Dal Maso, Luigino, Kelsey, Karl, McClean, Michael D, Vaughan, Thomas, Lazarus, Philip, Muscat, Joshua, Ramroth, Heribert, Chen, Chu, Schwartz, Stephen M, Eluf-Neto, Jose, Hayes, Richard B, Purdue, Mark, Boccia, Stefania, Cadoni, Gabriella, Zaridze, David, Koifman, Sergio, Curado, Maria Paula, Ahrens, Wolfgang, Benhamou, Simone, Matos, Elena, Lagiou, Pagona, Szeszenia-Dabrowska, Neonilla, Olshan, Andrew F, Fernandez, Leticia, Menezes, Ana, Agudo, Antonio, Daudt, Alexander W, Merletti, Franco, Macfarlane, Gary J, Kjaerheim, Kristina, Mates, Dana, Holcatova, Ivana, Schantz, Stimson, Yu, Guo-Pei, Simonato, Lorenzo, Brenner, Hermann, Mueller, Heiko, Conway, David I, Thomson, Peter, Fabianova, Eleonora, Znaor, Ariana, Rudnai, Peter, Healy, Claire M, Ferro, Gilles, Brennan, Paul, Boffetta, Paolo, and Hashibe, Mia
Subjects: Adult, Male, Red meat, Epidemiology, Prevention, Processed meat, Oncology and Carcinogenesis, Middle Aged, Diet, Head and Neck Neoplasms, Risk Factors, Clinical Research, Case-Control Studies, Fruit and vegetable, Public Health and Health Services, Humans, Female, Dental/Oral and Craniofacial Disease, Head and neck cancer, Aged, Cancer, Nutrition
Abstract: We investigated the association between diet and head and neck cancer (HNC) risk using data from the International Head and Neck Cancer Epidemiology (INHANCE) consortium. The INHANCE pooled data included 22 case-control studies with 14,520 cases and 22,737 controls. Center-specific quartiles among the controls were used for food groups, and frequencies per week were used for single food items. A dietary pattern score combining high fruit and vegetable intake and low red meat intake was created. Odds ratios (OR) and 95% confidence intervals (CI) for the dietary items on the risk of HNC were estimated with a two-stage random-effects logistic regression model. An inverse association was observed for higher-frequency intake of fruit (4th vs. 1st quartile OR = 0.52, 95% CI = 0.43-0.62, p (trend) < 0.01) and vegetables (OR = 0.66, 95% CI = 0.49-0.90, p (trend) = 0.01). Intake of red meat (OR = 1.40, 95% CI = 1.13-1.74, p (trend) = 0.13) and processed meat (OR = 1.37, 95% CI = 1.14-1.65, p (trend) < 0.01) was positively associated with HNC risk. Higher dietary pattern scores, reflecting high fruit/vegetable and low red meat intake, were associated with reduced HNC risk (per score increment OR = 0.90, 95% CI = 0.84-0.97).
Published: 2012

24. Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis

Author: Escala-Garcia, Maria, Canisius, Sander, Keeman, Renske, Beesley, Jonathan, Anton-Culver, Hoda, Arndt, Volker, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, D��rk, Thilo, Dunning, Alison M, Easton, Douglas F, Ekici, Arif B, Eliassen, A Heather, Fasching, Peter A, Flyger, Henrik, Gago-Dominguez, Manuela, Garc��a-Closas, Montserrat, Garc��a-S��enz, Jos�� A, Geisler, J��rgen, Giles, Graham G, Grip, Mervi, G��ndert, Melanie, Hahnen, Eric, Haiman, Christopher A, H��kansson, Niclas, Hall, Per, Hamann, Ute, Hartikainen, Jaana M, Heemskerk-Gerritsen, Bernadette A M, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Hunter, David J, Jacot, William, Jakubowska, Anna, John, Esther M, Jung, Audrey Y, Kaaks, Rudolf, Khusnutdinova, Elza, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Luben, Robert N, Lubi��ski, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Muranen, Taru A, Nevanlinna, Heli, Olshan, Andrew F, Olsson, H��kan, Park-Simon, Tjoung-Won, Patel, Alpa V, Peterlongo, Paolo, Pharoah, Paul D P, Punie, Kevin, Radice, Paolo, Rennert, Gad, Rennert, Hedy S, Romero, Atocha, Roylance, Rebecca, R��diger, Thomas, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schoemaker, Minouk J, Scott, Christopher, Southey, Melissa C, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Teras, Lauren R, Thomas, Emilie, Tomlinson, Ian, Troester, Melissa A, Vachon, Celine M, Wang, Qin, Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Michailidou, Kyriaki, Chenevix-Trench, Georgia, Bachelot, Thomas, and Schmidt, Marjanka K
Subjects: skin and connective tissue diseases, 3. Good health
Abstract: Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 �� 10-8 and 4.42 �� 10-8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations.

25. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women

Author: Adedokun, Babatunde, Du, Zhaohui, Gao, Guimin, Ahearn, Thomas U, Lunetta, Kathryn L, Zirpoli, Gary, Figueroa, Jonine, John, Esther M, Bernstein, Leslie, Zheng, Wei, Hu, Jennifer J, Ziegler, Regina G, Nyante, Sarah, Bandera, Elisa V, Ingles, Sue A, Press, Michael F, Deming-Halverson, Sandra L, Rodriguez-Gil, Jorge L, Yao, Song, Ogundiran, Temidayo O, Ojengbede, Oladosu, Blot, William, Troester, Melissa A, Nathanson, Katherine L, Hennis, Anselm, Nemesure, Barbara, Ambs, Stefan, Fiorica, Peter N, Sucheston-Campbell, Lara E, Bensen, Jeannette T, Kushi, Lawrence H, Torres-Mejia, Gabriela, Hu, Donglei, Fejerman, Laura, Bolla, Manjeet K, Dennis, Joe, Dunning, Alison M, Easton, Douglas F, Michailidou, Kyriaki, Pharoah, Paul D P, Wang, Qin, Sandler, Dale P, Taylor, Jack A, O'Brien, Katie M, Kitahara, Cari M, Falusi, Adeyinka G, Babalola, Chinedum, Yarney, Joel, Awuah, Baffour, Addai-Wiafe, Beatrice, Chanock, Stephen J, Olshan, Andrew F, Ambrosone, Christine B, Conti, David V, Ziv, Elad, Olopade, Olufunmilayo I, Garcia-Closas, Montserrat, Palmer, Julie R, Haiman, Christopher A, and Huo, Dezheng
Subjects: Quantitative Trait Loci, European Continental Ancestry Group, Breast Neoplasms, 16. Peace & justice, Polymorphism, Single Nucleotide, Introns, 3. Good health, 13. Climate action, Humans, Genetic Predisposition to Disease, Female, skin and connective tissue diseases, African Continental Ancestry Group, Genome-Wide Association Study
Abstract: Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P

26. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Author: Escala-Garcia, Maria, Abraham, Jean, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Ashworth, Alan, Auer, Paul L, Auvinen, Päivi, Beckmann, Matthias W, Beesley, Jonathan, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Blot, William, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brucker, Sara Y, Burwinkel, Barbara, Caldas, Carlos, Canzian, Federico, Chang-Claude, Jenny, Chanock, Stephen J, Chin, Suet-Feung, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dunn, Janet A, Dunning, Alison M, Dwek, Miriam, Earl, Helena M, Eccles, Diana M, Eliassen, A Heather, Ellberg, Carolina, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, George, Angela, Giles, Graham G, Goldgar, David E, González-Neira, Anna, Grip, Mervi, Guénel, Pascal, Guo, Qi, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Harrington, Patricia A, Hiller, Louise, Hooning, Maartje J, Hopper, John L, Howell, Anthony, Huang, Chiun-Sheng, Huang, Guanmengqian, Hunter, David J, Jakubowska, Anna, John, Esther M, Kaaks, Rudolf, Kapoor, Pooja Middha, Keeman, Renske, Kitahara, Cari M, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Lambrechts, Diether, Le Marchand, Loic, Lejbkowicz, Flavio, Lindblom, Annika, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Maurer, Tabea, Mavroudis, Dimitrios, Meindl, Alfons, Milne, Roger L, Mulligan, Anna Marie, Neuhausen, Susan L, Nevanlinna, Heli, Newman, William G, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Orr, Nick, Peterlongo, Paolo, Petridis, Christos, Prentice, Ross L, Presneau, Nadege, Punie, Kevin, Ramachandran, Dhanya, Rennert, Gad, Romero, Atocha, Sachchithananthan, Mythily, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schwentner, Lukas, Scott, Christopher, Simard, Jacques, Sohn, Christof, Southey, Melissa C, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William J, Teixeira, Manuel R, Terry, Mary Beth, Thorne, Heather, Tollenaar, Rob AEM, Tomlinson, Ian, Troester, Melissa A, Truong, Thérèse, Turnbull, Clare, Vachon, Celine M, Van Der Kolk, Lizet E, Wang, Qin, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R, Ziogas, Argyrios, Pharoah, Paul DP, Hall, Per, Wessels, Lodewyk FA, Chenevix-Trench, Georgia, Bader, Gary D, Dörk, Thilo, Easton, Douglas F, Canisius, Sander, and Schmidt, Marjanka K
Subjects: Genotype, Computational Biology, Genetic Variation, Apoptosis, Breast Neoplasms, Prognosis, GTP-Binding Protein alpha Subunits, 3. Good health, Germ Cells, Receptors, Estrogen, Circadian Clocks, GTP-Binding Protein alpha Subunits, Gq-G11, Humans, Female, Gene Regulatory Networks, Genome-Wide Association Study, Signal Transduction
Abstract: Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.

27. Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment

Author: Morra, Anna, Escala-Garcia, Maria, Beesley, Jonathan, Keeman, Renske, Canisius, Sander, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Auer, Paul L., Augustinsson, Annelie, Beane Freeman, Laura E., Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bojesen, Stig E., Bolla, Manjeet K., Brenner, Hermann, Brüning, Thomas, Buys, Saundra S., Caan, Bette, Campa, Daniele, Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Cheng, Ting-Yuan David, Clarke, Christine L., Colonna, Sarah V., Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Dennis, Joe, Dörk, Thilo, Dossus, Laure, Dunning, Alison M., Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Flyger, Henrik, Fritschi, Lin, Gago-Dominguez, Manuela, García-Sáenz, José A., Giles, Graham G., Grip, Mervi, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Hart, Steven N., Hartikainen, Jaana M., Hartmann, Arndt, He, Wei, Hooning, Maartje J., Hoppe, Reiner, Hopper, John L., Howell, Anthony, Hunter, David J., Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Jung, Audrey Y., Kaaks, Rudolf, Keupers, Machteld, Kitahara, Cari M., Koutros, Stella, Kraft, Peter, Kristensen, Vessela N., Kurian, Allison W., Lacey, James V., Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Linet, Martha, Luben, Robert N., Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, Michailidou, Kyriaki, Milne, Roger L., Mulligan, Anna Marie, Muranen, Taru A., Nevanlinna, Heli, Newman, William G., Nielsen, Sune F., Nordestgaard, Børge G., Olshan, Andrew F., Olsson, Håkan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa V., Peissel, Bernard, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Presneau, Nadege, Rack, Brigitte, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Roylance, Rebecca, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Schneeweiss, Andreas, Scott, Christopher, Shah, Mitul, Smichkoska, Snezhana, Southey, Melissa C., Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Teras, Lauren R., Terry, Mary Beth, Tollenaar, Rob A. E. M., Tomlinson, Ian, Troester, Melissa A., Truong, Thérèse, Vachon, Celine M., Wang, Qin, Hurson, Amber N., Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Brauch, Hiltrud, García-Closas, Montserrat, Pharoah, Paul D. P., Easton, Douglas F., Chenevix-Trench, Georgia, Schmidt, Marjanka K., Børresen-Dale, Anne-Lise, Sahlberg, Kristine K., Ottestad, Lars, Kåresen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebråten, Olav, Naume, Bjørn, Fosså, Alexander, Kiserud, Cecile E., Reinertsen, Kristin V., Helland, Åslaug, Riis, Margit, Geisler, Jürgen, Grenaker Alnæs, Grethe I., Clarke, Christine, Marsh, Deborah, Scott, Rodney, Baxter, Robert, Yip, Desmond, Carpenter, Jane, Davis, Alison, Pathmanathan, Nirmala, Simpson, Peter, Graham, J. Dinny, and Sachchithananthan, Mythily
Subjects: Tumor biology, Systemic treatment, Common germline genetic variants, Patient subgroups, 3. Good health, Research Article, Breast cancer-specific survival
Abstract: Funder: FP7 Ideas: European Research Council; doi: http://dx.doi.org/10.13039/100011199; Grant(s): HEALTH-F2-2009-223175, Background: Given the high heterogeneity among breast tumors, associations between common germline genetic variants and survival that may exist within specific subgroups could go undetected in an unstratified set of breast cancer patients. Methods: We performed genome-wide association analyses within 15 subgroups of breast cancer patients based on prognostic factors, including hormone receptors, tumor grade, age, and type of systemic treatment. Analyses were based on 91,686 female patients of European ancestry from the Breast Cancer Association Consortium, including 7531 breast cancer-specific deaths over a median follow-up of 8.1 years. Cox regression was used to assess associations of common germline variants with 15-year and 5-year breast cancer-specific survival. We assessed the probability of these associations being true positives via the Bayesian false discovery probability (BFDP < 0.15). Results: Evidence of associations with breast cancer-specific survival was observed in three patient subgroups, with variant rs5934618 in patients with grade 3 tumors (15-year-hazard ratio (HR) [95% confidence interval (CI)] 1.32 [1.20, 1.45], P = 1.4E−08, BFDP = 0.01, per G allele); variant rs4679741 in patients with ER-positive tumors treated with endocrine therapy (15-year-HR [95% CI] 1.18 [1.11, 1.26], P = 1.6E−07, BFDP = 0.09, per G allele); variants rs1106333 (15-year-HR [95% CI] 1.68 [1.39,2.03], P = 5.6E−08, BFDP = 0.12, per A allele) and rs78754389 (5-year-HR [95% CI] 1.79 [1.46,2.20], P = 1.7E−08, BFDP = 0.07, per A allele), in patients with ER-negative tumors treated with chemotherapy. Conclusions: We found evidence of four loci associated with breast cancer-specific survival within three patient subgroups. There was limited evidence for the existence of associations in other patient subgroups. However, the power for many subgroups is limited due to the low number of events. Even so, our results suggest that the impact of common germline genetic variants on breast cancer-specific survival might be limited.

28. Breast Cancer Polygenic Risk Score and Contralateral Breast Cancer Risk

Author: Kramer, Iris, Hooning, Maartje J, Mavaddat, Nasim, Hauptmann, Michael, Keeman, Renske, Steyerberg, Ewout W, Giardiello, Daniele, Antoniou, Antonis C, Pharoah, Paul DP, Canisius, Sander, Abu-Ful, Zumuruda, Andrulis, Irene L, Anton-Culver, Hoda, Aronson, Kristan J, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Bonanni, Bernardo, Brauch, Hiltrud, Bremer, Michael, Brucker, Sara Y, Burwinkel, Barbara, Castelao, Jose E, Chan, Tsun L, Chang-Claude, Jenny, Chanock, Stephen J, Chenevix-Trench, Georgia, Choi, Ji-Yeob, Clarke, Christine L, NBCS Collaborators, Collée, J Margriet, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Devilee, Peter, Dörk, Thilo, Dos-Santos-Silva, Isabel, Dunning, Alison M, Dwek, Miriam, Eccles, Diana M, Evans, D Gareth, Fasching, Peter A, Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Giles, Graham G, Goldgar, David E, González-Neira, Anna, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Hartman, Mikael, Heemskerk-Gerritsen, Bernadette AM, Hollestelle, Antoinette, Hopper, John L, Hou, Ming-Feng, Howell, Anthony, ABCTB Investigators, KConFab Investigators, Ito, Hidemi, Jakimovska, Milena, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jung, Audrey, Kang, Daehee, Kets, C Marleen, Khusnutdinova, Elza, Ko, Yon-Dschun, Kristensen, Vessela N, Kurian, Allison W, Kwong, Ava, Lambrechts, Diether, Le Marchand, Loic, Li, Jingmei, Lindblom, Annika, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Matsuo, Keitaro, Mavroudis, Dimitrios, Meindl, Alfons, Milne, Roger L, Mulligan, Anna Marie, Muranen, Taru A, Neuhausen, Susan L, Nevanlinna, Heli, Newman, William G, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Park-Simon, Tjoung-Won, Peto, Julian, Petridis, Christos, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Pylkäs, Katri, Radice, Paolo, Rennert, Gad, Romero, Atocha, Roylance, Rebecca, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schwentner, Lukas, Scott, Christopher, See, Mee-Hoong, Shah, Mitul, Shen, Chen-Yang, Shu, Xiao-Ou, Siesling, Sabine, Slager, Susan, Sohn, Christof, Southey, Melissa C, Spinelli, John J, Stone, Jennifer, Tapper, William J, Tengström, Maria, Teo, Soo Hwang, Terry, Mary Beth, Tollenaar, Rob AEM, Tomlinson, Ian, Troester, Melissa A, Vachon, Celine M, Van Ongeval, Chantal, Van Veen, Elke M, Winqvist, Robert, Wolk, Alicja, Zheng, Wei, Ziogas, Argyrios, Easton, Douglas F, Hall, Per, and Schmidt, Marjanka K
Subjects: Adult, Multifactorial Inheritance, Receptor, ErbB-2, Gene Expression, Breast Neoplasms, Risk Assessment, White People, Cohort Studies, Asian People, parasitic diseases, Humans, Genetic Predisposition to Disease, Aged, Proportional Hazards Models, Genome, Human, Estrogen Receptor alpha, Neoplasms, Second Primary, Middle Aged, Prognosis, Neoadjuvant Therapy, 3. Good health, polygenic risk score, contralateral breast cancer, epidemiology, Female, genetic, Receptors, Progesterone, Genome-Wide Association Study
Abstract: Previous research has shown that polygenic risk scores (PRSs) can be used to stratify women according to their risk of developing primary invasive breast cancer. This study aimed to evaluate the association between a recently validated PRS of 313 germline variants (PRS313) and contralateral breast cancer (CBC) risk. We included 56,068 women of European ancestry diagnosed with first invasive breast cancer from 1990 onward with follow-up from the Breast Cancer Association Consortium. Metachronous CBC risk (N = 1,027) according to the distribution of PRS313 was quantified using Cox regression analyses. We assessed PRS313 interaction with age at first diagnosis, family history, morphology, ER status, PR status, and HER2 status, and (neo)adjuvant therapy. In studies of Asian women, with limited follow-up, CBC risk associated with PRS313 was assessed using logistic regression for 340 women with CBC compared with 12,133 women with unilateral breast cancer. Higher PRS313 was associated with increased CBC risk: hazard ratio per standard deviation (SD) = 1.25 (95%CI = 1.18-1.33) for Europeans, and an OR per SD = 1.15 (95%CI = 1.02-1.29) for Asians. The absolute lifetime risks of CBC, accounting for death as competing risk, were 12.4% for European women at the 10th percentile and 20.5% at the 90th percentile of PRS313. We found no evidence of confounding by or interaction with individual characteristics, characteristics of the primary tumor, or treatment. The C-index for the PRS313 alone was 0.563 (95%CI = 0.547-0.586). In conclusion, PRS313 is an independent factor associated with CBC risk and can be incorporated into CBC risk prediction models to help improve stratification and optimize surveillance and treatment strategies.

29. Combined Associations of a Polygenic Risk Score and Classical Risk Factors With Breast Cancer Risk

Author: Kapoor, Pooja Middha, Mavaddat, Nasim, Choudhury, Parichoy Pal, Wilcox, Amber N, Lindström, Sara, Behrens, Sabine, Michailidou, Kyriaki, Dennis, Joe, Bolla, Manjeet K, Wang, Qin, Jung, Audrey, Abu-Ful, Zomoroda, Ahearn, Thomas, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Auer, Paul L, Freeman, Laura E Beane, Becher, Heiko, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Benitez, Javier, Bernstein, Leslie, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Cai, Qiuyin, Campa, Daniele, Canzian, Federico, Carracedo, Angel, Carter, Brian D, Castelao, Jose E, Chanock, Stephen J, Chatterjee, Nilanjan, Chenevix-Trench, Georgia, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Dai, James Y, Earp, H Shelton, Ekici, Arif B, Eliassen, A Heather, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M, Gaudet, Mia M, Giles, Graham G, González-Neira, Anna, Guénel, Pascal, Haeberle, Lothar, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hatse, Sigrid, Heyworth, Jane, Holleczek, Bernd, Hoover, Robert N, Hopper, John L, Howell, Anthony, Hunter, David J, ABCTB Investigators, KConFab/AOCS Investigators, John, Esther M, Jones, Michael E, Kaaks, Rudolf, Keeman, Renske, Kitahara, Cari M, Ko, Yon-Dschun, Koutros, Stella, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lee, Eunjung, Lejbkowicz, Flavio, Linet, Martha, Lissowska, Jolanta, Llaneza, Ana, MacInnis, Robert J, Martinez, Maria Elena, Maurer, Tabea, McLean, Catriona, Neuhausen, Susan L, Newman, William G, Norman, Aaron, O'Brien, Katie M, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Orr, Nick, Perou, Charles M, Pita, Guillermo, Polley, Eric C, Prentice, Ross L, Rennert, Gad, Rennert, Hedy S, Ruddy, Kathryn J, Sandler, Dale P, Saunders, Christobel, Schoemaker, Minouk J, Schöttker, Ben, Schumacher, Fredrick, Scott, Christopher, Scott, Rodney J, Shu, Xiao-Ou, Smeets, Ann, Southey, Melissa C, Spinelli, John J, Stone, Jennifer, Swerdlow, Anthony J, Tamimi, Rulla M, Taylor, Jack A, Troester, Melissa A, Vachon, Celine M, Van Veen, Elke M, Wang, Xiaoliang, Weinberg, Clarice R, Weltens, Caroline, Willett, Walter, Winham, Stacey J, Wolk, Alicja, Yang, Xiaohong R, Zheng, Wei, Ziogas, Argyrios, Dunning, Alison M, Pharoah, Paul DP, Schmidt, Marjanka K, Kraft, Peter, Easton, Douglas F, Milne, Roger L, García-Closas, Montserrat, and Chang-Claude, Jenny
Subjects: Aged, 80 and over, Breast Neoplasms, Middle Aged, Polymorphism, Single Nucleotide, White People, 3. Good health, Body Mass Index, Logistic Models, Receptors, Estrogen, Risk Factors, Case-Control Studies, Humans, Female, Genetic Predisposition to Disease, 10. No inequality, Medical History Taking, Aged
Abstract: We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.

30. Two truncating variants in FANCC and breast cancer risk

Author: Dörk, Thilo, Peterlongo, Paolo, Mannermaa, Arto, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Ahearn, Thomas, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Augustinsson, Annelie, Freeman, Laura E. Beane, Beckmann, Matthias W., Beeghly-Fadiel, Alicia, Behrens, Sabine, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Stig E., Brauch, Hiltrud, Brenner, Hermann, Burwinkel, Barbara, Canzian, Federico, Chan, Tsun L., Chang-Claude, Jenny, Chanock, Stephen J., Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L., Couch, Fergus J., Czene, Kamila, Daly, Mary B., Dos-Santos-Silva, Isabel, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M., García-Closas, Montserrat, García-Sáenz, José A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Goldgar, David E., Guénel, Pascal, Haeberle, Lothar, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Hartman, Mikael, Hauke, Jan, Hein, Alexander, Hillemanns, Peter, Hogervorst, Frans B. L., Hooning, Maartje J., Hopper, John L., Howell, Tony, Huo, Dezheng, Ito, Hidemi, Iwasaki, Motoki, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Kapoor, Pooja Middha, Khusnutdinova, Elza, Kim, Sung-Won, Kitahara, Cari M., Koutros, Stella, Kraft, Peter, Kristensen, Vessela N., Kwong, Ava, Lambrechts, Diether, Marchand, Loic Le, Li, Jingmei, Lindström, Sara, Linet, Martha, Lo, Wing-Yee, Long, Jirong, Lophatananon, Artitaya, Lubiński, Jan, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Elena, Matsuo, Keitaro, Mavroudis, Dimitris, Meindl, Alfons, Menon, Usha, Milne, Roger L., Mohd Taib, Nur Aishah, Muir, Kenneth, Mulligan, Anna Marie, Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Offit, Kenneth, Olopade, Olufunmilayo I., Olshan, Andrew F., Olson, Janet E., Olsson, Håkan, Park, Sue K., Park-Simon, Tjoung-Won, Peto, Julian, Plaseska-Karanfilska, Dijana, Pohl-Rescigno, Esther, Presneau, Nadege, Rack, Brigitte, Radice, Paolo, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Romero, Atocha, Ruebner, Matthias, Saloustros, Emmanouil, Schmidt, Marjanka K., Schmutzler, Rita K., Schneider, Michael O., Schoemaker, Minouk J., Scott, Christopher, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Slager, Susan, Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Teo, Soo H., Terry, Mary Beth, Toland, Amanda E., Tollenaar, Rob A. E. M., Torres, Diana, Torres-Mejía, Gabriela, Troester, Melissa A., Truong, Thérèse, Tsugane, Shoichiro, Untch, Michael, Vachon, Celine M., Ouweland, Ans M. W. Van Den, Veen, Elke M. Van, Vijai, Joseph, Wendt, Camilla, Wolk, Alicja, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, Argyrios, Ziv, Elad, Dunning, Alison M., Pharoah, Paul D. P., Schindler, Detlev, Devilee, Peter, Easton, Douglas F., Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Børresen-Dale, Anne-Lise, Grenaker Alnæs, Grethe I., Sahlberg, Kristine K., Ottestad, Lars, Kåresen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebråten, Olav, Naume, Bjørn, Fosså, Alexander, Kiserud, Cecile E., Reinertsen, Kristin V., Helland, Åslaug, Riis, Margit, and Geisler, Jürgen
Subjects: 45, article, 45/47, 692/499, 3. Good health, 692/4028
Abstract: Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

31. CYP3A7*1C allele: linking premenopausal oestrone and progesterone levels with risk of hormone receptor-positive breast cancers

Author: Johnson, Nichola, Maguire, Sarah, Morra, Anna, Kapoor, Pooja Middha, Tomczyk, Katarzyna, Jones, Michael E, Schoemaker, Minouk J, Gilham, Clare, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Ahearn, Thomas U, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Baynes, Caroline, Freeman, Laura E Beane, Beckmann, Matthias W, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Boeckx, Bram, Bogdanova, Natalia V, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Burwinkel, Barbara, Campa, Daniele, Canzian, Federico, Castelao, Jose E, Chanock, Stephen J, Chenevix-Trench, Georgia, Clarke, Christine L, NBCS Collaborators, Conroy, Don M, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Dörk, Thilo, Eliassen, A Heather, Engel, Christoph, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Floris, Giuseppe, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Closas, Montserrat, Gaudet, Mia M, Giles, Graham G, Goldberg, Mark S, González-Neira, Anna, AOCS Group, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A, Hart, Steven N, Hooning, Maartje J, Hopper, John L, Howell, Anthony, Hunter, David J, ABCTB Investigators, KConFab Investigators, Jager, Agnes, Jakubowska, Anna, John, Esther M, Kaaks, Rudolf, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M, Kosma, Veli-Matti, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Linet, Martha, Lubiński, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John WM, Mavroudis, Dimitrios, Mayes, Rebecca, Meindl, Alfons, Milne, Roger L, Neuhausen, Susan L, Nevanlinna, Heli, Newman, William G, Nielsen, Sune F, Nordestgaard, Børge G, Obi, Nadia, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Orban, Ester, Park-Simon, Tjoung-Won, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Pylkäs, Katri, Rennert, Gad, Rennert, Hedy S, Ruddy, Kathryn J, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schmutzler, Rita K, Scott, Christopher, Shu, Xiao-Ou, Simard, Jacques, Smichkoska, Snezhana, Sohn, Christof, Southey, Melissa C, Spinelli, John J, Stone, Jennifer, Tamimi, Rulla M, Taylor, Jack A, Tollenaar, Rob AEM, Tomlinson, Ian, Troester, Melissa A, Truong, Thérèse, Vachon, Celine M, Van Veen, Elke M, Wang, Sophia S, Weinberg, Clarice R, Wendt, Camilla, Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Zheng, Wei, Ziogas, Argyrios, Dunning, Alison M, Pharoah, Paul DP, Easton, Douglas F, Howie, A Forbes, Peto, Julian, Dos-Santos-Silva, Isabel, Swerdlow, Anthony J, Chang-Claude, Jenny, Schmidt, Marjanka K, Orr, Nick, and Fletcher, Olivia
Subjects: Estrone, Breast Neoplasms, Polymorphism, Single Nucleotide, 3. Good health, Premenopause, Receptors, Estrogen, Case-Control Studies, Cytochrome P-450 CYP3A, Humans, Pregnanediol, Female, Receptors, Progesterone, Alleles, Progesterone, Genome-Wide Association Study
Abstract: BACKGROUND: Epidemiological studies provide strong evidence for a role of endogenous sex hormones in the aetiology of breast cancer. The aim of this analysis was to identify genetic variants that are associated with urinary sex-hormone levels and breast cancer risk. METHODS: We carried out a genome-wide association study of urinary oestrone-3-glucuronide and pregnanediol-3-glucuronide levels in 560 premenopausal women, with additional analysis of progesterone levels in 298 premenopausal women. To test for the association with breast cancer risk, we carried out follow-up genotyping in 90,916 cases and 89,893 controls from the Breast Cancer Association Consortium. All women were of European ancestry. RESULTS: For pregnanediol-3-glucuronide, there were no genome-wide significant associations; for oestrone-3-glucuronide, we identified a single peak mapping to the CYP3A locus, annotated by rs45446698. The minor rs45446698-C allele was associated with lower oestrone-3-glucuronide (-49.2%, 95% CI -56.1% to -41.1%, P = 3.1 × 10-18); in follow-up analyses, rs45446698-C was also associated with lower progesterone (-26.7%, 95% CI -39.4% to -11.6%, P = 0.001) and reduced risk of oestrogen and progesterone receptor-positive breast cancer (OR = 0.86, 95% CI 0.82-0.91, P = 6.9 × 10-8). CONCLUSIONS: The CYP3A7*1C allele is associated with reduced risk of hormone receptor-positive breast cancer possibly mediated via an effect on the metabolism of endogenous sex hormones in premenopausal women.

32. Is family history of breast cancer a marker of susceptibility to exposures in the incidence of de Novo adult acute leukemia?

Author: Rauscher, Garth H., Sandler, Dale P., Charles Poole, James Pankow, David Shore, Bloomfield, Clara D., and Olshan, Andrew F.

33. Feasibility of neonatal dried blood spot retrieval amid evolving state policies (2009-2010): A Children's Oncology Group study

Author: Linabery, Amy M., Slater, Megan E., Logan Spector, Olshan, Andrew F., Stork, Susan K., Roesler, Michelle A., Reaman, Gregory H., and Ross, Julie A.
Subjects: Parents, Adolescent, Lymphoma, State Health Plans, Medical Oncology, behavioral disciplines and activities, Article, Translocation, Genetic, Young Adult, Neonatal Screening, Humans, Genetic Predisposition to Disease, Child, Blood Specimen Collection, Informed Consent, Leukemia, Health Policy, Infant, Newborn, Infant, United States, nervous system diseases, surgical procedures, operative, nervous system, Child, Preschool, Feasibility Studies, therapeutics
Abstract: Dried blood spots (DBS) are collected uniformly from US newborns to test for metabolic and other disorders. Because evidence exists for prenatal origins of some diseases, DBS may provide unique prenatal exposure records. Some states retain residual DBS and permit their use in aetiological studies. The primary study aim was to assess the feasibility of obtaining residual DBS from state newborn screening programmes for paediatric and adolescent cancer patients nationwide with parental/subject consent/assent. Families of leukaemia and lymphoma patients aged ≤21 years diagnosed from 1998 to 2007 at randomly selected Children's Oncology Group institutions across the US were questioned (n = 947). Parents/guardians and patients aged ≥18 years were asked to release DBS to investigators in spring 2009. DBS were then requested from states. Overall, 299 families (32%) released DBS. Consenting/assenting patients were born in 39 US states and 46 DBS were obtained from five states; 124 DBS were unobtainable because patients were born prior to dates of state retention. State policies are rapidly evolving and there is ongoing discussion regarding DBS storage and secondary research uses. Currently, population-based DBS studies can be conducted in a limited number of states; fortunately, many have large populations to provide reasonably sized paediatric subject groups.

34. Interaction between known risk factors for head and neck cancer and socioeconomic status: the Carolina Head and Neck Cancer Study

Author: Stanford-Moore, Gaelen, Bradshaw, Patrick T, Weissler, Mark C, Zevallos, Jose P, Brennan, Paul, Anantharaman, Devasena, Abedi-Ardekani, Behnoush, and Olshan, Andrew F
Subjects: Adult, Male, Alcohol Drinking, Epidemiology, Oral Health, Young Adult, Risk Factors, Tobacco, North Carolina, Odds Ratio, Humans, Head and neck cancer, Aged, Aged, 80 and over, Squamous Cell Carcinoma of Head and Neck, Smoking, Middle Aged, 3. Good health, Case–control studies, Logistic Models, Social Class, Head and Neck Neoplasms, Case-Control Studies, Socioeconomic status, Carcinoma, Squamous Cell, Income, Female, Alcohol
Abstract: Prior studies of squamous cell carcinoma of the head and neck (SCCHN) have explored the effect of socioeconomic status (SES) as an independent risk factor; however, none have investigated the interaction of known risk factors with SES. We examined this using the North Carolina Head and Neck Cancer Epidemiology Study, a population-based case-control study. Incident cases of SCCHN from North Carolina between 2002 and 2006 (n = 1,153) were identified and age, sex, and race-matched controls (n = 1,267) were selected from driver license records. SES measures included household income, educational attainment, and health insurance. Logistic regression was used to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI). Current smoking was more strongly associated with SCCHN among those households making < $20,000/year [OR 5.11 (3.61-6.61)] compared to household incomes > $50,000/year [OR 2.47 (1.69-3.25); p interaction < 0.001]. Current drinking was more strongly associated with SCCHN in household incomes < $20,000 [OR 2.91 (2.05-3.78)] compared to > $50,000/year [1.28 (0.97-1.58); p interaction < 0.001]. Current drinkers with less than high school education or income < $20,000 had nearly threefold odds of never-drinkers in the same SES category [OR 2.91 (2.05-3.78); 2.09 (1.39-2.78), respectively]. Our results suggest that the relationship of smoking and alcohol use may be stronger among those of lower SES.

35. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Author: Escala-Garcia, Maria, Abraham, Jean, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Ashworth, Alan, Auer, Paul L, Auvinen, Päivi, Beckmann, Matthias W, Beesley, Jonathan, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Blot, William, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brucker, Sara Y, Burwinkel, Barbara, Caldas, Carlos, Canzian, Federico, Chang-Claude, Jenny, Chanock, Stephen J, Chin, Suet-Feung, Clarke, Christine L, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dunn, Janet A, Dunning, Alison M, Dwek, Miriam, Earl, Helena M, Eccles, Diana M, Eliassen, A Heather, Ellberg, Carolina, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, George, Angela, Giles, Graham G, Goldgar, David E, González-Neira, Anna, Grip, Mervi, Guénel, Pascal, Guo, Qi, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Harrington, Patricia A, Hiller, Louise, Hooning, Maartje J, Hopper, John L, Howell, Anthony, Huang, Chiun-Sheng, Huang, Guanmengqian, Hunter, David J, Jakubowska, Anna, John, Esther M, Kaaks, Rudolf, Kapoor, Pooja Middha, Keeman, Renske, Kitahara, Cari M, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Lambrechts, Diether, Le Marchand, Loic, Lejbkowicz, Flavio, Lindblom, Annika, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Maurer, Tabea, Mavroudis, Dimitrios, Meindl, Alfons, Milne, Roger L, Mulligan, Anna Marie, Neuhausen, Susan L, Nevanlinna, Heli, Newman, William G, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Orr, Nick, Peterlongo, Paolo, Petridis, Christos, Prentice, Ross L, Presneau, Nadege, Punie, Kevin, Ramachandran, Dhanya, Rennert, Gad, Romero, Atocha, Sachchithananthan, Mythily, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schwentner, Lukas, Scott, Christopher, Simard, Jacques, Sohn, Christof, Southey, Melissa C, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William J, Teixeira, Manuel R, Terry, Mary Beth, Thorne, Heather, Tollenaar, Rob A E M, Tomlinson, Ian, Troester, Melissa A, Truong, Thérèse, Turnbull, Clare, Vachon, Celine M, Van Der Kolk, Lizet E, Wang, Qin, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R, Ziogas, Argyrios, Pharoah, Paul D P, Hall, Per, Wessels, Lodewyk F A, Chenevix-Trench, Georgia, Bader, Gary D, Dörk, Thilo, Easton, Douglas F, Canisius, Sander, and Schmidt, Marjanka K
Subjects: 3. Good health
Abstract: Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.

36. Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis

Author: Escala-Garcia, Maria, Canisius, Sander, Keeman, Renske, Beesley, Jonathan, Anton-Culver, Hoda, Arndt, Volker, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bermisheva, Marina, Bojesen, Stig E., Bolla, Manjeet K., Brenner, Hermann, Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Couch, Fergus J., Czene, Kamila, Daly, Mary B., Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dunning, Alison M., Easton, Douglas F., Ekici, Arif B., Eliassen, A. Heather, Fasching, Peter A., Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A., Geisler, Jürgen, Giles, Graham G., Grip, Mervi, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Hartikainen, Jaana M., Heemskerk-Gerritsen, Bernadette A. M., Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L., Hunter, David J., Jacot, William, Jakubowska, Anna, John, Esther M., Jung, Audrey Y., Kaaks, Rudolf, Khusnutdinova, Elza, Koppert, Linetta B., Kraft, Peter, Kristensen, Vessela N., Kurian, Allison W., Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Luben, Robert N., Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Muranen, Taru A., Nevanlinna, Heli, Olshan, Andrew F., Olsson, Håkan, Park-Simon, Tjoung-Won, Patel, Alpa V., Peterlongo, Paolo, Pharoah, Paul D. P., Punie, Kevin, Radice, Paolo, Rennert, Gad, Rennert, Hedy S., Romero, Atocha, Roylance, Rebecca, Rüdiger, Thomas, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Schoemaker, Minouk J., Scott, Christopher, Southey, Melissa C., Surowy, Harald, Swerdlow, Anthony J., Tamimi, Rulla M., Teras, Lauren R., Thomas, Emilie, Tomlinson, Ian, Troester, Melissa A., Vachon, Celine M., Wang, Qin, Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Michailidou, Kyriaki, Chenevix-Trench, Georgia, Bachelot, Thomas, and Schmidt, Marjanka K.
Subjects: 631/67/322, 631/67/68, article, 631/67/1347, skin and connective tissue diseases, 3. Good health
Abstract: Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 × 10−8 and 4.42 × 10−8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations.

37. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women

Author: Adedokun, Babatunde, Du, Zhaohui, Gao, Guimin, Ahearn, Thomas U., Lunetta, Kathryn L., Zirpoli, Gary, Figueroa, Jonine, John, Esther M., Bernstein, Leslie, Zheng, Wei, Hu, Jennifer J., Ziegler, Regina G., Nyante, Sarah, Bandera, Elisa V., Ingles, Sue A., Press, Michael F., Deming-Halverson, Sandra L., Rodriguez-Gil, Jorge L., Yao, Song, Ogundiran, Temidayo O., Ojengbede, Oladosu, Blot, William, Troester, Melissa A., Nathanson, Katherine L., Hennis, Anselm, Nemesure, Barbara, Ambs, Stefan, Fiorica, Peter N., Sucheston-Campbell, Lara E., Bensen, Jeannette T., Kushi, Lawrence H., Torres-Mejia, Gabriela, Hu, Donglei, Fejerman, Laura, Bolla, Manjeet K., Dennis, Joe, Dunning, Alison M., Easton, Douglas F., Michailidou, Kyriaki, Pharoah, Paul D. P., Wang, Qin, Sandler, Dale P., Taylor, Jack A., O’Brien, Katie M., Kitahara, Cari M., Falusi, Adeyinka G., Babalola, Chinedum, Yarney, Joel, Awuah, Baffour, Addai-Wiafe, Beatrice, Chanock, Stephen J., Olshan, Andrew F., Ambrosone, Christine B., Conti, David V., Ziv, Elad, Olopade, Olufunmilayo I., Garcia-Closas, Montserrat, Palmer, Julie R., Haiman, Christopher A., and Huo, Dezheng
Subjects: 45/43, article, 631/67/1347, 3. Good health, 692/4028/67/2324
Abstract: Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.

38. Additional file 2 of Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment

Author: Morra, Anna, Escala-Garcia, Maria, Beesley, Jonathan, Keeman, Renske, Canisius, Sander, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Auer, Paul L., Augustinsson, Annelie, Beane Freeman, Laura E., Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bojesen, Stig E., Bolla, Manjeet K., Brenner, Hermann, Brüning, Thomas, Buys, Saundra S., Caan, Bette, Campa, Daniele, Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Cheng, Ting-Yuan David, Clarke, Christine L., Colonna, Sarah V., Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Dennis, Joe, Dörk, Thilo, Dossus, Laure, Dunning, Alison M., Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Flyger, Henrik, Fritschi, Lin, Gago-Dominguez, Manuela, García-Sáenz, José A., Giles, Graham G., Grip, Mervi, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Hart, Steven N., Hartikainen, Jaana M., Hartmann, Arndt, He, Wei, Hooning, Maartje J., Hoppe, Reiner, Hopper, John L., Howell, Anthony, Hunter, David J., Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Jung, Audrey Y., Kaaks, Rudolf, Keupers, Machteld, Kitahara, Cari M., Koutros, Stella, Kraft, Peter, Kristensen, Vessela N., Kurian, Allison W., Lacey, James V., Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Linet, Martha, Luben, Robert N., Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, Michailidou, Kyriaki, Milne, Roger L., Mulligan, Anna Marie, Muranen, Taru A., Nevanlinna, Heli, Newman, William G., Nielsen, Sune F., Nordestgaard, Børge G., Olshan, Andrew F., Olsson, Håkan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa V., Peissel, Bernard, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Presneau, Nadege, Rack, Brigitte, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Roylance, Rebecca, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Schneeweiss, Andreas, Scott, Christopher, Shah, Mitul, Smichkoska, Snezhana, Southey, Melissa C., Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Teras, Lauren R., Terry, Mary Beth, Tollenaar, Rob A. E. M., Tomlinson, Ian, Troester, Melissa A., Truong, Thérèse, Vachon, Celine M., Wang, Qin, Hurson, Amber N., Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Brauch, Hiltrud, García-Closas, Montserrat, Pharoah, Paul D. P., Easton, Douglas F., Chenevix-Trench, Georgia, and Schmidt, Marjanka K.
Subjects: 3. Good health
Abstract: Additional file 2: Supplementary Methods, Supplementary Table S5, Supplementary Table S6, Supplementary Table S7, Supplementary Figure S1, Supplementary Figure S2, Supplementary Figure S3, Supplementary Figure S4, Supplementary Figure S5, Supplementary Figure S6, Supplementary Figure S7, Supplementary Figure S8, Supplementary Figure S9, Supplementary Figure S10, Supplementary Figure S11, Supplementary Figure S12. The Supplementary methods section includes details about: multiple imputation of missing data; power calculations. Supplementary Table S5. Shows an overview of number of breast cancer patients, breast cancer deaths and follow-up information by subgroup and endpoint. Supplementary Table S6. Shows a list of imputed variables with corresponding percentage of missing values, imputation method and processing. Supplementary Table S7. Shows an overview of the GWAS significant associations (P 5E-08) variants from the 15-year and 5-year genome-wide breast cancer-specific survival analyses. Supplementary Figure S7 shows the unadjusted association of variant rs5934618 with 15-year breast cancer-specific survival by tumor grade and in all breast cancer patients. Supplementary Figure S8. Shows the functional annotation and position of variants rs5934618, rs4830644, rs3810742, rs4830642, and rs72611496 relative to TBL1X. Supplementary Figure S9. Shows Kaplan-Meier distant metastasis-free survival plots (based on KMPlotter data) for high versus low expression level of gene TBL1X by tumor grade. Supplementary Figure S10. Shows the association of genetic variants with TBL1X expression, based on GTEx v8 data on samples of normal breast tissue from 396 individuals (male and female). Supplementary Figure S11. Shows a Kaplan-Meier distant metastasis-free survival plot for high versus low expression level of gene GRIP2, restricted to patients with an ER- tumor who received chemotherapy (based on KMPlotter data). Supplementary Figure S12. Shows a Kaplan-Meier distant metastasis-free survival plot for high versus low expression level of gene ARAP2, restricted to patients with an ER- tumor who received chemotherapy (based on KMPlotter data).

39. CYP3A7*1C allele: linking premenopausal oestrone and progesterone levels with risk of hormone receptor-positive breast cancers

Author: Johnson, Nichola, Maguire, Sarah, Morra, Anna, Kapoor, Pooja Middha, Tomczyk, Katarzyna, Jones, Michael E., Schoemaker, Minouk J., Gilham, Clare, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Aronson, Kristan J., Augustinsson, Annelie, Baynes, Caroline, Freeman, Laura E. Beane, Beckmann, Matthias W., Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Boeckx, Bram, Bogdanova, Natalia V., Bojesen, Stig E., Brauch, Hiltrud, Brenner, Hermann, Burwinkel, Barbara, Campa, Daniele, Canzian, Federico, Castelao, Jose E., Chanock, Stephen J., Chenevix-Trench, Georgia, Clarke, Christine L., Conroy, Don M., Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Dörk, Thilo, Eliassen, A. Heather, Engel, Christoph, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Floris, Giuseppe, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M., García-Closas, Montserrat, Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., González-Neira, Anna, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A., Hart, Steven N., Hooning, Maartje J., Hopper, John L., Howell, Anthony, Hunter, David J., Jager, Agnes, Jakubowska, Anna, John, Esther M., Kaaks, Rudolf, Keeman, Renske, Khusnutdinova, Elza, Kitahara, Cari M., Kosma, Veli-Matti, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N., Kurian, Allison W., Lambrechts, Diether, Le Marchand, Loic, Linet, Martha, Lubiński, Jan, Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Mavroudis, Dimitrios, Mayes, Rebecca, Meindl, Alfons, Milne, Roger L., Neuhausen, Susan L., Nevanlinna, Heli, Newman, William G., Nielsen, Sune F., Nordestgaard, Børge G., Obi, Nadia, Olshan, Andrew F., Olson, Janet E., Olsson, Håkan, Orban, Ester, Park-Simon, Tjoung-Won, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Pylkäs, Katri, Rennert, Gad, Rennert, Hedy S., Ruddy, Kathryn J., Saloustros, Emmanouil, Sandler, Dale P., Sawyer, Elinor J., Schmutzler, Rita K., Scott, Christopher, Shu, Xiao-Ou, Simard, Jacques, Smichkoska, Snezhana, Sohn, Christof, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Tamimi, Rulla M., Taylor, Jack A., Tollenaar, Rob A. E. M., Tomlinson, Ian, Troester, Melissa A., Truong, Thérèse, Vachon, Celine M., Van Veen, Elke M., Wang, Sophia S., Weinberg, Clarice R., Wendt, Camilla, Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Zheng, Wei, Ziogas, Argyrios, Dunning, Alison M., Pharoah, Paul D. P., Easton, Douglas F., Howie, A. Forbes, Peto, Julian, Dos-Santos-Silva, Isabel, Swerdlow, Anthony J., Chang-Claude, Jenny, Schmidt, Marjanka K., Orr, Nick, Fletcher, Olivia, Børresen-Dale, Anne-Lise, Alnæs, Grethe I. Grenaker, Sahlberg, Kristine K., Ottestad, Lars, Kåresen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebråten, Olav, Naume, Bjørn, Fosså, Alexander, Kiserud, Cecile E., Reinertsen, Kristin V., Helland, Åslaug, Riis, Margit, Geisler, Jürgen, Bowtell, David D. L., DeFazio, Anna, Webb, Penelope M., Clarke, Christine, Marsh, Deborah, Scott, Rodney, Baxter, Robert, Yip, Desmond, Carpenter, Jane, Davis, Alison, Pathmanathan, Nirmala, Simpson, Peter, Graham, Dinny, Sachchithananthan, Mythily, Amor, David, Andrews, Lesley, Antill, Yoland, Balleine, Rosemary, Beesley, Jonathan, Bennett, Ian, Bogwitz, Michael, Botes, Leon, Brennan, Meagan, Brown, Melissa, Buckley, Michael, Burke, Jo, Butow, Phyllis, Caldon, Liz, Campbell, Ian, Chauhan, Deepa, Chauhan, Manisha, Christian, Alice, Cohen, Paul, Colley, Alison, Crook, Ashley, Cui, James, Cummings, Margaret, Dawson, Sarah-Jane, Delatycki, Martin, Dickson, Rebecca, Dixon, Joanne, Edkins, Ted, 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, Hayward, Nick, Hopper, John, Hoskins, Cass, Hunt, Clare, James, Paul, Jenkins, Mark, Kidd, Alexa, Kirk, Judy, Koehler, Jessica, Kollias, James, Lakhani, Sunil, Lawrence, Mitchell, Lindeman, Geoff, Lipton, Lara, Lobb, Liz, Mann, Graham, McLachlan, Sue Anne, Meiser, Bettina, Milne, Roger, Nightingale, Sophie, O’Connell, Shona, O’Sullivan, Sarah, Ortega, David Gallego, Pachter, Nick, Patterson, Briony, Pearn, Amy, Phillips, Kelly, Pieper, Ellen, Rickard, Edwina, Robinson, Bridget, Saleh, Mona, Salisbury, Elizabeth, Saunders, Christobel, Saunus, Jodi, Scott, Clare, Sexton, Adrienne, Shelling, Andrew, Southey, Melissa, Spurdle, Amanda, Taylor, Jessica, Taylor, Renea, Thorne, Heather, Trainer, Alison, Tucker, Kathy, Visvader, Jane, Walker, Logan, Williams, Rachael, Winship, Ingrid, and Young, Mary Ann
Subjects: 631/67/68, article, 631/67/2324, 631/67/1347, 3. Good health
Abstract: Funder: Breast Cancer Now (BCN); doi: https://doi.org/10.13039/100009794, Funder: Cancer Research UK (CRUK); doi: https://doi.org/10.13039/501100000289, Funder: RCUK | Medical Research Council (MRC); doi: https://doi.org/10.13039/501100000265, Funder: U.S. Department of Health & Human Services | National Institutes of Health (NIH), Funder: Wellcome Trust (Wellcome); doi: https://doi.org/10.13039/100004440, Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): HEALTH-F2-2009-223175, HEALTH-F2-2009-223175, Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762, Funder: Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada); doi: https://doi.org/10.13039/501100000024, Funder: Quebec Breast cancer Foundation Genome Quebec, Funder: U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM); doi: https://doi.org/10.13039/100000092, Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)), Funder: European Union’s Horizon 2020, Funder: Deutsche Krebshilfe (German Cancer Aid); doi: https://doi.org/10.13039/501100005972, Funder: BCAST - European Union’s Horizon 2020, Funder: Breast Cancer Now; doi: https://doi.org/10.13039/501100007913, Background: Epidemiological studies provide strong evidence for a role of endogenous sex hormones in the aetiology of breast cancer. The aim of this analysis was to identify genetic variants that are associated with urinary sex-hormone levels and breast cancer risk. Methods: We carried out a genome-wide association study of urinary oestrone-3-glucuronide and pregnanediol-3-glucuronide levels in 560 premenopausal women, with additional analysis of progesterone levels in 298 premenopausal women. To test for the association with breast cancer risk, we carried out follow-up genotyping in 90,916 cases and 89,893 controls from the Breast Cancer Association Consortium. All women were of European ancestry. Results: For pregnanediol-3-glucuronide, there were no genome-wide significant associations; for oestrone-3-glucuronide, we identified a single peak mapping to the CYP3A locus, annotated by rs45446698. The minor rs45446698-C allele was associated with lower oestrone-3-glucuronide (−49.2%, 95% CI −56.1% to −41.1%, P = 3.1 × 10–18); in follow-up analyses, rs45446698-C was also associated with lower progesterone (−26.7%, 95% CI −39.4% to −11.6%, P = 0.001) and reduced risk of oestrogen and progesterone receptor-positive breast cancer (OR = 0.86, 95% CI 0.82–0.91, P = 6.9 × 10–8). Conclusions: The CYP3A7*1C allele is associated with reduced risk of hormone receptor-positive breast cancer possibly mediated via an effect on the metabolism of endogenous sex hormones in premenopausal women.

40. A network analysis to identify mediators of germline-driven differences in breast cancer prognosis

Author: Escala-Garcia, Maria, Abraham, Jean, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Ashworth, Alan, Auer, Paul L., Auvinen, Päivi, Beckmann, Matthias W., Beesley, Jonathan, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Blot, William, Bogdanova, Natalia V., Bojesen, Stig E., Bolla, Manjeet K., Børresen-Dale, Anne-Lise, Brauch, Hiltrud, Brenner, Hermann, Brucker, Sara Y., Burwinkel, Barbara, Caldas, Carlos, Canzian, Federico, Chang-Claude, Jenny, Chanock, Stephen J., Chin, Suet-Feung, Clarke, Christine L., Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Dennis, Joe, Devilee, Peter, Dunn, Janet A., Dunning, Alison M., Dwek, Miriam, Earl, Helena M., Eccles, Diana M., Eliassen, A. Heather, Ellberg, Carolina, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Gago-Dominguez, Manuela, Gapstur, Susan M., García-Closas, Montserrat, García-Sáenz, José A., Gaudet, Mia M., George, Angela, Giles, Graham G., Goldgar, David E., González-Neira, Anna, Grip, Mervi, Guénel, Pascal, Guo, Qi, Haiman, Christopher A., Håkansson, Niclas, Hamann, Ute, Harrington, Patricia A., Hiller, Louise, Hooning, Maartje J., Hopper, John L., Howell, Anthony, Huang, Chiun-Sheng, Huang, Guanmengqian, Hunter, David J., Jakubowska, Anna, John, Esther M., Kaaks, Rudolf, Kapoor, Pooja Middha, Keeman, Renske, Kitahara, Cari M., Koppert, Linetta B., Kraft, Peter, Kristensen, Vessela N., Lambrechts, Diether, Le Marchand, Loic, Lejbkowicz, Flavio, Lindblom, Annika, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Maurer, Tabea, Mavroudis, Dimitrios, Meindl, Alfons, Milne, Roger L., Mulligan, Anna Marie, Neuhausen, Susan L., Nevanlinna, Heli, Newman, William G., Olshan, Andrew F., Olson, Janet E., Olsson, Håkan, Orr, Nick, Peterlongo, Paolo, Petridis, Christos, Prentice, Ross L., Presneau, Nadege, Punie, Kevin, Ramachandran, Dhanya, Rennert, Gad, Romero, Atocha, Sachchithananthan, Mythily, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Schwentner, Lukas, Scott, Christopher, Simard, Jacques, Sohn, Christof, Southey, Melissa C., Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Teixeira, Manuel R., Terry, Mary Beth, Thorne, Heather, Tollenaar, Rob A. E. M., Tomlinson, Ian, Troester, Melissa A., Truong, Thérèse, Turnbull, Clare, Vachon, Celine M., Van Der Kolk, Lizet E., Wang, Qin, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Ziogas, Argyrios, Pharoah, Paul D. P., Hall, Per, Wessels, Lodewyk F. A., Chenevix-Trench, Georgia, Bader, Gary D., Dörk, Thilo, Easton, Douglas F., Canisius, Sander, and Schmidt, Marjanka K.
Subjects: 45, 631/208/205/2138, 45/43, article, 692/4028/67/1347, 631/114, 3. Good health
Abstract: Identifying the underlying genetic drivers of the heritability of breast cancer prognosis remains elusive. We adapt a network-based approach to handle underpowered complex datasets to provide new insights into the potential function of germline variants in breast cancer prognosis. This network-based analysis studies ~7.3 million variants in 84,457 breast cancer patients in relation to breast cancer survival and confirms the results on 12,381 independent patients. Aggregating the prognostic effects of genetic variants across multiple genes, we identify four gene modules associated with survival in estrogen receptor (ER)-negative and one in ER-positive disease. The modules show biological enrichment for cancer-related processes such as G-alpha signaling, circadian clock, angiogenesis, and Rho-GTPases in apoptosis.

41. The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Author: Figlioli, Gisella, Bogliolo, Massimo, Catucci, Irene, Caleca, Laura, Lasheras, Sandra Viz, Pujol, Roser, Kiiski, Johanna I., Muranen, Taru A., Barnes, Daniel R., Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K., Leslie, Goska, Aalfs, Cora M., Adank, Muriel A., Adlard, Julian, Agata, Simona, Cadoo, Karen, Agnarsson, Bjarni A., Ahearn, Thomas, Aittomäki, Kristiina, Ambrosone, Christine B., Andrews, Lesley, Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J., Arun, Banu K., Asseryanis, Ella, Auber, Bernd, Auvinen, Päivi, Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B., Barrowdale, Daniel, Barwell, Julian, Beane Freeman, Laura E., Beauparlant, Charles Joly, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Berger, Raanan, Bermisheva, Marina, Blanco, Amie M., Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Anders, Bojesen, Stig E., Bonanni, Bernardo, Borg, Ake, Brady, Angela F., Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Caldés, Trinidad, Caliebe, Almuth, Caligo, Maria A., Campa, Daniele, Campbell, Ian G., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Claes, Kathleen B. M., Clarke, Christine L., Collavoli, Anita, Conner, Thomas A., Cox, David G., Cybulski, Cezary, Czene, Kamila, Daly, Mary B., De La Hoya, Miguel, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Dite, Gillian S., Ditsch, Nina, Domchek, Susan M., Dorfling, Cecilia M., Dos-Santos-Silva, Isabel, Durda, Katarzyna, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Foulkes, William D., Friebel, Tara M., Friedman, Eitan, Gabrielson, Marike, Gaddam, Pragna, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M., Garber, Judy, García-Closas, Montserrat, García-Sáenz, José A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Guénel, Pascal, Gutierrez-Barrera, Angelica M., Haeberle, Lothar, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A., Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hopper, John L., Hosgood, H. Dean, Howell, Anthony, Hu, Chunling, Hulick, Peter J., Hunter, David J., Imyanitov, Evgeny N., Isaacs, Claudine, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Karlan, Beth Y., Khusnutdinova, Elza, Kitahara, Cari M., Konstantopoulou, Irene, Koutros, Stella, Kraft, Peter, Lambrechts, Diether, Lazaro, Conxi, Le Marchand, Loic, Lester, Jenny, Lesueur, Fabienne, Lilyquist, Jenna, Loud, Jennifer T., Lu, Karen H., Luben, Robert N., Lubinski, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Maurer, Tabea, Mavroudis, Dimitrios, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Montagna, Marco, Nathanson, Katherine L., Neuhausen, Susan L., Newman, William G., Nguyen-Dumont, Tu, Nielsen, Finn Cilius, Nielsen, Sarah, Nikitina-Zake, Liene, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I., Olshan, Andrew F., Olson, Janet E., Olsson, Håkan, Osorio, Ana, Ottini, Laura, Peissel, Bernard, Peixoto, Ana, Peto, Julian, Plaseska-Karanfilska, Dijana, Pocza, Timea, Presneau, Nadege, Pujana, Miquel Angel, Punie, Kevin, Rack, Brigitte, Rantala, Johanna, Rashid, Muhammad U., Rau-Murthy, Rohini, Rennert, Gad, Lejbkowicz, Flavio, Rhenius, Valerie, Romero, Atocha, Rookus, Matti A., Ross, Eric A., Rossing, Maria, Rudaitis, Vilius, Ruebner, Matthias, Saloustros, Emmanouil, Sanden, Kristin, Santamariña, Marta, Scheuner, Maren T., Schmutzler, Rita K., Schneider, Michael, Scott, Christopher, Senter, Leigha, Shah, Mitul, Sharma, Priyanka, Shu, Xiao-Ou, Simard, Jacques, Singer, Christian F., Sohn, Christof, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Steele, Linda, Stoppa-Lyonnet, Dominique, Tapper, William J., Teixeira, Manuel R., Terry, Mary Beth, Thomassen, Mads, Thompson, Jennifer, Thull, Darcy L., Tischkowitz, Marc, Tollenaar, Rob A.E.M., Torres, Diana, Troester, Melissa A., Truong, Thérèse, Tung, Nadine, Untch, Michael, Vachon, Celine M., Van Rensburg, Elizabeth J., Van Veen, Elke M., Vega, Ana, Viel, Alessandra, Wappenschmidt, Barbara, Weitzel, Jeffrey N., Wendt, Camilla, Wieme, Greet, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Ziogas, Argyrios, Zorn, Kristin K., Dunning, Alison M., Lush, Michael, Wang, Qin, McGuffog, Lesley, Parsons, Michael T., Pharoah, Paul D. P., Fostira, Florentia, Toland, Amanda E., Andrulis, Irene L., Ramus, Susan J., Swerdlow, Anthony J., Greene, Mark H., Chung, Wendy K., Milne, Roger L., Chenevix-Trench, Georgia, Dörk, Thilo, Schmidt, Marjanka K., Easton, Douglas F., Radice, Paolo, Hahnen, Eric, Antoniou, Antonis C., Couch, Fergus J., Nevanlinna, Heli, Surrallés, Jordi, Peterlongo, Paolo, Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Belotti, Muriel, Bertrand, Ophélie, Birot, Anne-Marie, Buecher, Bruno, Caputo, Sandrine, Dupré, Anaïs, Fourme, Emmanuelle, Gauthier-Villars, Marion, Golmard, Lisa, Le Mentec, Marine, Moncoutier, Virginie, De Pauw, Antoine, Saule, Claire, Boutry-Kryza, Nadia, Calender, Alain, Giraud, Sophie, Léone, Mélanie, Bressac-De-Paillerets, Brigitte, Caron, Olivier, Guillaud-Bataille, Marine, Bignon, Yves-Jean, Uhrhammer, Nancy, Bonadona, Valérie, Lasset, Christine, Berthet, Pascaline, Castera, Laurent, Vaur, Dominique, Bourdon, Violaine, Noguès, Catherine, Noguchi, Tetsuro, Popovici, Cornel, Remenieras, Audrey, Sobol, Hagay, Coupier, Isabelle, Pujol, Pascal, Adenis, Claude, Dumont, Aurélie, Révillion, Françoise, Muller, Danièle, Barouk-Simonet, Emmanuelle, Bonnet, Françoise, Bubien, Virginie, Longy, Michel, Sevenet, Nicolas, Gladieff, Laurence, Guimbaud, Rosine, Feillel, Viviane, Toulas, Christine, Dreyfus, Hélène, Leroux, Christine Dominique, Peysselon, Magalie, Rebischung, Christine, Legrand, Clémentine, Baurand, Amandine, Bertolone, Geoffrey, Coron, Fanny, Faivre, Laurence, Jacquot, Caroline, Lizard, Sarab, Kientz, Caroline, Lebrun, Marine, Prieur, Fabienne, Fert-Ferrer, Sandra, Mari, Véronique, Vénat-Bouvet, Laurence, Bézieau, Stéphane, Delnatte, Capucine, Mortemousque, Isabelle, Colas, Chrystelle, Coulet, Florence, Soubrier, Florent, Warcoin, Mathilde, Bronner, Myriam, Sokolowska, Johanna, Collonge-Rame, Marie-Agnès, Damette, Alexandre, Gesta, Paul, Lallaoui, Hakima, Chiesa, Jean, Molina-Gomes, Denise, Ingster, Olivier, Manouvrier-Hanu, Sylvie, Lejeune, Sophie, Aghmesheh, Morteza, Greening, Sian, Amor, David, Gattas, Mike, Botes, Leon, Buckley, Michael, Friedlander, Michael, Koehler, Jessica, Meiser, Bettina, Saleh, Mona, Salisbury, Elizabeth, Trainer, Alison, Tucker, Kathy, Antill, Yoland, Dobrovic, Alexander, Fellows, Andrew, Fox, Stephen, Harris, Marion, Nightingale, Sophie, Phillips, Kelly, Sambrook, Joe, Thorne, Heather, Armitage, Shane, Arnold, Leanne, Kefford, Rick, Kirk, Judy, Rickard, Edwina, Bastick, Patti, Beesley, Jonathan, Hayward, Nick, Spurdle, Amanda, Walker, Logan, Beilby, John, Saunders, Christobel, Bennett, Ian, Blackburn, Anneke, Bogwitz, Michael, Gaff, Clara, Lindeman, Geoff, Pachter, Nick, Scott, Clare, Sexton, Adrienne, Visvader, Jane, Taylor, Jessica, Winship, Ingrid, Brennan, Meagan, Brown, Melissa, French, Juliet, Edwards, Stacey, Burgess, Matthew, Burke, Jo, Patterson, Briony, Butow, Phyllis, Culling, Bronwyn, Caldon, Liz, Callen, David, Chauhan, Deepa, Eisenbruch, Maurice, Heiniger, Louise, Chauhan, Manisha, Christian, Alice, Dixon, Joanne, Kidd, Alexa, Cohen, Paul, Colley, Alison, Fenton, Georgina, Crook, Ashley, Dickson, Rebecca, Field, Michael, Cui, James, Cummings, Margaret, Dawson, Sarah-Jane, DeFazio, Anna, Delatycki, Martin, Dudding, Tracy, Edkins, Ted, Farshid, Gelareh, Flanagan, James, Fong, Peter, Forrest, Laura, Gallego-Ortega, David, George, Peter, Gill, Grantley, Kollias, James, Haan, Eric, Hart, Stewart, Jenkins, Mark, Hunt, Clare, Lakhani, Sunil, Lipton, Lara, Lobb, Liz, Mann, Graham, McLachlan, Sue Anne, O’Connell, Shona, O’Sullivan, Sarah, Pieper, Ellen, Robinson, Bridget, Saunus, Jodi, Scott, Elizabeth, Shelling, Andrew, Williams, Rachael, and Young, Mary Ann
Subjects: 692/4028/67/68, 631/67/68, article, nutritional and metabolic diseases, 631/208/68, skin and connective tissue diseases, 3. Good health
Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.

42. Germline variants and breast cancer survival in patients with distant metastases at primary breast cancer diagnosis

Author: Escala-Garcia, Maria, Canisius, Sander, Keeman, Renske, Beesley, Jonathan, Anton-Culver, Hoda, Arndt, Volker, Augustinsson, Annelie, Becher, Heiko, Beckmann, Matthias W, Behrens, Sabine, Bermisheva, Marina, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Dennis, Joe, Devilee, Peter, Dörk, Thilo, Dunning, Alison M, Easton, Douglas F, Ekici, Arif B, Eliassen, A Heather, Fasching, Peter A, Flyger, Henrik, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Geisler, Jürgen, Giles, Graham G, Grip, Mervi, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hartikainen, Jaana M, Heemskerk-Gerritsen, Bernadette AM, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Hunter, David J, Jacot, William, Jakubowska, Anna, John, Esther M, Jung, Audrey Y, Kaaks, Rudolf, Khusnutdinova, Elza, Koppert, Linetta B, Kraft, Peter, Kristensen, Vessela N, Kurian, Allison W, Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Luben, Robert N, Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Mavroudis, Dimitrios, Muranen, Taru A, Nevanlinna, Heli, Olshan, Andrew F, Olsson, Håkan, Park-Simon, Tjoung-Won, Patel, Alpa V, Peterlongo, Paolo, Pharoah, Paul DP, Punie, Kevin, Radice, Paolo, Rennert, Gad, Rennert, Hedy S, Romero, Atocha, Roylance, Rebecca, Rüdiger, Thomas, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J, Schmutzler, Rita K, Schoemaker, Minouk J, Scott, Christopher, Southey, Melissa C, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Teras, Lauren R, Thomas, Emilie, Tomlinson, Ian, Troester, Melissa A, Vachon, Celine M, Wang, Qin, Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, KConFab/AOCS Investigators, Michailidou, Kyriaki, Chenevix-Trench, Georgia, Bachelot, Thomas, and Schmidt, Marjanka K
Subjects: Germ Cells, Cancer Survivors, Biomarkers, Tumor, Genetic Variation, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease, Kaplan-Meier Estimate, skin and connective tissue diseases, Polymorphism, Single Nucleotide, Germ-Line Mutation, 3. Good health
Abstract: Breast cancer metastasis accounts for most of the deaths from breast cancer. Identification of germline variants associated with survival in aggressive types of breast cancer may inform understanding of breast cancer progression and assist treatment. In this analysis, we studied the associations between germline variants and breast cancer survival for patients with distant metastases at primary breast cancer diagnosis. We used data from the Breast Cancer Association Consortium (BCAC) including 1062 women of European ancestry with metastatic breast cancer, 606 of whom died of breast cancer. We identified two germline variants on chromosome 1, rs138569520 and rs146023652, significantly associated with breast cancer-specific survival (P = 3.19 × 10-8 and 4.42 × 10-8). In silico analysis suggested a potential regulatory effect of the variants on the nearby target genes SDE2 and H3F3A. However, the variants showed no evidence of association in a smaller replication dataset. The validation dataset was obtained from the SNPs to Risk of Metastasis (StoRM) study and included 293 patients with metastatic primary breast cancer at diagnosis. Ultimately, larger replication studies are needed to confirm the identified associations.

43. Additional file 2 of Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment

Author: Morra, Anna, Escala-Garcia, Maria, Beesley, Jonathan, Keeman, Renske, Canisius, Sander, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Auer, Paul L., Augustinsson, Annelie, Beane Freeman, Laura E., Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bojesen, Stig E., Bolla, Manjeet K., Brenner, Hermann, Brüning, Thomas, Buys, Saundra S., Caan, Bette, Campa, Daniele, Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Cheng, Ting-Yuan David, Clarke, Christine L., Colonna, Sarah V., Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Dennis, Joe, Dörk, Thilo, Dossus, Laure, Dunning, Alison M., Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Flyger, Henrik, Fritschi, Lin, Gago-Dominguez, Manuela, García-Sáenz, José A., Giles, Graham G., Grip, Mervi, Guénel, Pascal, Gündert, Melanie, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Hart, Steven N., Hartikainen, Jaana M., Hartmann, Arndt, He, Wei, Hooning, Maartje J., Hoppe, Reiner, Hopper, John L., Howell, Anthony, Hunter, David J., Jager, Agnes, Jakubowska, Anna, Janni, Wolfgang, John, Esther M., Jung, Audrey Y., Kaaks, Rudolf, Keupers, Machteld, Kitahara, Cari M., Koutros, Stella, Kraft, Peter, Kristensen, Vessela N., Kurian, Allison W., Lacey, James V., Lambrechts, Diether, Le Marchand, Loic, Lindblom, Annika, Linet, Martha, Luben, Robert N., Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Margolin, Sara, Martens, John W. M., Martinez, Maria Elena, Mavroudis, Dimitrios, Michailidou, Kyriaki, Milne, Roger L., Mulligan, Anna Marie, Muranen, Taru A., Nevanlinna, Heli, Newman, William G., Nielsen, Sune F., Nordestgaard, Børge G., Olshan, Andrew F., Olsson, Håkan, Orr, Nick, Park-Simon, Tjoung-Won, Patel, Alpa V., Peissel, Bernard, Peterlongo, Paolo, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Presneau, Nadege, Rack, Brigitte, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Roylance, Rebecca, Ruebner, Matthias, Saloustros, Emmanouil, Sawyer, Elinor J., Schmutzler, Rita K., Schneeweiss, Andreas, Scott, Christopher, Shah, Mitul, Smichkoska, Snezhana, Southey, Melissa C., Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J., Tamimi, Rulla M., Tapper, William J., Teras, Lauren R., Terry, Mary Beth, Tollenaar, Rob A. E. M., Tomlinson, Ian, Troester, Melissa A., Truong, Thérèse, Vachon, Celine M., Wang, Qin, Hurson, Amber N., Winqvist, Robert, Wolk, Alicja, Ziogas, Argyrios, Brauch, Hiltrud, García-Closas, Montserrat, Pharoah, Paul D. P., Easton, Douglas F., Chenevix-Trench, Georgia, and Schmidt, Marjanka K.
Subjects: 3. Good health
Abstract: Additional file 2: Supplementary Methods, Supplementary Table S5, Supplementary Table S6, Supplementary Table S7, Supplementary Figure S1, Supplementary Figure S2, Supplementary Figure S3, Supplementary Figure S4, Supplementary Figure S5, Supplementary Figure S6, Supplementary Figure S7, Supplementary Figure S8, Supplementary Figure S9, Supplementary Figure S10, Supplementary Figure S11, Supplementary Figure S12. The Supplementary methods section includes details about: multiple imputation of missing data; power calculations. Supplementary Table S5. Shows an overview of number of breast cancer patients, breast cancer deaths and follow-up information by subgroup and endpoint. Supplementary Table S6. Shows a list of imputed variables with corresponding percentage of missing values, imputation method and processing. Supplementary Table S7. Shows an overview of the GWAS significant associations (P 5E-08) variants from the 15-year and 5-year genome-wide breast cancer-specific survival analyses. Supplementary Figure S7 shows the unadjusted association of variant rs5934618 with 15-year breast cancer-specific survival by tumor grade and in all breast cancer patients. Supplementary Figure S8. Shows the functional annotation and position of variants rs5934618, rs4830644, rs3810742, rs4830642, and rs72611496 relative to TBL1X. Supplementary Figure S9. Shows Kaplan-Meier distant metastasis-free survival plots (based on KMPlotter data) for high versus low expression level of gene TBL1X by tumor grade. Supplementary Figure S10. Shows the association of genetic variants with TBL1X expression, based on GTEx v8 data on samples of normal breast tissue from 396 individuals (male and female). Supplementary Figure S11. Shows a Kaplan-Meier distant metastasis-free survival plot for high versus low expression level of gene GRIP2, restricted to patients with an ER- tumor who received chemotherapy (based on KMPlotter data). Supplementary Figure S12. Shows a Kaplan-Meier distant metastasis-free survival plot for high versus low expression level of gene ARAP2, restricted to patients with an ER- tumor who received chemotherapy (based on KMPlotter data).

44. Two truncating variants in FANCC and breast cancer risk

Author: Dörk, Thilo, Peterlongo, Paolo, Mannermaa, Arto, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, Ahearn, Thomas, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Augustinsson, Annelie, Freeman, Laura E Beane, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Behrens, Sabine, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Burwinkel, Barbara, Canzian, Federico, Chan, Tsun L, Chang-Claude, Jenny, Chanock, Stephen J, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L, Couch, Fergus J, Czene, Kamila, Daly, Mary B, Dos-Santos-Silva, Isabel, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, Giles, Graham G, Goldberg, Mark S, Goldgar, David E, Guénel, Pascal, Haeberle, Lothar, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hartman, Mikael, Hauke, Jan, Hein, Alexander, Hillemanns, Peter, Hogervorst, Frans BL, Hooning, Maartje J, Hopper, John L, Howell, Tony, Huo, Dezheng, Ito, Hidemi, Iwasaki, Motoki, Jakubowska, Anna, Janni, Wolfgang, John, Esther M, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Kapoor, Pooja Middha, Khusnutdinova, Elza, Kim, Sung-Won, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Kwong, Ava, Lambrechts, Diether, Marchand, Loic Le, Li, Jingmei, Lindström, Sara, Linet, Martha, Lo, Wing-Yee, Long, Jirong, Lophatananon, Artitaya, Lubiński, Jan, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Elena, Matsuo, Keitaro, Mavroudis, Dimitris, Meindl, Alfons, Menon, Usha, Milne, Roger L, Mohd Taib, Nur Aishah, Muir, Kenneth, Mulligan, Anna Marie, Neuhausen, Susan L, Nevanlinna, Heli, Neven, Patrick, Newman, William G, Offit, Kenneth, Olopade, Olufunmilayo I, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Park, Sue K, Park-Simon, Tjoung-Won, Peto, Julian, Plaseska-Karanfilska, Dijana, Pohl-Rescigno, Esther, Presneau, Nadege, Rack, Brigitte, Radice, Paolo, Rashid, Muhammad U, Rennert, Gad, Rennert, Hedy S, Romero, Atocha, Ruebner, Matthias, Saloustros, Emmanouil, Schmidt, Marjanka K, Schmutzler, Rita K, Schneider, Michael O, Schoemaker, Minouk J, Scott, Christopher, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Slager, Susan, Smichkoska, Snezhana, Southey, Melissa C, Spinelli, John J, Stone, Jennifer, Surowy, Harald, Swerdlow, Anthony J, Tamimi, Rulla M, Tapper, William J, Teo, Soo H, Terry, Mary Beth, Toland, Amanda E, Tollenaar, Rob AEM, Torres, Diana, Torres-Mejía, Gabriela, Troester, Melissa A, Truong, Thérèse, Tsugane, Shoichiro, Untch, Michael, Vachon, Celine M, Ouweland, Ans MW Van Den, Veen, Elke M Van, Vijai, Joseph, Wendt, Camilla, Wolk, Alicja, Yu, Jyh-Cherng, Zheng, Wei, Ziogas, Argyrios, Ziv, Elad, ABCTB Investigators, NBCS Collaborators, Dunning, Alison M, Pharoah, Paul DP, Schindler, Detlev, Devilee, Peter, and Easton, Douglas F
Subjects: BRCA2 Protein, Fanconi Anemia, BRCA1 Protein, Case-Control Studies, Fanconi Anemia Complementation Group C Protein, Genetic Variation, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease, 3. Good health, Sequence Deletion
Abstract: Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44-1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

45. Shared heritability and functional enrichment across six solid cancers

Author: Jiang, Xia, Finucane, Hilary K, Schumacher, Fredrick R, Schmit, Stephanie L, Tyrer, Jonathan P, Han, Younghun, Michailidou, Kyriaki, Lesseur, Corina, Kuchenbaecker, Karoline B, Dennis, Joe, Conti, David V, Casey, Graham, Gaudet, Mia M, Huyghe, Jeroen R, Albanes, Demetrius, Aldrich, Melinda C, Andrew, Angeline S, Andrulis, Irene L, Anton-Culver, Hoda, Antoniou, Antonis C, Antonenkova, Natalia N, Arnold, Susanne M, Aronson, Kristan J, Arun, Banu K, Bandera, Elisa V, Barkardottir, Rosa B, Barnes, Daniel R, Batra, Jyotsna, Beckmann, Matthias W, Benitez, Javier, Benlloch, Sara, Berchuck, Andrew, Berndt, Sonja I, Bickeböller, Heike, Bien, Stephanie A, Blomqvist, Carl, Boccia, Stefania, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Brauch, Hiltrud, Brenner, Hermann, Brenton, James D, Brook, Mark N, Brunet, Joan, Brunnström, Hans, Buchanan, Daniel D, Burwinkel, Barbara, Butzow, Ralf, Cadoni, Gabriella, Caldés, Trinidad, Caligo, Maria A, Campbell, Ian, Campbell, Peter T, Cancel-Tassin, Géraldine, Cannon-Albright, Lisa, Campa, Daniele, Caporaso, Neil, Carvalho, André L, Chan, Andrew T, Chang-Claude, Jenny, Chanock, Stephen J, Chen, Chu, Christiani, David C, Claes, Kathleen BM, Claessens, Frank, Clements, Judith, Collée, J Margriet, Correa, Marcia Cruz, Couch, Fergus J, Cox, Angela, Cunningham, Julie M, Cybulski, Cezary, Czene, Kamila, Daly, Mary B, DeFazio, Anna, Devilee, Peter, Diez, Orland, Gago-Dominguez, Manuela, Donovan, Jenny L, Dörk, Thilo, Duell, Eric J, Dunning, Alison M, Dwek, Miriam, Eccles, Diana M, Edlund, Christopher K, Edwards, Digna R Velez, Ellberg, Carolina, Evans, D Gareth, Fasching, Peter A, Ferris, Robert L, Liloglou, Triantafillos, Figueiredo, Jane C, Fletcher, Olivia, Fortner, Renée T, Fostira, Florentia, Franceschi, Silvia, Friedman, Eitan, Gallinger, Steven J, Ganz, Patricia A, Garber, Judy, García-Sáenz, José A, Gayther, Simon A, Giles, Graham G, Godwin, Andrew K, Goldberg, Mark S, Goldgar, David E, Goode, Ellen L, Goodman, Marc T, Goodman, Gary, Grankvist, Kjell, Greene, Mark H, Gronberg, Henrik, Gronwald, Jacek, Guénel, Pascal, Håkansson, Niclas, Hall, Per, Hamann, Ute, Hamdy, Freddie C, Hamilton, Robert J, Hampe, Jochen, Haugen, Aage, Heitz, Florian, Herrero, Rolando, Hillemanns, Peter, Hoffmeister, Michael, Høgdall, Estrid, Hong, Yun-Chul, Hopper, John L, Houlston, Richard, Hulick, Peter J, Hunter, David J, Huntsman, David G, Idos, Gregory, Imyanitov, Evgeny N, Ingles, Sue Ann, Isaacs, Claudine, Jakubowska, Anna, James, Paul, Jenkins, Mark A, Johansson, Mattias, Johansson, Mikael, John, Esther M, Joshi, Amit D, Kaneva, Radka, Karlan, Beth Y, Kelemen, Linda E, Kühl, Tabea, Khaw, Kay-Tee, Khusnutdinova, Elza, Kibel, Adam S, Kiemeney, Lambertus A, Kim, Jeri, Kjaer, Susanne K, Knight, Julia A, Kogevinas, Manolis, Kote-Jarai, Zsofia, Koutros, Stella, Kristensen, Vessela N, Kupryjanczyk, Jolanta, Lacko, Martin, Lam, Stephan, Lambrechts, Diether, Landi, Maria Teresa, Lazarus, Philip, Le, Nhu D, Lee, Eunjung, Lejbkowicz, Flavio, Lenz, Heinz-Josef, Leslie, Goska, Lessel, Davor, Lester, Jenny, Levine, Douglas A, Li, Li, Li, Christopher I, Lindblom, Annika, Lindor, Noralane M, Liu, Geoffrey, Loupakis, Fotios, Lubiński, Jan, Maehle, Lovise, Maier, Christiane, Mannermaa, Arto, Marchand, Loic Le, Margolin, Sara, May, Taymaa, McGuffog, Lesley, Meindl, Alfons, Middha, Pooja, Miller, Austin, Milne, Roger L, MacInnis, Robert J, Modugno, Francesmary, Montagna, Marco, Moreno, Victor, Moysich, Kirsten B, Mucci, Lorelei, Muir, Kenneth, Mulligan, Anna Marie, Nathanson, Katherine L, Neal, David E, Ness, Andrew R, Neuhausen, Susan L, Nevanlinna, Heli, Newcomb, Polly A, Newcomb, Lisa F, Nielsen, Finn Cilius, Nikitina-Zake, Liene, Nordestgaard, Børge G, Nussbaum, Robert L, Offit, Kenneth, Olah, Edith, Olama, Ali Amin Al, Olopade, Olufunmilayo I, Olshan, Andrew F, Olsson, Håkan, Osorio, Ana, Pandha, Hardev, Park, Jong Y, Pashayan, Nora, Parsons, Michael T, Pejovic, Tanja, Penney, Kathryn L, Peters, Wilbert HM, Phelan, Catherine M, Phipps, Amanda I, Plaseska-Karanfilska, Dijana, Pring, Miranda, Prokofyeva, Darya, Radice, Paolo, Stefansson, Kari, Ramus, Susan J, Raskin, Leon, Rennert, Gad, Rennert, Hedy S, Van Rensburg, Elizabeth J, Riggan, Marjorie J, Risch, Harvey A, Risch, Angela, Roobol, Monique J, Rosenstein, Barry S, Rossing, Mary Anne, De Ruyck, Kim, Saloustros, Emmanouil, Sandler, Dale P, Sawyer, Elinor J, Schabath, Matthew B, Schleutker, Johanna, Schmidt, Marjanka K, Setiawan, V Wendy, Shen, Hongbing, Siegel, Erin M, Sieh, Weiva, Singer, Christian F, Slattery, Martha L, Sorensen, Karina Dalsgaard, Southey, Melissa C, Spurdle, Amanda B, Stanford, Janet L, Stevens, Victoria L, Stintzing, Sebastian, Stone, Jennifer, Sundfeldt, Karin, Sutphen, Rebecca, Swerdlow, Anthony J, Tajara, Eloiza H, Tangen, Catherine M, Tardon, Adonina, Taylor, Jack A, Teare, M Dawn, Teixeira, Manuel R, Terry, Mary Beth, Terry, Kathryn L, Thibodeau, Stephen N, Thomassen, Mads, Bjørge, Line, Tischkowitz, Marc, Toland, Amanda E, Torres, Diana, Townsend, Paul A, Travis, Ruth C, Tung, Nadine, Tworoger, Shelley S, Ulrich, Cornelia M, Usmani, Nawaid, Vachon, Celine M, Van Nieuwenhuysen, Els, Vega, Ana, Aguado-Barrera, Miguel Elías, Wang, Qin, Webb, Penelope M, Weinberg, Clarice R, Weinstein, Stephanie, Weissler, Mark C, Weitzel, Jeffrey N, West, Catharine ML, White, Emily, Whittemore, Alice S, Wichmann, H-Erich, Wiklund, Fredrik, Winqvist, Robert, Wolk, Alicja, Woll, Penella, Woods, Michael, Wu, Anna H, Wu, Xifeng, Yannoukakos, Drakoulis, Zheng, Wei, Zienolddiny, Shanbeh, Ziogas, Argyrios, Zorn, Kristin K, Lane, Jacqueline M, Saxena, Richa, Thomas, Duncan, Hung, Rayjean J, Diergaarde, Brenda, McKay, James, Peters, Ulrike, Hsu, Li, García-Closas, Montserrat, Eeles, Rosalind A, Chenevix-Trench, Georgia, Brennan, Paul J, Haiman, Christopher A, Simard, Jacques, Easton, Douglas F, Gruber, Stephen B, Pharoah, Paul DP, Price, Alkes L, Pasaniuc, Bogdan, Amos, Christopher I, Kraft, Peter, and Lindström, Sara
Subjects: Male, Ovarian Neoplasms, Lung Neoplasms, Mental Disorders, Smoking, Inheritance Patterns, Prostatic Neoplasms, Breast Neoplasms, Polymorphism, Single Nucleotide, White People, 3. Good health, Neoplasm Proteins, Phenotype, Head and Neck Neoplasms, Case-Control Studies, Humans, Female, Genetic Predisposition to Disease, Colorectal Neoplasms, Genome-Wide Association Study
Abstract: Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, here we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (rg = 0.57, p = 4.6 × 10-8), breast and ovarian cancer (rg = 0.24, p = 7 × 10-5), breast and lung cancer (rg = 0.18, p =1.5 × 10-6) and breast and colorectal cancer (rg = 0.15, p = 1.1 × 10-4). We also found that multiple cancers are genetically correlated with non-cancer traits including smoking, psychiatric diseases and metabolic characteristics. Functional enrichment analysis revealed a significant excess contribution of conserved and regulatory regions to cancer heritability. Our comprehensive analysis of cross-cancer heritability suggests that solid tumors arising across tissues share in part a common germline genetic basis.

46. The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Author: Figlioli, Gisella, Bogliolo, Massimo, Catucci, Irene, Caleca, Laura, Lasheras, Sandra Viz, Pujol, Roser, Kiiski, Johanna I, Muranen, Taru A, Barnes, Daniel R, Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K, Leslie, Goska, Aalfs, Cora M, ABCTB Investigators, Adank, Muriel A, Adlard, Julian, Agata, Simona, Cadoo, Karen, Agnarsson, Bjarni A, Ahearn, Thomas, Aittomäki, Kristiina, Ambrosone, Christine B, Andrews, Lesley, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Arnold, Norbert, Aronson, Kristan J, Arun, Banu K, Asseryanis, Ella, Auber, Bernd, Auvinen, Päivi, Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B, Barrowdale, Daniel, Barwell, Julian, Beane Freeman, Laura E, Beauparlant, Charles Joly, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Berger, Raanan, Bermisheva, Marina, Blanco, Amie M, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Anders, Bojesen, Stig E, Bonanni, Bernardo, Borg, Ake, Brady, Angela F, Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S, Caldés, Trinidad, Caliebe, Almuth, Caligo, Maria A, Campa, Daniele, Campbell, Ian G, Canzian, Federico, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Claes, Kathleen BM, Clarke, Christine L, Collavoli, Anita, Conner, Thomas A, Cox, David G, Cybulski, Cezary, Czene, Kamila, Daly, Mary B, De La Hoya, Miguel, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Dite, Gillian S, Ditsch, Nina, Domchek, Susan M, Dorfling, Cecilia M, Dos-Santos-Silva, Isabel, Durda, Katarzyna, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Ellberg, Carolina, Eriksson, Mikael, Evans, D Gareth, Fasching, Peter A, Figueroa, Jonine, Flyger, Henrik, Foulkes, William D, Friebel, Tara M, Friedman, Eitan, Gabrielson, Marike, Gaddam, Pragna, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M, Garber, Judy, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, Gayther, Simon A, GEMO Study Collaborators, Giles, Graham G, Glendon, Gord, Godwin, Andrew K, Goldberg, Mark S, Goldgar, David E, Guénel, Pascal, Gutierrez-Barrera, Angelica M, Haeberle, Lothar, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A, Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hopper, John L, Hosgood, H Dean, Howell, Anthony, Hu, Chunling, Hulick, Peter J, Hunter, David J, Imyanitov, Evgeny N, KConFab, Isaacs, Claudine, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M, Jones, Michael E, Jung, Audrey, Kaaks, Rudolf, Karlan, Beth Y, Khusnutdinova, Elza, Kitahara, Cari M, Konstantopoulou, Irene, Koutros, Stella, Kraft, Peter, Lambrechts, Diether, Lazaro, Conxi, Le Marchand, Loic, Lester, Jenny, Lesueur, Fabienne, Lilyquist, Jenna, Loud, Jennifer T, Lu, Karen H, Luben, Robert N, Lubinski, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martens, John WM, Maurer, Tabea, Mavroudis, Dimitrios, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Montagna, Marco, Nathanson, Katherine L, Neuhausen, Susan L, Newman, William G, Nguyen-Dumont, Tu, Nielsen, Finn Cilius, Nielsen, Sarah, Nikitina-Zake, Liene, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I, Olshan, Andrew F, Olson, Janet E, Olsson, Håkan, Osorio, Ana, Ottini, Laura, Peissel, Bernard, Peixoto, Ana, Peto, Julian, Plaseska-Karanfilska, Dijana, Pocza, Timea, Presneau, Nadege, Pujana, Miquel Angel, Punie, Kevin, Rack, Brigitte, Rantala, Johanna, Rashid, Muhammad U, Rau-Murthy, Rohini, Rennert, Gad, Lejbkowicz, Flavio, Rhenius, Valerie, Romero, Atocha, Rookus, Matti A, Ross, Eric A, Rossing, Maria, Rudaitis, Vilius, Ruebner, Matthias, Saloustros, Emmanouil, Sanden, Kristin, Santamariña, Marta, Scheuner, Maren T, Schmutzler, Rita K, Schneider, Michael, Scott, Christopher, Senter, Leigha, Shah, Mitul, Sharma, Priyanka, Shu, Xiao-Ou, Simard, Jacques, Singer, Christian F, Sohn, Christof, Soucy, Penny, Southey, Melissa C, Spinelli, John J, Steele, Linda, Stoppa-Lyonnet, Dominique, Tapper, William J, Teixeira, Manuel R, Terry, Mary Beth, Thomassen, Mads, Thompson, Jennifer, Thull, Darcy L, Tischkowitz, Marc, Tollenaar, Rob AEM, Torres, Diana, Troester, Melissa A, Truong, Thérèse, Tung, Nadine, Untch, Michael, Vachon, Celine M, Van Rensburg, Elizabeth J, Van Veen, Elke M, Vega, Ana, Viel, Alessandra, Wappenschmidt, Barbara, Weitzel, Jeffrey N, Wendt, Camilla, Wieme, Greet, Wolk, Alicja, Yang, Xiaohong R, Zheng, Wei, Ziogas, Argyrios, Zorn, Kristin K, Dunning, Alison M, Lush, Michael, Wang, Qin, McGuffog, Lesley, Parsons, Michael T, Pharoah, Paul DP, Fostira, Florentia, Toland, Amanda E, Andrulis, Irene L, Ramus, Susan J, Swerdlow, Anthony J, Greene, Mark H, Chung, Wendy K, Milne, Roger L, Chenevix-Trench, Georgia, Dörk, Thilo, Schmidt, Marjanka K, Easton, Douglas F, Radice, Paolo, Hahnen, Eric, Antoniou, Antonis C, Couch, Fergus J, Nevanlinna, Heli, Surrallés, Jordi, and Peterlongo, Paolo
Subjects: nutritional and metabolic diseases, skin and connective tissue diseases, Cancer genetics, 3. Good health
Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM -/- patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.

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