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1. Identification of nine new susceptibility loci for endometrial cancer

Author

Tracy A. O’Mara, Dylan M. Glubb, Frederic Amant, Daniela Annibali, Katie Ashton, John Attia, Paul L. Auer, Matthias W. Beckmann, Amanda Black, Manjeet K. Bolla, Hiltrud Brauch, Hermann Brenner, Louise Brinton, Daniel D. Buchanan, Barbara Burwinkel, Jenny Chang-Claude, Stephen J. Chanock, Chu Chen, Maxine M. Chen, Timothy H. T. Cheng, Christine L. Clarke, Mark Clendenning, Linda S. Cook, Fergus J. Couch, Angela Cox, Marta Crous-Bous, Kamila Czene, Felix Day, Joe Dennis, Jeroen Depreeuw, Jennifer Anne Doherty, Thilo Dörk, Sean C. Dowdy, Matthias Dürst, Arif B. Ekici, Peter A. Fasching, Brooke L. Fridley, Christine M. Friedenreich, Lin Fritschi, Jenny Fung, Montserrat García-Closas, Mia M. Gaudet, Graham G. Giles, Ellen L. Goode, Maggie Gorman, Christopher A. Haiman, Per Hall, Susan E. Hankison, Catherine S. Healey, Alexander Hein, Peter Hillemanns, Shirley Hodgson, Erling A. Hoivik, Elizabeth G. Holliday, John L. Hopper, David J. Hunter, Angela Jones, Camilla Krakstad, Vessela N. Kristensen, Diether Lambrechts, Loic Le Marchand, Xiaolin Liang, Annika Lindblom, Jolanta Lissowska, Jirong Long, Lingeng Lu, Anthony M. Magliocco, Lynn Martin, Mark McEvoy, Alfons Meindl, Kyriaki Michailidou, Roger L. Milne, Miriam Mints, Grant W. Montgomery, Rami Nassir, Håkan Olsson, Irene Orlow, Geoffrey Otton, Claire Palles, John R. B. Perry, Julian Peto, Loreall Pooler, Jennifer Prescott, Tony Proietto, Timothy R. Rebbeck, Harvey A. Risch, Peter A. W. Rogers, Matthias Rübner, Ingo Runnebaum, Carlotta Sacerdote, Gloria E. Sarto, Fredrick Schumacher, Rodney J. Scott, V. Wendy Setiawan, Mitul Shah, Xin Sheng, Xiao-Ou Shu, Melissa C. Southey, Anthony J. Swerdlow, Emma Tham, Jone Trovik, Constance Turman, Jonathan P. Tyrer, Celine Vachon, David VanDen Berg, Adriaan Vanderstichele, Zhaoming Wang, Penelope M. Webb, Nicolas Wentzensen, Henrica M. J. Werner, Stacey J. Winham, Alicja Wolk, Lucy Xia, Yong-Bing Xiang, Hannah P. Yang, Herbert Yu, Wei Zheng, Paul D. P. Pharoah, Alison M. Dunning, Peter Kraft, Immaculata De Vivo, Ian Tomlinson, Douglas F. Easton, Amanda B. Spurdle, and Deborah J. Thompson

Subjects
Science
Abstract

Endometrial cancer is the most common invasive gynaecological cancer in developed countries. Here a meta-analysis identifies an additional nine novel endometrial cancer risk loci and eQTL analysis reveals risk variants associate with reduced expression of negative regulators of oncogenic signal transduction proteins.

Published
2018
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2. When the Ideal Meets the Feasible: Constructing a Protocol for Developmental Assessment at Early School-Age

Author

Adel Farhi, Saralee Glasser, Shay Frank, Galit Hirsh-Yechezkel, Louise Brinton, Bert Scoccia, Rafael Ron-El, Liat Lerner-Geva, and Lidia V. Gabis

Subjects
assessment, child development, cognitive, health, parents, telephone interview, Pediatrics, RJ1-570
Abstract

Objective: To describe development of a methodology for an outcome study of children born following in-vitro fertilization or spontaneously-conceived, as a model for defining normal and below-normal development of school-age children for research purposes.Study Design: The main issues addressed were defining the major health and developmental domains to be investigated, selection of age-appropriate validated instruments, considering time constraints to maximize compliance, and budgetary limitations. The final protocol included a half-hour structured telephone interview with mothers of all 759 children and a 2-h developmental assessment of 294 of them. Each of the instruments and recruiting methods are described in terms of the abovementioned considerations.Results: Almost all of the mothers who agreed to be interviewed completed it within the half-hour allotted; however only about half of those who agreed to bring the child for the developmental assessment actually did so. The entire examination battery, assessing cognitive ability, executive functions, attention, and learning skills, was completed by almost all 294 children. There was a significant degree of agreement between the maternal report of the child's reading, writing and arithmetic skills and the in-person examination, as well as regarding the child's weight and height measurements.Conclusion: The findings lend support for a low-budget study, relying on telephone interviews. However, limitations such as the validity of maternal report and recall bias must be taken into consideration.

Published
2018
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3. Exome-wide association study of endometrial cancer in a multiethnic population.

Author

Maxine M Chen, Marta Crous-Bou, Veronica W Setiawan, Jennifer Prescott, Sara H Olson, Nicolas Wentzensen, Amanda Black, Louise Brinton, Chu Chen, Constance Chen, Linda S Cook, Jennifer Doherty, Christine M Friedenreich, Susan E Hankinson, Patricia Hartge, Brian E Henderson, David J Hunter, Loic Le Marchand, Xiaolin Liang, Jolanta Lissowska, Lingeng Lu, Irene Orlow, Stacey Petruzella, Silvia Polidoro, Loreall Pooler, Timothy R Rebbeck, Harvey Risch, Carlotta Sacerdote, Frederick Schumacher, Xin Sheng, Xiao-Ou Shu, Noel S Weiss, Lucy Xia, David Van Den Berg, Hannah P Yang, Herbert Yu, Stephen Chanock, Christopher Haiman, Peter Kraft, and Immaculata De Vivo

Subjects
Medicine, Science
Abstract

Endometrial cancer (EC) contributes substantially to total burden of cancer morbidity and mortality in the United States. Family history is a known risk factor for EC, thus genetic factors may play a role in EC pathogenesis. Three previous genome-wide association studies (GWAS) have found only one locus associated with EC, suggesting that common variants with large effects may not contribute greatly to EC risk. Alternatively, we hypothesize that rare variants may contribute to EC risk. We conducted an exome-wide association study (EXWAS) of EC using the Infinium HumanExome BeadChip in order to identify rare variants associated with EC risk. We successfully genotyped 177,139 variants in a multiethnic population of 1,055 cases and 1,778 controls from four studies that were part of the Epidemiology of Endometrial Cancer Consortium (E2C2). No variants reached global significance in the study, suggesting that more power is needed to detect modest associations between rare genetic variants and risk of EC.

Published
2014
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4. MicroRNA related polymorphisms and breast cancer risk.

Author

Sofia Khan, Dario Greco, Kyriaki Michailidou, Roger L Milne, Taru A Muranen, Tuomas Heikkinen, Kirsimari Aaltonen, Joe Dennis, Manjeet K Bolla, Jianjun Liu, Per Hall, Astrid Irwanto, Keith Humphreys, Jingmei Li, Kamila Czene, Jenny Chang-Claude, Rebecca Hein, Anja Rudolph, Petra Seibold, Dieter Flesch-Janys, Olivia Fletcher, Julian Peto, Isabel dos Santos Silva, Nichola Johnson, Lorna Gibson, Zoe Aitken, John L Hopper, Helen Tsimiklis, Minh Bui, Enes Makalic, Daniel F Schmidt, Melissa C Southey, Carmel Apicella, Jennifer Stone, Quinten Waisfisz, Hanne Meijers-Heijboer, Muriel A Adank, Rob B van der Luijt, Alfons Meindl, Rita K Schmutzler, Bertram Müller-Myhsok, Peter Lichtner, Clare Turnbull, Nazneen Rahman, Stephen J Chanock, David J Hunter, Angela Cox, Simon S Cross, Malcolm W R Reed, Marjanka K Schmidt, Annegien Broeks, Laura J Van't Veer, Frans B Hogervorst, Peter A Fasching, Michael G Schrauder, Arif B Ekici, Matthias W Beckmann, Stig E Bojesen, Børge G Nordestgaard, Sune F Nielsen, Henrik Flyger, Javier Benitez, Pilar M Zamora, Jose I A Perez, Christopher A Haiman, Brian E Henderson, Fredrick Schumacher, Loic Le Marchand, Paul D P Pharoah, Alison M Dunning, Mitul Shah, Robert Luben, Judith Brown, Fergus J Couch, Xianshu Wang, Celine Vachon, Janet E Olson, Diether Lambrechts, Matthieu Moisse, Robert Paridaens, Marie-Rose Christiaens, Pascal Guénel, Thérèse Truong, Pierre Laurent-Puig, Claire Mulot, Frederick Marme, Barbara Burwinkel, Andreas Schneeweiss, Christof Sohn, Elinor J Sawyer, Ian Tomlinson, Michael J Kerin, Nicola Miller, Irene L Andrulis, Julia A Knight, Sandrine Tchatchou, Anna Marie Mulligan, Thilo Dörk, Natalia V Bogdanova, Natalia N Antonenkova, Hoda Anton-Culver, Hatef Darabi, Mikael Eriksson, Montserrat Garcia-Closas, Jonine Figueroa, Jolanta Lissowska, Louise Brinton, Peter Devilee, Robert A E M Tollenaar, Caroline Seynaeve, Christi J van Asperen, Vessela N Kristensen, kConFab Investigators, Australian Ovarian Cancer Study Group, Susan Slager, Amanda E Toland, Christine B Ambrosone, Drakoulis Yannoukakos, Annika Lindblom, Sara Margolin, Paolo Radice, Paolo Peterlongo, Monica Barile, Paolo Mariani, Maartje J Hooning, John W M Martens, J Margriet Collée, Agnes Jager, Anna Jakubowska, Jan Lubinski, Katarzyna Jaworska-Bieniek, Katarzyna Durda, Graham G Giles, Catriona McLean, Hiltrud Brauch, Thomas Brüning, Yon-Dschun Ko, GENICA Network, Hermann Brenner, Aida Karina Dieffenbach, Volker Arndt, Christa Stegmaier, Anthony Swerdlow, Alan Ashworth, Nick Orr, Michael Jones, Jacques Simard, Mark S Goldberg, France Labrèche, Martine Dumont, Robert Winqvist, Katri Pylkäs, Arja Jukkola-Vuorinen, Mervi Grip, Vesa Kataja, Veli-Matti Kosma, Jaana M Hartikainen, Arto Mannermaa, Ute Hamann, Georgia Chenevix-Trench, Carl Blomqvist, Kristiina Aittomäki, Douglas F Easton, and Heli Nevanlinna

Subjects
Medicine, Science
Abstract

Genetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility to cancer. We investigated associations between miRNA related SNPs and breast cancer risk. First we evaluated 2,196 SNPs in a case-control study combining nine genome wide association studies (GWAS). Second, we further investigated 42 SNPs with suggestive evidence for association using 41,785 cases and 41,880 controls from 41 studies included in the Breast Cancer Association Consortium (BCAC). Combining the GWAS and BCAC data within a meta-analysis, we estimated main effects on breast cancer risk as well as risks for estrogen receptor (ER) and age defined subgroups. Five miRNA binding site SNPs associated significantly with breast cancer risk: rs1045494 (odds ratio (OR) 0.92; 95% confidence interval (CI): 0.88-0.96), rs1052532 (OR 0.97; 95% CI: 0.95-0.99), rs10719 (OR 0.97; 95% CI: 0.94-0.99), rs4687554 (OR 0.97; 95% CI: 0.95-0.99, and rs3134615 (OR 1.03; 95% CI: 1.01-1.05) located in the 3' UTR of CASP8, HDDC3, DROSHA, MUSTN1, and MYCL1, respectively. DROSHA belongs to miRNA machinery genes and has a central role in initial miRNA processing. The remaining genes are involved in different molecular functions, including apoptosis and gene expression regulation. Further studies are warranted to elucidate whether the miRNA binding site SNPs are the causative variants for the observed risk effects.

Published
2014
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5. Data from Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk

Author

Paul D.P. Pharoah, Simon A. Gayther, Matthew L. Freedman, Alvaro N.A. Monteiro, Thomas A. Sellers, Argyrios Ziogas, Wei Zheng, Hannah Yang, Anna Wu, Xifeng Wu, Yin-Ling Woo, Lynne R. Wilkens, Kristine G. Wicklund, Alice S. Whittemore, Nicolas Wentzensen, Christine Walsh, Shan Wang-Gohrke, Robert A. Vierkant, Ignace Vergote, Els Van Nieuwenhuysen, Anne M. van Altena, Shelley S. Tworoger, Ya-Yu Tsai, Agnieszka Timorek, Pamela J. Thompson, Kathryn L. Terry, Soo-Hwang Teo, Ingvild L. Tangen, Lara E. Sucheston-Campbell, Melissa C. Southey, Honglin Song, Weiva Sieh, Nadeem Siddiqui, Yurii B. Shvetsov, Xiao-Ou Shu, Ira Schwaab, Joellen M. Schildkraut, Helga B. Salvesen, Iwona K. Rzepecka, Ingo B. Runnebaum, Anja Rudolph, Joseph H. Rothstein, Mary Anne Rossing, Barry Rosen, Harvey A. Risch, Susan J. Ramus, Elizabeth M. Poole, Malcolm C. Pike, Catherine M. Phelan, Jennifer Permuth-Wey, Liisa M. Pelttari, Tanja Pejovic, Celeste Leigh Pearce, Rachel Palmieri Weber, Sandra Orsulic, Irene Orlow, Sara H. Olson, Kunle Odunsi, Heli Nevanlinna, Roberta B. Ness, Lotte Nedergaard, Steven A. Narod, Kirsten B. Moysich, Francesmary Modugno, Usha Menon, Iain A. McNeish, John R. McLaughlin, Valerie McGuire, Keitaro Matsuo, Leon Massuger, Lene Lundvall, Jan Lubinski, Karen Lu, Jolanta Lissowska, Dong Liang, Douglas A. Levine, Jenny Lester, Arto Leminen, Shashi Lele, Alice W. Lee, Nhu D. Le, Sandrina Lambrechts, Diether Lambrechts, Jolanta Kupryjanczyk, Camilla Krakstad, Lambertus A. Kiemeney, Joseph Kelley, Melissa Kellar, Linda E. Kelemen, Susanne K. Kjaer, Beth Y. Karlan, Bu-Tian Ji, Allan Jensen, James Paul, Anna Jakubowska, Edwin S. Iversen, Satoyo Hosono, Claus K. Hogdall, Estrid Hogdall, Peter Hillemanns, Michelle A.T. Hildebrandt, Florian Heitz, Alexander Hein, Philipp Harter, Patricia Harrington, Jacek Grownwald, Marc T. Goodman, Ellen L. Goode, Rosalind Glasspool, Graham G. Giles, Aleksandra Gentry-Maharaj, Yu-Tang Gao, Brooke L. Fridley, Peter A. Fasching, Arif B. Ekici, Robert P. Edwards, Douglas F. Easton, Diana Eccles, Matthias Dürst, Andreas du Bois, Thilo Dörk, Jennifer A. Doherty, Ed Dicks, Joe Dennis, Agnieszka Dansonka-Mieszkowska, Cezary Cybulski, Julie M. Cunningham, Daniel Cramer, Linda S. Cook, Zhihua Chen, Yian Ann Chen, Jenny Chang-Claude, Karen Carty, Ian Campbell, Ralf Butzow, Angela Brooks-Wilson, Louise Brinton, Natalia Bogdanova, Line Bjørge, Maria Bisogna, Andrew Berchuck, Matthias W. Beckmann, Yukie T. Bean, Elisa V. Bandera, Helen Baker, Georgia Chenevix-Trench, Natalia Antonenkova, Hoda Anton-Culver, Katja K.H. Aben, Kate Lawrenson, Qiyuan Li, Jonathan P. Tyrer, and Siddhartha P. Kar

Abstract

Background: Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations.Methods: We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls).Results: Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network.Conclusion: We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development.Impact: Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization. Cancer Epidemiol Biomarkers Prev; 24(10); 1574–84. ©2015 AACR.

Published
2023

6. Supplementary Figures 1-5, Tables 1-8 from Genome-wide Analysis Identifies Novel Loci Associated with Ovarian Cancer Outcomes: Findings from the Ovarian Cancer Association Consortium

Author

Georgia Chenevix-Trench, Penelope M. Webb, Anna deFazio, Ellen L. Goode, Paul D.P. Pharoah, Stuart MacGregor, Andrew Berchuck, Yoke-Eng Chiew, Catherine Kennedy, Thomas Sellers, Rosalind Glasspool, Nadeem Siddiqui, Karen Carty, James Paul, Ian McNeish, Lene Lundvall, Claus Høgdall, Yukie Bean, Tanja Pejovic, Irene Orlow, Elisa V. Bandera, Daniel W. Cramer, Kathryn L. Terry, Edwin S. Iversen, Joellen M. Schildkraut, Robert A. Vierkant, Julie M. Cunningham, Brooke L. Fridley, Susanne Kruger Kjaer, Allan Jensen, Estrid Høgdall, Zachary C. Fogarty, Melissa C. Larson, Madalene Earp, Stacey J. Winham, Sandra Orsulic, Jenny Lester, Christine Walsh, Beth Y. Karlan, Peter Hillemanns, Jacobus Pisterer, Philipp Harter, Ira Schwaab, Andreas du Bois, Florian Heitz, Pamela J. Thompson, Michael E. Carney, Lynne R. Wilkens, Marc T. Goodman, Beata Spiewankiewicz, Iwona K. Rzepecka, Agnieszka Dansonka-Mieszkowska, Jolanta Kupryjanczyk, Anna H. Wu, Daniel O. Stram, Malcolm C. Pike, Celeste L. Pearce, Susan J. Ramus, Usha Menon, Aleksandra Gentry-Maharaj, Simon A. Gayther, Argyrios Ziogas, Hoda Anton-Culver, Rebecca Sutphen, Joseph H. Rothstein, Valerie McGuire, Alice S. Whittemore, Weiva Sieh, Diana Eccles, Ian Campbell, Valerie Rhenius, Honglin Song, Nicolas Wentzensen, Jolanta Lissowska, Louise Brinton, Cezary Cybulski, Anna Jakubowska, Jan Lubiński, Jacek Gronwald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Douglas A. Levine, Kirsten B. Moysich, Roberta B. Ness, Francesmary Modugno, Jenny Chang-Claude, Jennifer A. Doherty, Mary Anne Rossing, Sandrina Lambrechts, Ignace Vergote, Els Van Nieuwenhuysen, Diether Lambrechts, Matthias W. Beckmann, Arif B. Ekici, Alexander Hein, Peter A. Fasching, Bo Gao, Yi Lu, Jonathan Beesley, Siddhartha Kar, Jonathan P. Tyrer, and Sharon E. Johnatty

Abstract

Supplementary Figures 1-5, Tables 1-8. Supplementary Figure 1: Overview of the analytic approach. Supplementary Figure 2: QQ plots of SNPs with MAF ≥0.02 and imputation r2 ≥0.9 associated with Overall Survival in A. Supplementary Figure 3: ‘All OCAC’ histology-adjusted analysis. Supplementary Figure 4: Forest plots of promising SNPs. Supplementary Figure 5: KM-Plotter graphs of significant associations with outcome. Supplementary Table 1: All studies (OCAC & TCGA) eligible for analyses according to first-line chemotherapy. Supplementary Table 2: Description of individual OCAC studies included in the secondary 'all OCAC' analysis. Supplementary Table 3a: Overall Survival estimates for selected SNPs (MAF ≥0.02) comparing iCOGS imputed (r2 ≥0.3) and iPLEX genotyped samples. Supplementary Table 3b: Progression-free Survival estimates for selected SNPs (MAF ≥0.02) comparing iCOGS imputed (r2 ≥0.3) and iPLEX genotyped samples. Supplementary Table 4: SNPs with imputation r2 ≥0.9, EAF ≥0.02 and p ≤ 1E-05 for at least one of four outcomes analyzed in cases selected according to first-line chemotherapy. Supplementary Table 5: Meta-analysis of largest possible sample (TCGA, non-overlapping iCOGS and iplex genotyped) for selected promising SNPs analyzed in cases selected according to first-line chemotherapy. Supplementary Table 6: Significant association between protein-coding genes within 1Mb of promising SNPs and ovarian cancer outcomes. Supplementary Table 7: SNPs with imputation r-sq≥0.9 and p ≤ 1E-05 for Overall Survival in histology-adj 'all OCAC' analysis. Supplementary Table 8: iCOGS estimates for SNPs previously identified to be associated with response to chemotherapy as reported in the aNHGRI GWAS catalog.

Published
2023

7. Supplementary Table 1 from Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

Author

Wei Zheng, Douglas F. Easton, Alison M. Dunning, Georgia Chenevix-Trench, Jacques Simard, Paul D.P. Pharoah, Per Hall, Ying Zheng, M. Pilar Zamora, Cheng Har Yip, Anna Wu, Robert Winqvist, Wanqing Wen, Ans van den Ouweland, Chiu-chen Tseng, Thérèse Truong, Ian P.M. Tomlinson, Robert A.E.M. Tollenaar, Amanda Ewart Toland, Bernard Thienpont, Soo Hwang Teo, Anthony Swerdlow, Melissa C. Southey, Martha J. Shrubsole, Jiajun Shi, Chen-Yang Shen, Rita K. Schmutzler, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Thomas Choudary Putti, Paolo Peterlongo, Nick Orr, Janet E. Olson, Silje Nord, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Alfons Meindl, Catriona A. McLean, Keitaro Matsuo, Frederik Marme, Sara Margolin, Siranoush Manoukian, Arto Mannermaa, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Veli-Matti Kosma, Julia A. Knight, Sofia Khan, Daehee Kang, Maria Kabisch, Nichola Johnson, Anna Jakubowska, Hidemi Ito, Chia-Ni Hsiung, John L. Hopper, Antoinette Hollestelle, Mikael Hartman, Ute Hamann, Christopher A. Haiman, Pascal Guénel, Mervi Grip, Graham G. Giles, Montserrat García-Closas, Valerie Gaborieau, Florentia Fostira, Henrik Flyger, Olivia Fletcher, Peter A. Fasching, Thilo Dörk, Arnaud Droit, Peter Devilee, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, Fergus J. Couch, Ji-Yeob Choi, Jenny Chang-Claude, Sander Canisius, Hui Cai, Barbara Burwinkel, Thomas Brüning, Annegien Broeks, Louise Brinton, Hermann Brenner, Hiltrud Brauch, Stig E. Bojesen, Natalia Bogdanova, William Blot, Javier Benitez, Alicia Beeghly-Fadiel, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene L. Andrulis, Siddhartha P. Kar, Jonathan Beesley, Qiuyin Cai, Xiao-Ou Shu, Roger L. Milne, Qin Wang, Manjeet K. Bolla, Maya Ghoussaini, Kyriaki Michailidou, Chenjie Zeng, Jirong Long, and Xingyi Guo

Abstract

Summary results for all SNPs at the 4q24 locus associated with breast cancer risk at P

Published
2023

8. Data from Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

Author

Wei Zheng, Douglas F. Easton, Alison M. Dunning, Georgia Chenevix-Trench, Jacques Simard, Paul D.P. Pharoah, Per Hall, Ying Zheng, M. Pilar Zamora, Cheng Har Yip, Anna Wu, Robert Winqvist, Wanqing Wen, Ans van den Ouweland, Chiu-chen Tseng, Thérèse Truong, Ian P.M. Tomlinson, Robert A.E.M. Tollenaar, Amanda Ewart Toland, Bernard Thienpont, Soo Hwang Teo, Anthony Swerdlow, Melissa C. Southey, Martha J. Shrubsole, Jiajun Shi, Chen-Yang Shen, Rita K. Schmutzler, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Thomas Choudary Putti, Paolo Peterlongo, Nick Orr, Janet E. Olson, Silje Nord, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Alfons Meindl, Catriona A. McLean, Keitaro Matsuo, Frederik Marme, Sara Margolin, Siranoush Manoukian, Arto Mannermaa, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Veli-Matti Kosma, Julia A. Knight, Sofia Khan, Daehee Kang, Maria Kabisch, Nichola Johnson, Anna Jakubowska, Hidemi Ito, Chia-Ni Hsiung, John L. Hopper, Antoinette Hollestelle, Mikael Hartman, Ute Hamann, Christopher A. Haiman, Pascal Guénel, Mervi Grip, Graham G. Giles, Montserrat García-Closas, Valerie Gaborieau, Florentia Fostira, Henrik Flyger, Olivia Fletcher, Peter A. Fasching, Thilo Dörk, Arnaud Droit, Peter Devilee, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, Fergus J. Couch, Ji-Yeob Choi, Jenny Chang-Claude, Sander Canisius, Hui Cai, Barbara Burwinkel, Thomas Brüning, Annegien Broeks, Louise Brinton, Hermann Brenner, Hiltrud Brauch, Stig E. Bojesen, Natalia Bogdanova, William Blot, Javier Benitez, Alicia Beeghly-Fadiel, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene L. Andrulis, Siddhartha P. Kar, Jonathan Beesley, Qiuyin Cai, Xiao-Ou Shu, Roger L. Milne, Qin Wang, Manjeet K. Bolla, Maya Ghoussaini, Kyriaki Michailidou, Chenjie Zeng, Jirong Long, and Xingyi Guo

Abstract

Background: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored.Methods: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium.Results: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10−4; OR, 1.04; 95% confidence interval (CI), 1.02–1.07] and rs77928427 (P = 1.86 × 10−4; OR, 1.04; 95% CI, 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor–binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue.Conclusion: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2.Impact: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk. Cancer Epidemiol Biomarkers Prev; 24(11); 1680–91. ©2015 AACR.

Published
2023

9. Supplemental Figure 1 from Assessment of Multifactor Gene–Environment Interactions and Ovarian Cancer Risk: Candidate Genes, Obesity, and Hormone-Related Risk Factors

Author

Brooke L. Fridley, Ellen L. Goode, Paul Pharoah, Joellen M. Schildkraut, Celeste Leigh Pearce, Hannah Yang, Anna H. Wu, Lynne R. Wilkens, Alice S. Whittemore, Nicolas Wentzensen, Shan Wang-Gohrke, Robert A. Vierkant, David J. van den Berg, Pamela J. Thompson, Honglin Song, Joseph Rothstein, Mary Anne Rossing, Susan J. Ramus, Malcolm C. Pike, Roberta B. Ness, Kirsten B. Moysich, Francesmary Modugno, Usha Menon, Leon Massuger, Galina Lurie, Melissa C. Larson, Susanne K. Kjaer, Lambertus A. Kiemeney, Sharon E. Johnatty, Allan Jensen, Estrid Høgdall, Marc T. Goodman, Aleksandra Gentry-Maharaj, Simon A. Gayther, Robert P. Edwards, Jennifer A. Doherty, Anna DeFazio, Julie M. Cunningham, Louise Brinton, Andrew Berchuck, Hoda Anton-Culver, Anja Rudolph, Jenny Chang-Claude, Penelope Webb, Weiva Sieh, Valerie McGuire, Jonathan P. Tyrer, Rama Raghavan, and Joseph L. Usset

Abstract

Potential hormonal mechanism to motivate investigation of multi-factor obesity-hormone related risk factors - SNP interactions.

Published
2023

10. Data from Assessment of Multifactor Gene–Environment Interactions and Ovarian Cancer Risk: Candidate Genes, Obesity, and Hormone-Related Risk Factors

Author

Brooke L. Fridley, Ellen L. Goode, Paul Pharoah, Joellen M. Schildkraut, Celeste Leigh Pearce, Hannah Yang, Anna H. Wu, Lynne R. Wilkens, Alice S. Whittemore, Nicolas Wentzensen, Shan Wang-Gohrke, Robert A. Vierkant, David J. van den Berg, Pamela J. Thompson, Honglin Song, Joseph Rothstein, Mary Anne Rossing, Susan J. Ramus, Malcolm C. Pike, Roberta B. Ness, Kirsten B. Moysich, Francesmary Modugno, Usha Menon, Leon Massuger, Galina Lurie, Melissa C. Larson, Susanne K. Kjaer, Lambertus A. Kiemeney, Sharon E. Johnatty, Allan Jensen, Estrid Høgdall, Marc T. Goodman, Aleksandra Gentry-Maharaj, Simon A. Gayther, Robert P. Edwards, Jennifer A. Doherty, Anna DeFazio, Julie M. Cunningham, Louise Brinton, Andrew Berchuck, Hoda Anton-Culver, Anja Rudolph, Jenny Chang-Claude, Penelope Webb, Weiva Sieh, Valerie McGuire, Jonathan P. Tyrer, Rama Raghavan, and Joseph L. Usset

Abstract

Background: Many epithelial ovarian cancer (EOC) risk factors relate to hormone exposure and elevated estrogen levels are associated with obesity in postmenopausal women. Therefore, we hypothesized that gene–environment interactions related to hormone-related risk factors could differ between obese and non-obese women.Methods: We considered interactions between 11,441 SNPs within 80 candidate genes related to hormone biosynthesis and metabolism and insulin-like growth factors with six hormone-related factors (oral contraceptive use, parity, endometriosis, tubal ligation, hormone replacement therapy, and estrogen use) and assessed whether these interactions differed between obese and non-obese women. Interactions were assessed using logistic regression models and data from 14 case–control studies (6,247 cases; 10,379 controls). Histotype-specific analyses were also completed.Results: SNPs in the following candidate genes showed notable interaction: IGF1R (rs41497346, estrogen plus progesterone hormone therapy, histology = all, P = 4.9 × 10−6) and ESR1 (rs12661437, endometriosis, histology = all, P = 1.5 × 10−5). The most notable obesity–gene–hormone risk factor interaction was within INSR (rs113759408, parity, histology = endometrioid, P = 8.8 × 10−6).Conclusions: We have demonstrated the feasibility of assessing multifactor interactions in large genetic epidemiology studies. Follow-up studies are necessary to assess the robustness of our findings for ESR1, CYP11A1, IGF1R, CYP11B1, INSR, and IGFBP2. Future work is needed to develop powerful statistical methods able to detect these complex interactions.Impact: Assessment of multifactor interaction is feasible, and, here, suggests that the relationship between genetic variants within candidate genes and hormone-related risk factors may vary EOC susceptibility. Cancer Epidemiol Biomarkers Prev; 25(5); 780–90. ©2016 AACR.

Published
2023

11. Supplementary Figure 1 from Genome-Wide Association Study Identifies a Possible Susceptibility Locus for Endometrial Cancer

Author

Xiao-Ou Shu, Amanda B. Spurdle, Qiuyin Cai, Yu-Tang Gao, Douglas Easton, Alison Dunning, Wei Lu, Hui Cai, Anthony Proietto, Alexander Hein, Mari K. Halle, Rayna K. Matsuno, An Coosemans, Louise Brinton, Maggie Gorman, Ben Zhang, Jiajun Shi, Geoffrey Otton, Arif B. Ekici, Camilla Krakstad, Pamela J. Thompson, Matthias Dürst, Dilyara Kaidarova, Lieve Coenegrachts, Jolanta Lissowska, Lingeng Lu, Kimberly Howarth, Ping-Ping Bao, Bu-Tian Ji, Katie Ashton, Matthias W. Beckmann, Jone Trovik, Galina Lurie, Anita Schwake, Nurzhan Turmanov, Frederic Amant, Hannah P. Yang, Harvey Risch, Shirley Hodgson, Catherine S. Healey, Tracy O'Mara, Ying Zheng, Ryan Delahanty, Rodney J. Scott, Peter A. Fasching, Helga B. Salvesen, Marc T. Goodman, Natalia Dubrowinskaja, Thilo Dörk, Diether Lambrechts, Nicolas Wentzensen, Herbert Yu, Ian Tomlinson, Deborah Thompson, Felicity Lose, Yong-Bing Xiang, Wei Zheng, and Jirong Long

Abstract

PDF file, 53KB.

Published
2023

12. Data from Genome-wide Analysis Identifies Novel Loci Associated with Ovarian Cancer Outcomes: Findings from the Ovarian Cancer Association Consortium

Author

Georgia Chenevix-Trench, Penelope M. Webb, Anna deFazio, Ellen L. Goode, Paul D.P. Pharoah, Stuart MacGregor, Andrew Berchuck, Yoke-Eng Chiew, Catherine Kennedy, Thomas Sellers, Rosalind Glasspool, Nadeem Siddiqui, Karen Carty, James Paul, Ian McNeish, Lene Lundvall, Claus Høgdall, Yukie Bean, Tanja Pejovic, Irene Orlow, Elisa V. Bandera, Daniel W. Cramer, Kathryn L. Terry, Edwin S. Iversen, Joellen M. Schildkraut, Robert A. Vierkant, Julie M. Cunningham, Brooke L. Fridley, Susanne Kruger Kjaer, Allan Jensen, Estrid Høgdall, Zachary C. Fogarty, Melissa C. Larson, Madalene Earp, Stacey J. Winham, Sandra Orsulic, Jenny Lester, Christine Walsh, Beth Y. Karlan, Peter Hillemanns, Jacobus Pisterer, Philipp Harter, Ira Schwaab, Andreas du Bois, Florian Heitz, Pamela J. Thompson, Michael E. Carney, Lynne R. Wilkens, Marc T. Goodman, Beata Spiewankiewicz, Iwona K. Rzepecka, Agnieszka Dansonka-Mieszkowska, Jolanta Kupryjanczyk, Anna H. Wu, Daniel O. Stram, Malcolm C. Pike, Celeste L. Pearce, Susan J. Ramus, Usha Menon, Aleksandra Gentry-Maharaj, Simon A. Gayther, Argyrios Ziogas, Hoda Anton-Culver, Rebecca Sutphen, Joseph H. Rothstein, Valerie McGuire, Alice S. Whittemore, Weiva Sieh, Diana Eccles, Ian Campbell, Valerie Rhenius, Honglin Song, Nicolas Wentzensen, Jolanta Lissowska, Louise Brinton, Cezary Cybulski, Anna Jakubowska, Jan Lubiński, Jacek Gronwald, Leon F.A.G. Massuger, Lambertus A. Kiemeney, Douglas A. Levine, Kirsten B. Moysich, Roberta B. Ness, Francesmary Modugno, Jenny Chang-Claude, Jennifer A. Doherty, Mary Anne Rossing, Sandrina Lambrechts, Ignace Vergote, Els Van Nieuwenhuysen, Diether Lambrechts, Matthias W. Beckmann, Arif B. Ekici, Alexander Hein, Peter A. Fasching, Bo Gao, Yi Lu, Jonathan Beesley, Siddhartha Kar, Jonathan P. Tyrer, and Sharon E. Johnatty

Abstract

Purpose: Chemotherapy resistance remains a major challenge in the treatment of ovarian cancer. We hypothesize that germline polymorphisms might be associated with clinical outcome.Experimental Design: We analyzed approximately 2.8 million genotyped and imputed SNPs from the iCOGS experiment for progression-free survival (PFS) and overall survival (OS) in 2,901 European epithelial ovarian cancer (EOC) patients who underwent first-line treatment of cytoreductive surgery and chemotherapy regardless of regimen, and in a subset of 1,098 patients treated with ≥4 cycles of paclitaxel and carboplatin at standard doses. We evaluated the top SNPs in 4,434 EOC patients, including patients from The Cancer Genome Atlas. In addition, we conducted pathway analysis of all intragenic SNPs and tested their association with PFS and OS using gene set enrichment analysis.Results: Five SNPs were significantly associated (P ≤ 1.0 × 10−5) with poorer outcomes in at least one of the four analyses, three of which, rs4910232 (11p15.3), rs2549714 (16q23), and rs6674079 (1q22), were located in long noncoding RNAs (lncRNAs) RP11-179A10.1, RP11-314O13.1, and RP11-284F21.8, respectively (P ≤ 7.1 × 10−6). ENCODE ChIP-seq data at 1q22 for normal ovary show evidence of histone modification around RP11-284F21.8, and rs6674079 is perfectly correlated with another SNP within the super-enhancer MEF2D, expression levels of which were reportedly associated with prognosis in another solid tumor. YAP1- and WWTR1 (TAZ)-stimulated gene expression and high-density lipoprotein (HDL)-mediated lipid transport pathways were associated with PFS and OS, respectively, in the cohort who had standard chemotherapy (pGSEA ≤6 × 10−3).Conclusions: We have identified SNPs in three lncRNAs that might be important targets for novel EOC therapies. Clin Cancer Res; 21(23); 5264–76. ©2015 AACR.

Published
2023

13. Data from Genome-Wide Association Study Identifies a Possible Susceptibility Locus for Endometrial Cancer

Author

Xiao-Ou Shu, Amanda B. Spurdle, Qiuyin Cai, Yu-Tang Gao, Douglas Easton, Alison Dunning, Wei Lu, Hui Cai, Anthony Proietto, Alexander Hein, Mari K. Halle, Rayna K. Matsuno, An Coosemans, Louise Brinton, Maggie Gorman, Ben Zhang, Jiajun Shi, Geoffrey Otton, Arif B. Ekici, Camilla Krakstad, Pamela J. Thompson, Matthias Dürst, Dilyara Kaidarova, Lieve Coenegrachts, Jolanta Lissowska, Lingeng Lu, Kimberly Howarth, Ping-Ping Bao, Bu-Tian Ji, Katie Ashton, Matthias W. Beckmann, Jone Trovik, Galina Lurie, Anita Schwake, Nurzhan Turmanov, Frederic Amant, Hannah P. Yang, Harvey Risch, Shirley Hodgson, Catherine S. Healey, Tracy O'Mara, Ying Zheng, Ryan Delahanty, Rodney J. Scott, Peter A. Fasching, Helga B. Salvesen, Marc T. Goodman, Natalia Dubrowinskaja, Thilo Dörk, Diether Lambrechts, Nicolas Wentzensen, Herbert Yu, Ian Tomlinson, Deborah Thompson, Felicity Lose, Yong-Bing Xiang, Wei Zheng, and Jirong Long

Abstract

Background: Genome-wide association studies (GWAS) have identified more than 100 genetic loci for various cancers. However, only one is for endometrial cancer.Methods: We conducted a three-stage GWAS including 8,492 endometrial cancer cases and 16,596 controls. After analyzing 585,963 single-nucleotide polymorphisms (SNP) in 832 cases and 2,682 controls (stage I) from the Shanghai Endometrial Cancer Genetics Study, we selected the top 106 SNPs for in silico replication among 1,265 cases and 5,190 controls from the Australian/British Endometrial Cancer GWAS (stage II). Nine SNPs showed results consistent in direction with stage I with P < 0.1. These nine SNPs were investigated among 459 cases and 558 controls (stage IIIa) and six SNPs showed a direction of association consistent with stages I and II. These six SNPs, plus two additional SNPs selected on the basis of linkage disequilibrium and P values in stage II, were investigated among 5,936 cases and 8,166 controls from an additional 11 studies (stage IIIb).Results: SNP rs1202524, near the CAPN9 gene on chromosome 1q42.2, showed a consistent association with endometrial cancer risk across all three stages, with ORs of 1.09 [95% confidence interval (CI), 1.03–1.16] for the A/G genotype and 1.17 (95% CI, 1.05–1.30) for the G/G genotype (P = 1.6 × 10−4 in combined analyses of all samples). The association was stronger when limited to the endometrioid subtype, with ORs (95% CI) of 1.11 (1.04–1.18) and 1.21 (1.08–1.35), respectively (P = 2.4 × 10−5).Conclusions: Chromosome 1q42.2 may host an endometrial cancer susceptibility locus.Impact: This study identified a potential genetic locus for endometrial cancer risk. Cancer Epidemiol Biomarkers Prev; 21(6); 980–7. ©2012 AACR.

Published
2023

14. Supplementary Tables 1 - 4 from Genome-Wide Association Study Identifies a Possible Susceptibility Locus for Endometrial Cancer

Author

Xiao-Ou Shu, Amanda B. Spurdle, Qiuyin Cai, Yu-Tang Gao, Douglas Easton, Alison Dunning, Wei Lu, Hui Cai, Anthony Proietto, Alexander Hein, Mari K. Halle, Rayna K. Matsuno, An Coosemans, Louise Brinton, Maggie Gorman, Ben Zhang, Jiajun Shi, Geoffrey Otton, Arif B. Ekici, Camilla Krakstad, Pamela J. Thompson, Matthias Dürst, Dilyara Kaidarova, Lieve Coenegrachts, Jolanta Lissowska, Lingeng Lu, Kimberly Howarth, Ping-Ping Bao, Bu-Tian Ji, Katie Ashton, Matthias W. Beckmann, Jone Trovik, Galina Lurie, Anita Schwake, Nurzhan Turmanov, Frederic Amant, Hannah P. Yang, Harvey Risch, Shirley Hodgson, Catherine S. Healey, Tracy O'Mara, Ying Zheng, Ryan Delahanty, Rodney J. Scott, Peter A. Fasching, Helga B. Salvesen, Marc T. Goodman, Natalia Dubrowinskaja, Thilo Dörk, Diether Lambrechts, Nicolas Wentzensen, Herbert Yu, Ian Tomlinson, Deborah Thompson, Felicity Lose, Yong-Bing Xiang, Wei Zheng, and Jirong Long

Abstract

PDF file, 112KB.

Published
2023

15. Supplementary Figure 2 from Genome-Wide Association Study Identifies a Possible Susceptibility Locus for Endometrial Cancer

Author

Xiao-Ou Shu, Amanda B. Spurdle, Qiuyin Cai, Yu-Tang Gao, Douglas Easton, Alison Dunning, Wei Lu, Hui Cai, Anthony Proietto, Alexander Hein, Mari K. Halle, Rayna K. Matsuno, An Coosemans, Louise Brinton, Maggie Gorman, Ben Zhang, Jiajun Shi, Geoffrey Otton, Arif B. Ekici, Camilla Krakstad, Pamela J. Thompson, Matthias Dürst, Dilyara Kaidarova, Lieve Coenegrachts, Jolanta Lissowska, Lingeng Lu, Kimberly Howarth, Ping-Ping Bao, Bu-Tian Ji, Katie Ashton, Matthias W. Beckmann, Jone Trovik, Galina Lurie, Anita Schwake, Nurzhan Turmanov, Frederic Amant, Hannah P. Yang, Harvey Risch, Shirley Hodgson, Catherine S. Healey, Tracy O'Mara, Ying Zheng, Ryan Delahanty, Rodney J. Scott, Peter A. Fasching, Helga B. Salvesen, Marc T. Goodman, Natalia Dubrowinskaja, Thilo Dörk, Diether Lambrechts, Nicolas Wentzensen, Herbert Yu, Ian Tomlinson, Deborah Thompson, Felicity Lose, Yong-Bing Xiang, Wei Zheng, and Jirong Long

Abstract

PDF file, 45KB.

Published
2023

16. Supplementary Tables S1-6, Figures S1-2 from Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk

Author

Paul D.P. Pharoah, Simon A. Gayther, Matthew L. Freedman, Alvaro N.A. Monteiro, Thomas A. Sellers, Argyrios Ziogas, Wei Zheng, Hannah Yang, Anna Wu, Xifeng Wu, Yin-Ling Woo, Lynne R. Wilkens, Kristine G. Wicklund, Alice S. Whittemore, Nicolas Wentzensen, Christine Walsh, Shan Wang-Gohrke, Robert A. Vierkant, Ignace Vergote, Els Van Nieuwenhuysen, Anne M. van Altena, Shelley S. Tworoger, Ya-Yu Tsai, Agnieszka Timorek, Pamela J. Thompson, Kathryn L. Terry, Soo-Hwang Teo, Ingvild L. Tangen, Lara E. Sucheston-Campbell, Melissa C. Southey, Honglin Song, Weiva Sieh, Nadeem Siddiqui, Yurii B. Shvetsov, Xiao-Ou Shu, Ira Schwaab, Joellen M. Schildkraut, Helga B. Salvesen, Iwona K. Rzepecka, Ingo B. Runnebaum, Anja Rudolph, Joseph H. Rothstein, Mary Anne Rossing, Barry Rosen, Harvey A. Risch, Susan J. Ramus, Elizabeth M. Poole, Malcolm C. Pike, Catherine M. Phelan, Jennifer Permuth-Wey, Liisa M. Pelttari, Tanja Pejovic, Celeste Leigh Pearce, Rachel Palmieri Weber, Sandra Orsulic, Irene Orlow, Sara H. Olson, Kunle Odunsi, Heli Nevanlinna, Roberta B. Ness, Lotte Nedergaard, Steven A. Narod, Kirsten B. Moysich, Francesmary Modugno, Usha Menon, Iain A. McNeish, John R. McLaughlin, Valerie McGuire, Keitaro Matsuo, Leon Massuger, Lene Lundvall, Jan Lubinski, Karen Lu, Jolanta Lissowska, Dong Liang, Douglas A. Levine, Jenny Lester, Arto Leminen, Shashi Lele, Alice W. Lee, Nhu D. Le, Sandrina Lambrechts, Diether Lambrechts, Jolanta Kupryjanczyk, Camilla Krakstad, Lambertus A. Kiemeney, Joseph Kelley, Melissa Kellar, Linda E. Kelemen, Susanne K. Kjaer, Beth Y. Karlan, Bu-Tian Ji, Allan Jensen, James Paul, Anna Jakubowska, Edwin S. Iversen, Satoyo Hosono, Claus K. Hogdall, Estrid Hogdall, Peter Hillemanns, Michelle A.T. Hildebrandt, Florian Heitz, Alexander Hein, Philipp Harter, Patricia Harrington, Jacek Grownwald, Marc T. Goodman, Ellen L. Goode, Rosalind Glasspool, Graham G. Giles, Aleksandra Gentry-Maharaj, Yu-Tang Gao, Brooke L. Fridley, Peter A. Fasching, Arif B. Ekici, Robert P. Edwards, Douglas F. Easton, Diana Eccles, Matthias Dürst, Andreas du Bois, Thilo Dörk, Jennifer A. Doherty, Ed Dicks, Joe Dennis, Agnieszka Dansonka-Mieszkowska, Cezary Cybulski, Julie M. Cunningham, Daniel Cramer, Linda S. Cook, Zhihua Chen, Yian Ann Chen, Jenny Chang-Claude, Karen Carty, Ian Campbell, Ralf Butzow, Angela Brooks-Wilson, Louise Brinton, Natalia Bogdanova, Line Bjørge, Maria Bisogna, Andrew Berchuck, Matthias W. Beckmann, Yukie T. Bean, Elisa V. Bandera, Helen Baker, Georgia Chenevix-Trench, Natalia Antonenkova, Hoda Anton-Culver, Katja K.H. Aben, Kate Lawrenson, Qiyuan Li, Jonathan P. Tyrer, and Siddhartha P. Kar

Abstract

Supplementary Tables S1-6, Figures S1-2. Supplementary Table S1: Summary of serous EOC GWAS data sets; Supplementary Table S2: Genes in the six significant co-expression networks; Supplementary Table S3: GSEA results after LD-based clumping of SNPs; Supplementary Table S4: GSEA results for the replication data set (COGS); Supplementary Table S5: GSEA results for all networks with > 10 genes; Supplementary Table S6: Number of intragenic SNPs and genes covered by SNPs in the different analyses; Supplementary Figure S1: Q-Q plots of the minimum P-value among all SNPs in each gene with and without the modified Sidak correction; Supplementary Figure S2: Disease Association Protein-Protein Link Evaluator (DAPPLE) protein-protein interaction network

Published
2023

17. Supplementary Methods from Genome-Wide Association Study Identifies a Possible Susceptibility Locus for Endometrial Cancer

Author

Xiao-Ou Shu, Amanda B. Spurdle, Qiuyin Cai, Yu-Tang Gao, Douglas Easton, Alison Dunning, Wei Lu, Hui Cai, Anthony Proietto, Alexander Hein, Mari K. Halle, Rayna K. Matsuno, An Coosemans, Louise Brinton, Maggie Gorman, Ben Zhang, Jiajun Shi, Geoffrey Otton, Arif B. Ekici, Camilla Krakstad, Pamela J. Thompson, Matthias Dürst, Dilyara Kaidarova, Lieve Coenegrachts, Jolanta Lissowska, Lingeng Lu, Kimberly Howarth, Ping-Ping Bao, Bu-Tian Ji, Katie Ashton, Matthias W. Beckmann, Jone Trovik, Galina Lurie, Anita Schwake, Nurzhan Turmanov, Frederic Amant, Hannah P. Yang, Harvey Risch, Shirley Hodgson, Catherine S. Healey, Tracy O'Mara, Ying Zheng, Ryan Delahanty, Rodney J. Scott, Peter A. Fasching, Helga B. Salvesen, Marc T. Goodman, Natalia Dubrowinskaja, Thilo Dörk, Diether Lambrechts, Nicolas Wentzensen, Herbert Yu, Ian Tomlinson, Deborah Thompson, Felicity Lose, Yong-Bing Xiang, Wei Zheng, and Jirong Long

Abstract

PDF file, 123KB, Detailed Description of the Case and Control Sample Sets.

Published
2023

18. Supplementary Table 4 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

Supplementary Table 4 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

19. Data from Tagging Single Nucleotide Polymorphisms in Cell Cycle Control Genes and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Paul D.P. Pharoah, Andrew Berchuck, Georgia Chenevix-Trench, C. Leigh Pearce, Joellen Schildkraut, Bruce A.J. Ponder, Ian Jacobs, Douglas F. Easton, Beata Peplonska, Jolanta Lissowska, Louise Brinton, Montserrat Garcia-Closas, Jeffrey R. Marks, Edwin S. Iversen, Malcolm C. Pike, Anna H. Wu, Thomas A. Sellers, Julie M. Cunningham, Fergus J. Couch, Ellen L. Goode, Kirsten B. Moysich, Robert P. Edwards, Roberta B. Ness, Francesmary Modugno, Michael E. Carney, Galina Lurie, Marc T. Goodman, David C. Whiteman, Adele C. Green, Jonathan Beesley, Penelope M. Webb, Valerie McGuire, Richard DiCioccio, Jan Blaeker, Claus Hogdall, Estrid Hogdall, Danielle Shadforth, Jonathan Tyrer, Lydia Quaye, Alice S. Whittemore, Susan Krüger Kjaer, Susan J. Ramus, Honglin Song, and Simon A. Gayther

Abstract

High-risk susceptibility genes explain CCND1, CCND2, CCND3, CCNE1, CDK2, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, and CDKN2D—and risk of invasive epithelial ovarian cancer. We used a two-stage, multicenter, case-control study. In stage 1, 88 SNPs that tag common variation in these genes were genotyped in three studies from the United Kingdom, United States, and Denmark (∼1,500 cases and 2,500 controls). Genotype frequencies in cases and controls were compared using logistic regression. In stage 2, eight other studies from Australia, Poland, and the United States (∼2,000 cases and ∼3,200 controls) were genotyped for the five most significant SNPs from stage 1. No SNP was significant in the stage 2 data alone. Using the combined stages 1 and 2 data set, CDKN2A rs3731257 and CDKN1B rs2066827 were associated with disease risk (unadjusted P trend = 0.008 and 0.036, respectively), but these were not significant after adjusting for multiple testing. Carrying the minor allele of these SNPs was found to be associated with reduced risk [OR, 0.91 (0.85–0.98) for rs3731257; and OR, 0.93 (0.87–0.995) for rs2066827]. In conclusion, we have found evidence that a single tagged SNP in both the CDKN2A and CDKN1B genes may be associated with reduced ovarian cancer risk. This study highlights the need for multicenter collaborations for genetic association studies. [Cancer Res 2007;67(7):3027–35]

Published
2023

20. Supplementary Figure 1 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

Supplementary Figure 1 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

21. Supplementary Tables 1-4 from Tagging Single Nucleotide Polymorphisms in Cell Cycle Control Genes and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Paul D.P. Pharoah, Andrew Berchuck, Georgia Chenevix-Trench, C. Leigh Pearce, Joellen Schildkraut, Bruce A.J. Ponder, Ian Jacobs, Douglas F. Easton, Beata Peplonska, Jolanta Lissowska, Louise Brinton, Montserrat Garcia-Closas, Jeffrey R. Marks, Edwin S. Iversen, Malcolm C. Pike, Anna H. Wu, Thomas A. Sellers, Julie M. Cunningham, Fergus J. Couch, Ellen L. Goode, Kirsten B. Moysich, Robert P. Edwards, Roberta B. Ness, Francesmary Modugno, Michael E. Carney, Galina Lurie, Marc T. Goodman, David C. Whiteman, Adele C. Green, Jonathan Beesley, Penelope M. Webb, Valerie McGuire, Richard DiCioccio, Jan Blaeker, Claus Hogdall, Estrid Hogdall, Danielle Shadforth, Jonathan Tyrer, Lydia Quaye, Alice S. Whittemore, Susan Krüger Kjaer, Susan J. Ramus, Honglin Song, and Simon A. Gayther

Abstract

Supplementary Tables 1-4 from Tagging Single Nucleotide Polymorphisms in Cell Cycle Control Genes and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

22. Supplementary Table 2 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

Supplementary Table 2 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

23. Supplementary Table 3 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

Supplementary Table 3 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

24. Data from Risk of Ovarian Cancer and the NF-κB Pathway: Genetic Association with IL1A and TNFSF10

Author

Ellen L. Goode, Brooke L. Fridley, Julie M. Cunningham, Keith L. Knutson, Kirsten Moysich, Paul D.P. Pharoah, Linda E. Kelemen, Piotr Sobiczewski, Michelle A.T. Hildebrandt, Montserrat Garcia-Closas, Ignace Vergote, Joseph H. Rothstein, Grace Friel, Francesmary Modugno, Arto Leminen, Lynne R. Wilkens, Arif B. Ekici, Janusz Menkiszak, Urmila Chandran, Ira Schwaab, Aleksandra Gentry-Maharaj, Mari K. Halle, David van den Berg, Anne M. Van Altena, Liisa M. Pelttari, Matthias W. Beckmann, Hannah Yang, Sandrina Lambrechts, Lukasz M. Szafron, Shan Wang-Gohrke, Lene Lundvall, Andreas du Bois, Jenny Lester, Valerie McGuire, Robert Edwards, Lara Sucheston, Jie Lin, Cezary Cybulski, Elisabeth Wik, Susan J. Ramus, Malcolm C. Pike, Katja K. Aben, Angela Brooks-Wilson, Allison F. Vitonis, Jonathan Tyrer, Philipp Harter, Sara H. Olson, Agnieszka Dansonka-Mieszkowska, Anja Rudolph, Alexander Hein, Louise Brinton, Evelyn Despierre, Christine Walsh, Argyrios Ziogas, Galina Lurie, Yukie T. Bean, Heli Nevanlinna, Jan Lubiński, Allan Jensen, Andrew Berchuck, Kunle Odunsi, Dong Liang, Camilla Krakstad, Jennifer A. Doherty, Honglin Song, Leon F.A.G. Massuger, Robert Brown, Catherine M. Phelan, James M. Flanagan, Daniel Cramer, Susanne Kruger Kjaer, Douglas A. Levine, Celeste Leigh Pearce, Joellen Schildkraut, Usha Menon, Peter A. Fasching, Diether Lambrechts, Claus K. Hogdall, Jacek Gronwald, Hoda Anton-Culver, Beth Y. Karlan, Stanley B. Kaye, Florian Heitz, Estrid Hogdall, Simon A. Gayther, Anna H. Wu, James Paul, Diana Eccles, Ingo B. Runnebaum, Natalia Bogdanova, Clareann H. Bunker, Nhu D. Le, Ian Campbell, Tanja Pejovic, Thilo Dörk, Ralf Butzow, Karen Lu, Jolanta Kupryjanczyk, Steven A. Narod, Roberta B. Ness, Mary Anne Rossing, Linda S. Cook, Pamela J. Thompson, Marc T. Goodman, Kathryn Terry, Irene Orlow, Elisa V. Bandera, Jenny Chang-Claude, Weiva Sieh, Alice S. Whittemore, Georgia Chenevix-Trench, Nicolas Wentzensen, Britton Trabert, Gianluca Severi, Graham G. Giles, Laura Baglietto, Lambertus A. Kiemeney, Helga B. Salvesen, Harvey A. Risch, Elizabeth Poole, Shelley S. Tworoger, Thomas A. Sellers, David N. Rider, Zachary Fogarty, Kimberly R. Kalli, Robert A. Vierkant, William R. Bamlet, Matthew S. Block, and Bridget Charbonneau

Abstract

A missense single-nucleotide polymorphism (SNP) in the immune modulatory gene IL1A has been associated with ovarian cancer risk (rs17561). Although the exact mechanism through which this SNP alters risk of ovarian cancer is not clearly understood, rs17561 has also been associated with risk of endometriosis, an epidemiologic risk factor for ovarian cancer. Interleukin-1α (IL1A) is both regulated by and able to activate NF-κB, a transcription factor family that induces transcription of many proinflammatory genes and may be an important mediator in carcinogenesis. We therefore tagged SNPs in more than 200 genes in the NF-κB pathway for a total of 2,282 SNPs (including rs17561) for genotype analysis of 15,604 cases of ovarian cancer in patients of European descent, including 6,179 of high-grade serous (HGS), 2,100 endometrioid, 1,591 mucinous, 1,034 clear cell, and 1,016 low-grade serous, including 23,235 control cases spanning 40 studies in the Ovarian Cancer Association Consortium. In this large population, we confirmed the association between rs17561 and clear cell ovarian cancer [OR, 0.84; 95% confidence interval (CI), 0.76–0.93; P = 0.00075], which remained intact even after excluding participants in the prior study (OR, 0.85; 95% CI, 0.75–0.95; P = 0.006). Considering a multiple-testing–corrected significance threshold of P < 2.5 × 10−5, only one other variant, the TNFSF10 SNP rs6785617, was associated significantly with a risk of ovarian cancer (low malignant potential tumors OR, 0.85; 95% CI, 0.79–0.91; P = 0.00002). Our results extend the evidence that borderline tumors may have a distinct genetic etiology. Further investigation of how these SNPs might modify ovarian cancer associations with other inflammation-related risk factors is warranted. Cancer Res; 74(3); 852–61. ©2013 AACR.

Published
2023

25. Supplementary Figure 2 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

Supplementary Figure 2 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

26. Supplementary Tables 1 - 5 from Risk of Ovarian Cancer and the NF-κB Pathway: Genetic Association with IL1A and TNFSF10

Author

Ellen L. Goode, Brooke L. Fridley, Julie M. Cunningham, Keith L. Knutson, Kirsten Moysich, Paul D.P. Pharoah, Linda E. Kelemen, Piotr Sobiczewski, Michelle A.T. Hildebrandt, Montserrat Garcia-Closas, Ignace Vergote, Joseph H. Rothstein, Grace Friel, Francesmary Modugno, Arto Leminen, Lynne R. Wilkens, Arif B. Ekici, Janusz Menkiszak, Urmila Chandran, Ira Schwaab, Aleksandra Gentry-Maharaj, Mari K. Halle, David van den Berg, Anne M. Van Altena, Liisa M. Pelttari, Matthias W. Beckmann, Hannah Yang, Sandrina Lambrechts, Lukasz M. Szafron, Shan Wang-Gohrke, Lene Lundvall, Andreas du Bois, Jenny Lester, Valerie McGuire, Robert Edwards, Lara Sucheston, Jie Lin, Cezary Cybulski, Elisabeth Wik, Susan J. Ramus, Malcolm C. Pike, Katja K. Aben, Angela Brooks-Wilson, Allison F. Vitonis, Jonathan Tyrer, Philipp Harter, Sara H. Olson, Agnieszka Dansonka-Mieszkowska, Anja Rudolph, Alexander Hein, Louise Brinton, Evelyn Despierre, Christine Walsh, Argyrios Ziogas, Galina Lurie, Yukie T. Bean, Heli Nevanlinna, Jan Lubiński, Allan Jensen, Andrew Berchuck, Kunle Odunsi, Dong Liang, Camilla Krakstad, Jennifer A. Doherty, Honglin Song, Leon F.A.G. Massuger, Robert Brown, Catherine M. Phelan, James M. Flanagan, Daniel Cramer, Susanne Kruger Kjaer, Douglas A. Levine, Celeste Leigh Pearce, Joellen Schildkraut, Usha Menon, Peter A. Fasching, Diether Lambrechts, Claus K. Hogdall, Jacek Gronwald, Hoda Anton-Culver, Beth Y. Karlan, Stanley B. Kaye, Florian Heitz, Estrid Hogdall, Simon A. Gayther, Anna H. Wu, James Paul, Diana Eccles, Ingo B. Runnebaum, Natalia Bogdanova, Clareann H. Bunker, Nhu D. Le, Ian Campbell, Tanja Pejovic, Thilo Dörk, Ralf Butzow, Karen Lu, Jolanta Kupryjanczyk, Steven A. Narod, Roberta B. Ness, Mary Anne Rossing, Linda S. Cook, Pamela J. Thompson, Marc T. Goodman, Kathryn Terry, Irene Orlow, Elisa V. Bandera, Jenny Chang-Claude, Weiva Sieh, Alice S. Whittemore, Georgia Chenevix-Trench, Nicolas Wentzensen, Britton Trabert, Gianluca Severi, Graham G. Giles, Laura Baglietto, Lambertus A. Kiemeney, Helga B. Salvesen, Harvey A. Risch, Elizabeth Poole, Shelley S. Tworoger, Thomas A. Sellers, David N. Rider, Zachary Fogarty, Kimberly R. Kalli, Robert A. Vierkant, William R. Bamlet, Matthew S. Block, and Bridget Charbonneau

Abstract

PDF file - 145K, Supplementary Table 1. Studies in the Ovarian Cancer Association Consortium (OCAC) are listed, as well as the abbreviation, location, type, and number of cases and controls for each study. Supplementary Table 2. The number of cases included in the analysis from each OCAC study site is listed by histologic subtype. Supplementary Table 3. Gene symbols and IDs are listed for NF-κB pathway genes that were tagged in this study, as well as chromosome position, number of SNPs tagged, and bin coverage of each gene using Hapmap or 1000 genomes as a reference. Supplementary Table 4. Reasons and numbers of samples excluded from the analysis following the sample quality control are described. Supplementary Table 5. We evaluated rs17561 and rs6785617 for interactions with known epidemiologic risk factors for risk of clear cell and LMP tumors, respectively, and report interaction p-values in the table below.

Published
2023

27. Data from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

The p53 protein is critical for multiple cellular functions including cell growth and DNA repair. We assessed whether polymorphisms in the region encoding TP53 were associated with risk of invasive ovarian cancer. The study population includes a total of 5,206 invasive ovarian cancer cases (2,829 of which were serous) and 8,790 controls from 13 case-control or nested case-control studies participating in the Ovarian Cancer Association Consortium (OCAC). Three of the studies performed independent discovery investigations involving genotyping of up to 23 single nucleotide polymorphisms (SNP) in the TP53 region. Significant findings from this discovery phase were followed up for replication in the other OCAC studies. Mixed effects logistic regression was used to generate posterior median per allele odds ratios (OR), 95% probability intervals (PI), and Bayes factors (BF) for genotype associations. Five SNPs showed significant associations with risk in one or more of the discovery investigations and were followed up by OCAC. Mixed effects analysis confirmed associations with serous invasive cancers for two correlated (r2 = 0.62) SNPs: rs2287498 (median per allele OR, 1.30; 95% PI, 1.07–1.57) and rs12951053 (median per allele OR, 1.19; 95% PI, 1.01–1.38). Analyses of other histologic subtypes suggested similar associations with endometrioid but not with mucinous or clear cell cancers. This large study provides statistical evidence for a small increase in risk of ovarian cancer associated with common variants in the TP53 region. [Cancer Res 2009;69(6):2349–57]

Published
2023

28. Supplementary Table 1 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Author

Montserrat Garcia-Closas, Mark Sherman, Stephen Chanock, Brian Calingaert, Shelley S. Tworoger, Susan E. Hankinson, Daniel W. Cramer, Kathryn L. Terry, Argyrios Ziogas, Hoda Anton-Culver, Lydia Quaye, Valerie McGuire, Alice S. Whittemore, Paul D.P. Pharoah, Honglin Song, Douglas F. Easton, Claus Hogdall, Jan Blaakaer, Estrid Hogdall, Susanne Krüger Kjaer, Ian Jacobs, Susan J. Ramus, Simon A. Gayther, Pamela J. Thompson, Michael E. Carney, Galina Lurie, Marc T. Goodman, Rebecca Anderson, Christopher K. Elund, David Conti, David Van Den Berg, Anna H. Wu, Leigh Pearce, Thomas A. Sellers, Rebecca Sutphen, Catherine Phelan, Xiaoqing Chen, Jonathan Beesley, Penelope M. Webb, Georgia Chenevix-Trench, David N. Rider, Robert A. Vierkant, Julie M. Cunningham, Beata Peplonska, Louise Brinton, Jolanta Lissowska, Jeffrey R. Marks, Andrew Berchuck, Patricia G. Moorman, Edwin S. Iversen, Merlise A. Clyde, Ellen L. Goode, and Joellen M. Schildkraut

Abstract

Supplementary Table 1 from Single Nucleotide Polymorphisms in the TP53 Region and Susceptibility to Invasive Epithelial Ovarian Cancer

Published
2023

29. DBT

Author

Louise Brinton Clarke

Subjects
education, humanities
Abstract

This chapter describes the author’s personal experience in DBT, both the challenges and the successes. Having lived a life of trauma, accompanied by repeated patterns of invalidation from both without and within, the author entered DBT as a textbook case. Borderline personality disorder (BPD) was discussed when the author was 15 years old; she was diagnosed at age 18. She battled with the diagnosis and often focused on its perceived injustice, instead of addressing what could be changed. The author spent a year in DBT as a client, and a further year as a graduate facilitator. She uses the skills she learned regularly; she feels more in control and no longer makes things worse. The author recognizes that there are pros and cons to DBT treatment, and that DBT treatment may not be suitable for everyone.

Published
2018

30. Abstract LB-178: Performance of breast cancer polygenic risk score (PRS) in a Ghanaian population

Author

Thomas U. Ahearn, Andriy Derkach, Joel Yarney, Beatrice Wiafe Addai, Baffour Awuah, Louise Brinton, Nilanjan Chatterjee, Jonine D. Figueroa, and Montserrat Garcia-Closas

Subjects
Cancer Research, Oncology
Abstract

Background: Three breast cancer PRSs comprised of 313 single nucleotide polymorphisms (SNPs) have been developed and validated in women of European ancestry for predicting risk for overall, estrogen receptor-positive (ER+), and ER-negative (ER-) disease[1]. We evaluated the associations of these PRSs with breast cancer risk in Ghanaian women Methods: Analyses included 899 cases (296 ER+, 277 ER-, and 326 unknown ER status) diagnosed with invasive (n=888) or in situ (n=11) breast cancer and 1,630 population-based controls from the Ghana Breast Health Study (GBHS). The 313 SNPs were determined using the Illumina Global Screening Array (66 SNPs genotyped and 247 SNPs imputed to the 1000 genome phase 3 reference panel). Three PRSs were calculated based on 313 SNPs for overall, ER+ and ER- disease using log odds ratios (OR) published by the Breast Cancer Association Consortium (BCAC)[1]. Multivariable logistic regression was used to estimate ORs and 95% confidence intervals (95% CI) between percentiles of PRS and breast cancer risk. Results: The mean PRS was higher in GBHS controls than BCAC controls for overall PRS (GBHS: mean= 0.14, standard deviation (SD)=0.51; BCAC: mean=-0.42, SD=0.61), ER+ PRS (GBHS: mean= 0.10, SD=0.55; BCAC: mean=-0.41, SD=0.65), and ER- PRS (GBHS: mean= 0.30, SD=0.51, BCAC: mean=-0.31; SD=0.59). The shift in mean was explained by protective alleles tending to be more common in BCAC and risk alleles with the largest effect sizes tending to be more common in GBHS. The OR per SD in GBHS was 1.22 (95% CI=1.13-1.33) for overall, 1.34 (1.19-1.52) for ER+, and 1.14 (1.00-1.29) for ER- disease. These risk estimates are lower than previously reported in BCAC [1]. Based on the distributions of each of the three PRSs in the GBHS controls, women at the top 5% PRS percentile compared with women at average risk (40-60% PRS percentile) were at higher risk for overall (OR=2.17 (95% CI=1.51-3.11)), ER+(2.71 (1.63-4.50)), and ER- disease (1.47 (0.81-2.49)). On the other hand, women at the lowest 5% PRS percentile were not at a significantly decreased risk, as would have been expected, for overall (1.11 (0.73-1.69)), ER+(0.91 (0.46-1.83)), and ER- disease (0.99 (0.55-1.80)). Conclusion: Our results show that the breast cancer 313-SNP PRS developed in women of European ancestry predicts risk of breast cancer in Ghanaian women; however, the level of risk stratification is smaller, particularly for women with lower PRSs. These results are likely due to differences in linkage disequilibrium, allele frequencies, and/or genetic architecture between populations. Further work to develop population-specific PRSs is needed to improve risk stratification in women of West African ancestry. 1. Mavaddat, N., et al., Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes. Am J Hum Genet, 2018. Citation Format: Thomas U. Ahearn, Andriy Derkach, Joel Yarney, Beatrice Wiafe Addai, Baffour Awuah, Louise Brinton, Nilanjan Chatterjee, Jonine D. Figueroa, Montserrat Garcia-Closas. Performance of breast cancer polygenic risk score (PRS) in a Ghanaian population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-178.

Published
2019

31. RE. 'TWIN MEMBERSHIP AND BREAST CANCER RISK'

Author

M. Miles Braun, Neil E. Caporaso, Louise Brinton, and William F. Page

Subjects
Oncology, medicine.medical_specialty, Breast cancer, Text mining, Epidemiology, business.industry, Internal medicine, medicine, medicine.disease, business
Published
1994

32. Intake of fruits, and vegetables in relation to breast cancer risk by hormone receptor status.

Author

Mia Gaudet, Louise Brinton, Beata Peplonska, Mark Sherman, Neonila Szeszenia-Dabrowska, Witold Zatonski, and Montserrat Garcia-Closas

Subjects
MEDICAL research, BREAST cancer, DISEASE risk factors, ONCOLOGY
Abstract

Summary  The inconsistent associations between fruit and vegetable intake and breast cancer risk may be due to heterogeneity of associations by estrogen (ER) and progesterone receptor (PR) status of the tumors. We evaluated this hypothesis in a large (2,386 cases and 2,503 controls) population-based case-control study in Poland, conducted between 2000 and 2003. We observed significant associations between reduced overall risk of breast cancer and increasing levels of total fruit intake (odds ratio (OR) for highest versus lowest quartile = 0.76, 95%CI = 0.63–0.91; p-trend = 0.01), but not for total vegetable intake (1.13 (0.93–1.37), p-trend = 0.25), after controlling for age, energy intake and known risk factors for breast cancer. The inverse association with total fruit intake was stronger for risk of ER (0.69 (0.54–0.88), p-trend = 0.01) than ER− tumors (0.89 (0.67–1.19), p-trend = 0.57) (p-heterogeneity = 0.02). In conclusion, this study suggests that fruit intake might have differential associations for breast tumor subtypes defined by ER status. [ABSTRACT FROM AUTHOR]

Published
2008

33. Estimating age-specific breast cancer risks: a descriptive tool to identify age interactions.

Author

Rayna Matsuno, Mark Sherman, Mitchell Gail, Louise Brinton, Xiaohong Yang, Beata Peplonska, Bingshu Chen, Philip Rosenberg, Nilanjan Chatterjee, Neonila Szeszenia-Dąbrowska, Alicja Bardin-Mikolajczak, Witold Zatonski, Susan Devesa, and Montserrat García-Closas

Subjects
CANCER in women, CANCER patients, WOMEN'S history, BREAST cancer
Abstract

AbstractObjective??Clarifying age-specific female breast cancer risks and interactions may provide important etiologic clues.Method??Using a population-based case?control study in Poland (2000?2003) of 2,386 incident breast cancer cases and 2,502 control subjects aged 25?74 years, we estimated age-specific breast cancer incidence rates according to risk factors.Results??Breast cancer risks were elevated among women with positive family history (FH), younger age at menarche, older age at first full-term birth, nulliparity, exogenous hormonal usage, and reduced physical activity (PA). Notwithstanding overall risks, we observed statistically significant quantitative (non-crossover) and qualitative (crossover) age interactions for all risk factors except for FH and PA. For example, nulliparity compared to parity reduced breast cancer risk among women ages 25?39 years then rates crossed or reversed, after which nulliparity increased relative risks among women ages 40?74 years.Conclusion??Though quantitative age interactions could be expected, qualitative interactions were somewhat counterintuitive. If confirmed in other populations, qualitative interactions for a continuous covariate such as age will be difficult to reconcile in a sequential (multistep or monolithic) ?stochastic? breast cancer model. Alternatively, the reversal of relative risks among younger and older women suggests subgroup heterogeneity with different etiologic mechanisms for early-onset and late-onset breast cancer types. [ABSTRACT FROM AUTHOR]

Published
2007

34. Interrelationships between serum leptin, IGF-1, IGFBP3, C-peptide and prolactin and breast cancer risk in young women.

Author

Roni Falk, Louise Brinton, M. Madigan, Nancy Potischman, Susan Sturgeon, Kathleen Malone, and Janet Daling

Abstract

Epidemiologic evidence suggests obese premenopausal women experience a reduced risk of breast cancer. The mechanism underlying this protection is not fully understood although it is well documented that abdominal obesity may impair ovulatory function and reduce gonadal steroidogenesis. We measured levels of several metabolic markers that are modified by obesity [measured by body mass index (BMI, (weight (kg)/height (m2)))] and play a role in the reproductive axis, including, leptin, insulin-like growth factor I (IGF-I), insulin-like growth factor binding protein 3 (IGFBP3), C-peptide and prolactin in 233 cases and 251 controls participating in a retrospective study of breast cancer in young women conducted in the Seattle/Puget Sound region between 1990 and 1992. Consistent with the finding of a reduced risk with increasing BMI, risks declined with leptin levels, although to a lesser degree with odds ratios (OR) for the highest vs. lowest quartile of BMI=0.34 (95% C.I. 0.3–0.8) and for leptin=0.71 (95% C.I. 0.5–1.3). IGF-I, IGFBP3, C-peptide and prolactin were not related to breast cancer risk in a dose-dependent manner. With the possible exception of leptin, our findings do not suggest that these markers explain the breast cancer protection provided by obesity in premenopausal women. [ABSTRACT FROM AUTHOR]

Published
2006
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