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1. Double somatic mismatch repair gene pathogenic variants as common as Lynch syndrome among endometrial cancer patients

Author

Hampel, Heather, Pearlman, Rachel, de la Chapelle, Albert, Pritchard, Colin C, Zhao, Weiqiang, Jones, Dan, Yilmaz, Ahmet, Chen, Wei, Frankel, Wendy L, Suarez, Adrian A, Cosgrove, Casey, Backes, Floor, Copeland, Larry, Fowler, Jeffrey, O'Malley, David, Salani, Ritu, McElroy, Joseph P, Stanich, Peter P, Goodfellow, Paul, and Cohn, David E

Subjects
Adult, Oncology and Carcinogenesis, DNA Mismatch Repair, Mismatch repair, Paediatrics and Reproductive Medicine, Young Adult, Rare Diseases, Clinical Research, Double somatic, 80 and over, Genetics, Humans, 2.1 Biological and endogenous factors, Somatic, Oncology & Carcinogenesis, Aetiology, Germ-Line Mutation, Neoplasm Staging, Aged, Cancer, DNA Methylation, Middle Aged, Endometrial Neoplasms, Colo-Rectal Cancer, Hereditary Nonpolyposis, Lynch syndrome, Neoplasm, Female, Colorectal Neoplasms, MutL Protein Homolog 1, Digestive Diseases, Endometrial
Abstract

ObjectiveLynch syndrome is the most common cause of inherited endometrial cancer, attributable to germline pathogenic variants (PV) in mismatch repair (MMR) genes. Tumor microsatellite instability (MSI-high) and MMR IHC abnormalities are characteristics of Lynch syndrome. Double somatic MMR gene PV also cause MSI-high endometrial cancers. The aim of this study was to determine the relative frequency of Lynch syndrome and double somatic MMR PV.Methods341 endometrial cancer patients enrolled in the Ohio Colorectal Cancer Prevention Initiative at The Ohio State University Comprehensive Cancer Center from 1/1/13-12/31/16. All tumors underwent immunohistochemical (IHC) staining for the four MMR proteins, MSI testing, and MLH1 methylation testing if the tumor was MMR-deficient (dMMR). Germline genetic testing for Lynch syndrome was undertaken for all cases with dMMR tumors lacking MLH1 methylation. Tumor sequencing followed if a germline MMR gene PV was not identified.ResultsTwenty-seven percent (91/341) of tumors were either MSI-high or had abnormal IHC indicating dMMR. As expected, most dMMR tumors had MLH1 methylation; (69, 75.8% of the dMMR cases; 20.2% of total). Among the 22 (6.5%) cases with dMMR not explained by methylation, 10 (2.9% of total) were found to have Lynch syndrome (6 MSH6, 3 MSH2, 1 PMS2). Double somatic MMR PV accounted for the remaining 12 dMMR cases (3.5% of total).ConclusionsSince double somatic MMR gene PV are as common as Lynch syndrome among endometrial cancer patients, paired tumor and germline testing for patients with non-methylated dMMR tumor may be the most efficient approach for LS screening.

Published
2021

2. Functional characterization of recurrent FOXA2 mutations seen in endometrial cancers

Author

Neff, Robert, Rush, Craig M., Smith, Blair, Backes, Floor J., Cohn, David E., and Goodfellow, Paul J.

Subjects
Transcription, Genetic, respiratory system, Cadherins, Article, Cell Line, Endometrial Neoplasms, DNA-Binding Proteins, Protein Transport, HEK293 Cells, Cell Line, Tumor, embryonic structures, Mutation, Hepatocyte Nuclear Factor 3-beta, Humans, Female, reproductive and urinary physiology
Abstract

FOXA2, a member of the forkhead family of DNA-binding proteins, is frequently mutated in uterine cancers. Most of the mutations observed in uterine cancers are frameshifts and stops. FOXA2 is considered to be a driver gene in uterine cancers, functioning as a haploinsufficient tumor suppressor. The functional consequences of FOXA2 mutations, however, have not yet been determined. We evaluated the effects that frameshift mutations as well as a recurrent missense mutation have on FOXA2 transcriptional activity. Recurrent N-terminal frameshifts resulted in truncated proteins that failed to translocate to the nucleus and have no transcriptional activity using an E-cadherin/luciferase reporter assay. Protein abundance was reduced for the recurrent p.S169W mutation, as was transcriptional activity. A C-terminal frameshift mutation had increased FOXA2 levels evidenced by both Western blot and immunofluorescence. Given that FOXA2 is a recognized activator of E-cadherin (CDH1) expression and E-cadherin’s potential role in epithelial-to-mesenchymal transition in a wide range of cancer types, we tested the hypothesis that FOXA2 mutations in primary uterine cancer specimens would be associated with reduced CDH1 transcript levels. qRT-PCR revealed significantly lower levels of CDH1 expression in primary tumors with FOXA2 mutations. Our findings in vitro and in vivo suggest that reduced transcriptional activity associated with FOXA2 mutations in uterine cancers is likely to contribute to pro-tumorigenic changes in gene expression.

Published
2018

3. Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing

Author

Le Gallo, Matthieu, Rudd, Meghan L., Urick, Mary Ellen, Hansen, Nancy F., Zhang, Suiyuan, Lozy, Fred, Sgroi, Dennis C., Bel, August Vidal, Matias-Guiu, Xavier, Broaddus, Russell R., Lu, Karen H., Levine, Douglas A., Mutch, David G., Goodfellow, Paul J., Salvesen, Helga B., Mullikin, James C., and Bell, Daphne W.

Subjects
Mutation, Humans, Exome, Precision Medicine, Article, Adenocarcinoma, Clear Cell, Endometrial Neoplasms
Published
2017

4. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author

Milne, Roger L., Kuchenbaecker, Karoline B., Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindstrom, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary, Bolla, Manjeet K., McGuffog, Lesley, Wang, Qin, Aalfs, Cora M., Abctctb, Investigators, Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittom, Kristiina Äki, Fares, Al Ejeh, Allen, Jamie, Ambrosone, Christine B., Amos, Christopher I., Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J., Auber, Bernd, Auer, Paul L., Ausems, Margreet G.M., Azzollini, Jacopo, François, Bacot, Balma, Judith Nã, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B., Barrdahl, Myrto, Barnes, Daniel, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W., Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Bignon, Yves Jean, Blazer, Kathleen R., Blok, Marinus J., Blomqvist, Carl, Blot, William, Bobolis, Kristie, Boeckx, Bram, Bogdanova, Natalia V., Bojesen, Anders, Bojesen, Stig E., Bonanni, Bernardo, Anne-Lise, Børresen Dale, Bozsik, Aniko, Bradbury, Angela R., Brand, Judith S., Brauch, Hiltrud, Brenner, Hermann, Brigitte, Bressac De Paillerets, Brewer, Carole, Brinton, Louise, Broberg, Per, Angela, Brooks Wilson, Brunet, Joan, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byun, Jinyoung, Cai, Qiuyin, Cald, Trinidad És, Caligo, Maria A., Campbell, Ian, Canzian, Federico, Caron, Olivier, Carracedo, Angel, Carter, Brian D., Esteban, Castelao, Castera, Laurent, Virginie, Caux Moncoutier, Chan, Salina B., Jenny, Chang Claude, Chanock, Stephen J., Chen, Xiaoqing, Cheng, Ting Yuan David, Chiquette, Jocelyne, Christiansen, Hans, Claes, Kathleen B., Clarke, Christine L., Conner, Thomas, Conroy, Don M., Cook, Jackie, Cordina-Duverger, Emilie, Cornelissen, Sten, Coupier, Isabelle, Cox, Angela, Cox, David G., Cross, Simon S., Cuk, Katarina, Cunningham, J. M., Czene, Kamila, Daly, Mary B., Damiola, Francesca, Darabi, Hatef, Davidson, Rosemarie, Leeneer, Kim De L., Devilee, Peter, Dicks, Ed, Diez, Orland, Ding, Yuan Chun, Ditsch, Nina, Doheny, Kimberly F., Domchek, Susan M., Dorfling, Cecilia M., Dörk, Thilo, Dos-Santos-Silva, Isabel, Dubois, Stéphane, Dugué, Pierre Antoine, Dumont, Martine, Dunning, Alison M., Durcan, Lorraine, Dwek, Miriam, Dworniczak, Bernd, Eccles, Diana, Eeles, Ros, Ehrencrona, Hans, Eilber, Ursula, Ejlertsen, Bent, Ekici, Arif B., Eliassen, A. Heather, Engel, Christoph, Eriksson, Mikael, Fachal, Laura, Faivre, Laurence, Fasching, Peter A., Faust, Ulrike, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Foulkes, William D., Friedman, Eitan, Fritschi, Lin, Frost, Debra, Gabrielson, Marike, Gaddam, Pragna, Gammon, Marilie D., Ganz, Patricia A., Gapstur, Susan M., Garber, Judy, Garcia-Barberan, Vanesa, Garciá-Saénz, José A., Gaudet, Mia M., Gauthier-Villars, Marion, Gehrig, Andrea, Georgoulias, Vassilios, Gerdes, Anne Marie, Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., González-Neira, Anna, Goodfellow, Paul, Greene, Mark H., Grenaker, Grethe Alnæs I., Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Gschwantler, Daphne Kaulich, Guénel, Pascal, Guo, Qi, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hallberg, Emily, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Hansen, Thomas V., Harrington, Patricia, Hart, Steven N., Hartikainen, Jaana M., Healey, Catherine S., Hein, Alexander, Helbig, Sonja, Henderson, Alex, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Hodgson, Shirley, Hogervorst, Frans B., Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Bob, Hopper, John L., Hu, Chunling, Huang, Guanmengqian, Hulick, Peter J., Humphreys, Keith, Hunter, David J., Imyanitov, Evgeny N., Isaacs, Claudine, Iwasaki, Motoki, Izatt, Louise, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, Jensen, Uffe Birk, John, Esther M., Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kast, Karin, Keeman, Renske, Kerin, Michael J., Kets, Carolien M., Keupers, Mac Hteld, Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I., Kim, Sung Won, Knight, Julia A., Konstantopoulou, Irene, Kosma, Veli Matti, Kristensen, Vessela N., Kruse, Torben A., Kwong, Ava, Lænkholm, Anne Vibeke, Laitman, Yael, Lalloo, Fiona, Lambrechts, Diether, Landsman, Keren, Lasset, Christine, Lazaro, Conxi, Marchand, Loic Le, Lindström, Sara, Al-Ejeh, Fares, Margreet, G. M.Ausems, Bacot, François, Børresen-Dale, Anne Lise, Bressac-De, Brigitte Paillerets, Brooks-Wilson, Angela, Castelao, J. Esteban, Caux-Moncoutier, Virginie, Chang-Claude, Jenny, McLaes, Kathleen B., Leeneer, Kim De, Dieter, Flesch Janys, Gschwantler-Kaulich, Daphne, Keupers, MacHteld, Lecarpentier, Julie, Lee, Andrew, Lee, Eunjung, Won, Jong Lee, Lee, Min Hyuk, Lejbkowicz, Flavio, Lesueur, Fabienne, Li, Jingmei, Lilyquist, Jenna, Lincoln, Anne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing Yee, Loibl, Sibylle, Long, Jirong, Loud, Jennifer T., Lubinski, Jan, Luccarini, Craig, Lush, Michael, MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Malone, Kathleen E., Siranoush, Manoukian, Manson, Joann E., Margolin, Sara, Martens, John W., Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, Mazoyer, Sylvie, McLean, Catriona, Meijers-Heijboer, Hanne, Menéndez, Primitiva, Meyer, Jeffery, Miao, Hui, Miller, Austin, Miller, Nicola, Mitchell, Gillian, Montagna, Marco, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Nadesan, Sue, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Nevelsteen, Ines, Niederacher, Dieter, Nielsen, Sune F., Nordestgaard, Børge G., Norman, Aaron, Nussbaum, Robert L., Olah, Edith, Olopade, Olufunmilayo I., Olson, Janet E., Olswold, Curtis, Ong, Kai Ren, Oosterwijk, Jan C., Orr, Nick, Osorio, Ana, Pankratz, V. Shane, Papi, Laura, Park-Simon, Tjoung Won, Paulsson-Karlsson, Ylva, Lloyd, Rachel, Pedersen, Inge Søkilde, Peissel, Bernard, Peixoto, Ana, Perez, Jose I., Peterlongo, Paolo, Peto, Julian, Pfeiler, Georg, Phelan, Catherine M., Pinchev, Mila, Plaseska-Karanfilska, Dijana, Poppe, Bruce, Porteous, Mary E., Prentice, Ross, Presneau, Nadege, Prokofieva, Darya, Pugh, Elizabeth, Pujana, Miquel Angel, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rantala, Johanna, Rappaport-Fuerhauser, Christine, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Rhiem, Kerstin, Richardson, Andrea, Rodriguez, Gustavo C., Romero, Atocha, Romm, Jane, Rookus, Matti A., Rudolph, Anja, Ruediger, Thomas, Saloustros, Emmanouil, Sanders, Joyce, Sandler, Dale P., Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Daniel F., Schoemaker, Minouk J., Schumacher, Fredrick, Schürmann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J., Seal, Sheila, Senter, Leigha, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen Yang, Sheng, Xin, Shimelis, Hermela, Shrubsole, Martha J., Shu, Xiao Ou, Side, Lucy E., Singer, Christian F., Sohn, Christof, Southey, Melissa C., Spinelli, John J., Spurdle, Amanda B., Stegmaier, Christa, Stoppa-Lyonnet, Dominique, Sukiennicki, Grzegorz, Surowy, Harald, Sutter, Christian, Swerdlow, Anthony, Szabo, Csilla I., Tamimi, Rulla M., Tan, Yen Y., Taylor, Jack A., Tejada, Maria Isabel, Tengström, Maria, Teo, Soo H., Terry, Mary B., Tessier, Daniel C., Teul, Alex E., Thöne, Kathrin, Thull, Darcy L., Tibiletti, Maria Grazia, Tihomirova, Laima, Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A.M., Tomlinson, Ian, Tong, Ling, Torres, Diana, Tranchant, Martine, Truong, Thérèse, Tucker, Kathy, Tung, Nadine, Tyrer, Jonathan, Ulmer, Hans Ulrich, Vachon, Celine, Christi, Van Asperen J., Den Berg, David Van, Ouweland, Ans M.Vanden, Rensburg, Elizabeth J., Varesco, Liliana, Varon-Mateeva, Raymonda, Vega, Ana, Viel, Alessandra, Vijai, Joseph, Vincent, Daniel, Vollenweider, Jason, Walker, Lisa, Wang, Zhaoming, Wang-Gohrke, Shan, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wendt, Camilla, Wesseling, Jelle, Whittemore, Alice S., Wijnen, Juul T., Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Xia, Lucy, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zaffaroni, Daniela, Zheng, Wei, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Zorn, Kristin K., Gago-Dominguez, Manuela, Mannermaa, Arto, Olsson, Håkan, Teixeira, Manuel R., Stone, Jennifer, Offit, Kenneth, Ottini, Laura, Park, Sue K., Thomassen, Mads, Hall, Per, Meindl, Alfons, Schmutzler, Rita K., Droit, Arnaud, Bader, Gary D., Pharoah, Paul D., Couch, Fergus J., Easton, Douglas F., Kraft, Peter, Chenevix-Trench, Georgia, Garciá-Closas, Montserrat, Schmidt, Marjanka K., Antoniou, Antonis C., Simard, Jacques, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), Human Genetics, CCA - Cancer biology and immunology, Epidemiology and Data Science, Amsterdam Neuroscience - Complex Trait Genetics, Human genetics, Amsterdam Reproduction & Development (AR&D), Clinical Genetics, Medical Oncology, Internal Medicine, Obstetrics & Gynecology, MUMC+: DA KG Lab Centraal Lab (9), and RS: GROW - R4 - Reproductive and Perinatal Medicine

Subjects
0301 basic medicine, Oncology, Estrogen receptor, Genome-wide association study, consortium, Gene mutation, DISEASE, Breast cancer, Risk Factors, Receptors, common variants, BRCA2 MUTATION CARRIERS, Medicine and Health Sciences, CONFER SUSCEPTIBILITY, skin and connective tissue diseases, ovarian cancers, BRCA1 Protein, COMMON VARIANTS, Single Nucleotide, OVARIAN CANCERS, 3. Good health, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Receptors, Estrogen, functional variants, Female, estrogen receptor, SNPs, EXPRESSION, medicine.medical_specialty, Heterozygote, SUSCEPTIBILITY LOCI, European Continental Ancestry Group, Breast cancer, estrogen receptor, SNPs, Single-nucleotide polymorphism, Breast Neoplasms, Biology, Polymorphism, Single Nucleotide, White People, Article, Càncer de mama, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Internal medicine, expression, medicine, Genetic predisposition, Genetics, Journal Article, Humans, Genetic Predisposition to Disease, ddc:610, Risk factor, Polymorphism, GENOME-WIDE ASSOCIATION, FUNCTIONAL VARIANTS, disease, CONSORTIUM, Case-control study, Biology and Life Sciences, medicine.disease, confer susceptibility, Estrogen, susceptibility loci, 030104 developmental biology, Mutation, genome-wide association, brca2 mutation carriers, Genome-Wide Association Study
Abstract

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease1. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10−8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.

Published
2017

5. Frequent PIK3CA Mutations in Colorectal and Endometrial Cancer with Double Somatic Mismatch Repair Mutations

Author

Cohen, Stacey A., Turner, Emily H., Beightol, Mallory B., Jacobson, Angela, Gooley, Ted A., Salipante, Stephen J., Haraldsdottir, Sigurdis, Smith, Christina, Scroggins, Sheena, Tait, Jonathan F., Grady, William M., Lin, Edward H., Cohn, David E., Goodfellow, Paul J., Arnold, Mark W., de la Chapelle, Albert, Pearlman, Rachel, Hampel, Heather, and Pritchard, Colin C.

Subjects
Male, Proto-Oncogene Proteins B-raf, Class I Phosphatidylinositol 3-Kinases, DNA Mutational Analysis, PTEN Phosphohydrolase, Membrane Proteins, Colorectal Neoplasms, Hereditary Nonpolyposis, DNA Mismatch Repair, Article, Endometrial Neoplasms, GTP Phosphohydrolases, Proto-Oncogene Proteins p21(ras), Phosphatidylinositol 3-Kinases, Phenotype, Mutation, Humans, Female, Microsatellite Instability, Prospective Studies, Colorectal Neoplasms
Abstract

Some colorectal and endometrial tumors with microsatellite instability not attributable to MLH1 hypermethylation or germline mutations contain 2 or more somatic mutations in genes encoding mismatch repair (MMR) proteins. We sought to define the molecular phenotype of this newly recognized tumor subtype.From 2 prospective studies of the efficacy of screening for Lynch syndrome, we identified patients with colorectal and endometrial tumors who had 2 or more somatic (but not germline) mutations in genes encoding MMR proteins (double somatic). We determined the frequencies of tumor mutations in PIK3CA, BRAF, KRAS, NRAS, and PTEN by targeted next-generation sequencing and used logistic-regression models to compare them with those from patients with Lynch syndrome, MLH1-hypermethylated, or microsatellite-stable tumors. We validated our findings using independent data sets from The Cancer Genome Atlas.Among colorectal cancer cases, we found that 14 of 21 (67%) patients with double somatic tumors also had PIK3CA mutations, compared with 4 of 18 (22%) tumors from patients with Lynch syndrome, 2 of 10 (20%) tumors with MLH1 hypermethylation, and 12 of 78 (15%) tumors with microsatellite stability (P.0001 for patients with double somatic tumors vs other subgroups). Mutations in PIK3CA were detected in all 13 patients with double somatic endometrial cancers (P = .04 compared with other subgroups). We did not detect BRAF mutations in patients with double somatic colorectal tumors or Lynch syndrome. We found highly similar results in a validation cohort from The Cancer Genome Atlas (113 patients with colorectal tumors, 178 endometrial tumors); 100% of double somatic cases had a somatic mutation in PIK3CA (P.0001 compared with other subgroups).Most patients with colorectal or endometrial tumors with 2 or more somatic (but not germline) mutations in MMR proteins also have mutations in PIK3CA; mutations in PIK3CA are detected at substantially higher frequencies in these double somatic tumors than in other microsatellite-instability subgroups. PIK3CA mutation status might be used to identify a specific group of colorectal tumors, and to select treatment or determine prognosis.

Published
2016

6. System Walks and Sampling Colour

Author

Goodfellow, Paul, Yeung, Heather, and Collier, Mark

Subjects
W100, GeneralLiterature_MISCELLANEOUS
Abstract

This paper discusses some of the processes employed by the author, a Systems Artist, during the production of artwork made from walking. The authors approach to walking is discussed before describing the original drawing techniques, employed to sample digitally captured colours, on the walk, to produce drawings, colour field paintings and prints.

Published
2014

7. Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer

Author

Purrington, Kristen S, Slager, Susan, Eccles, Diana, Yannoukakos, Drakoulis, Fasching, Peter A, Miron, Penelope, Carpenter, Jane, Chang-Claude, Jenny, Martin, Nicholas G, Montgomery, Grant W, Kristensen, Vessela, Anton-Culver, Hoda, Goodfellow, Paul, Tapper, William J, Rafiq, Sajjad, Gerty, Susan M, Durcan, Lorraine, Konstantopoulou, Irene, Fostira, Florentia, Vratimos, Athanassios, Apostolou, Paraskevi, Konstanta, Irene, Kotoula, Vassiliki, Lakis, Sotiris, Dimopoulos, Meletios A, Skarlos, Dimosthenis, Pectasides, Dimitrios, Fountzilas, George, Beckmann, Matthias W, Hein, Alexander, Ruebner, Matthias, Ekici, Arif B, Hartmann, Arndt, Schulz-Wendtland, Ruediger, Renner, Stefan P, Janni, Wolfgang, Rack, Brigitte, Scholz, Christoph, Neugebauer, Julia, Andergassen, Ulrich, Lux, Michael P, Haeberle, Lothar, Clarke, Christine, Pathmanathan, Nirmala, Rudolph, Anja, Flesch-Janys, Dieter, Nickels, Stefan, Olson, Janet E, Ingle, James N, Olswold, Curtis, Slettedahl, Seth, Eckel-Passow, Jeanette E, Anderson, S Keith, Visscher, Daniel W, Cafourek, Victoria L, Sicotte, Hugues, Prodduturi, Naresh, Weiderpass, Elisabete, Bernstein, Leslie, Ziogas, Argyrios, Ivanovich, Jennifer, Giles, Graham G, Baglietto, Laura, Southey, Melissa, Kosma, Veli-Matti, Fischer, Hans-Peter, GENICA Network, Reed, Malcom WR, Cross, Simon S, Deming-Halverson, Sandra, Shrubsole, Martha, Cai, Qiuyin, Shu, Xiao-Ou, Daly, Mary, Weaver, Joellen, Ross, Eric, Klemp, Jennifer, Sharma, Priyanka, Torres, Diana, Rüdiger, Thomas, Wölfing, Heidrun, Ulmer, Hans-Ulrich, Försti, Asta, Khoury, Thaer, Kumar, Shicha, Pilarski, Robert, Shapiro, Charles L, Greco, Dario, Heikkilä, Päivi, Aittomäki, Kristiina, Blomqvist, Carl, Irwanto, Astrid, Liu, Jianjun, Pankratz, Vernon Shane, Wang, Xianshu, Severi, Gianluca, Mannermaa, Arto, Easton, Douglas, Hall, Per, Brauch, Hiltrud, Cox, Angela, Zheng, Wei, Godwin, Andrew K, Hamann, Ute, Ambrosone, Christine, Toland, Amanda Ewart, Nevanlinna, Heli, Vachon, Celine M, and Couch, Fergus J

Subjects
Adult, Aged, 80 and over, Quantitative Trait Loci, Oncology and Carcinogenesis, Estrogen Receptor alpha, Triple Negative Breast Neoplasms, Middle Aged, Polymorphism, Single Nucleotide, Young Adult, Case-Control Studies, Humans, Genetic Predisposition to Disease, Female, Oncology & Carcinogenesis, GENICA Network, Chromosomes, Human, Pair 19, Aged, Genome-Wide Association Study
Abstract

Triple-negative (TN) breast cancer is an aggressive subtype of breast cancer associated with a unique set of epidemiologic and genetic risk factors. We conducted a two-stage genome-wide association study of TN breast cancer (stage 1: 1529 TN cases, 3399 controls; stage 2: 2148 cases, 1309 controls) to identify loci that influence TN breast cancer risk. Variants in the 19p13.1 and PTHLH loci showed genome-wide significant associations (P < 5 × 10(-) (8)) in stage 1 and 2 combined. Results also suggested a substantial enrichment of significantly associated variants among the single nucleotide polymorphisms (SNPs) analyzed in stage 2. Variants from 25 of 74 known breast cancer susceptibility loci were also associated with risk of TN breast cancer (P < 0.05). Associations with TN breast cancer were confirmed for 10 loci (LGR6, MDM4, CASP8, 2q35, 2p24.1, TERT-rs10069690, ESR1, TOX3, 19p13.1, RALY), and we identified associations with TN breast cancer for 15 additional breast cancer loci (P < 0.05: PEX14, 2q24.1, 2q31.1, ADAM29, EBF1, TCF7L2, 11q13.1, 11q24.3, 12p13.1, PTHLH, NTN4, 12q24, BRCA2, RAD51L1-rs2588809, MKL1). Further, two SNPs independent of previously reported signals in ESR1 [rs12525163 odds ratio (OR) = 1.15, P = 4.9 × 10(-) (4)] and 19p13.1 (rs1864112 OR = 0.84, P = 1.8 × 10(-) (9)) were associated with TN breast cancer. A polygenic risk score (PRS) for TN breast cancer based on known breast cancer risk variants showed a 4-fold difference in risk between the highest and lowest PRS quintiles (OR = 4.03, 95% confidence interval 3.46-4.70, P = 4.8 × 10(-) (69)). This translates to an absolute risk for TN breast cancer ranging from 0.8% to 3.4%, suggesting that genetic variation may be used for TN breast cancer risk prediction.

Published
2014

8. Lithium and inhibition of GSK3β as a potential therapy for serous ovarian cancer

Author

Novetsky, Akiva P., Thompson, Dominic M., Zighelboim, Israel, Thaker, Premal H., Powell, Matthew A., Mutch, David G., and Goodfellow, Paul J.

Subjects
Ovarian Neoplasms, Glycogen Synthase Kinase 3, Glycogen Synthase Kinase 3 beta, Cell Cycle, Primary Cell Culture, Tumor Cells, Cultured, Humans, Female, Lithium Chloride, Protein Kinase Inhibitors, Article, Cell Proliferation, Cystadenocarcinoma, Serous
Abstract

Lithium chloride (LiCl) has been shown to demonstrate anticancer properties at supratherapeutic doses. This study was designed to determine whether LiCl, as a single agent or in combination with cytotoxic agents, reduces ovarian cancer cell growth and metabolic activity at clinically achievable levels.We studied the effects of LiCl on 2 high-grade serous ovarian cancer cell lines, SKOV3 and OVCA 433, and primary cultures developed from ascitic fluid collected from patients with metastatic high-grade serous ovarian cancer. We assessed proliferation and metabolism using cell cycle analysis, MTT assays, and cellular proliferation and clonogenic potential assays.Treatment with 1 mM LiCl had no effect on the cell cycle distribution or metabolic activity of the SKOV3 and OVCA 433 cell lines. Combination treatment with cisplatin or paclitaxel led to statistically significant decreases in metabolic activity in the OVCA 433 cell line and 50% of cultures investigated. The decreased metabolic activity was not, however, associated with decreased cell growth or clonogenic potential.Combination treatment with LiCl and cytotoxic agents at physiologically achievable drug concentrations reduces ovarian cancer cell metabolism but does not appear to affect cellular proliferation. The potential for combined lithium/cytoxic therapies appears to be limited based on our analysis of both established cell lines and short-term ovarian cancer cultures.

Published
2013

9. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML

Author

Link, Daniel C., Schuettpelz, Laura G., Shen, Dong, Wang, Jinling, Walter, Matthew J., Kulkarni, Shashikant, Payton, Jacqueline E., Ivanovich, Jennifer, Goodfellow, Paul J., Le Beau, Michelle, Koboldt, Daniel C., Dooling, David J., Fulton, Robert S., Bender, R. Hugh F., Fulton, Lucinda L., Delehaunty, Kimberly D., Fronick, Catrina C., Appelbaum, Elizabeth L., Schmidt, Heather, Abbott, Rachel, O'Laughlin, Michelle, Chen, Ken, McLellan, Michael D., Varghese, Nobish, Nagarajan, Rakesh, Heath, Sharon, Graubert, Timothy A., Ding, Li, Ley, Timothy J., Zambetti, Gerard P., Wilson, Richard K., and Mardis, Elaine R.

Subjects
Adult, Ovarian Neoplasms, Genome, Human, Breast Neoplasms, DNA, Neoplasm, Sequence Analysis, DNA, Genes, p53, Polymorphism, Single Nucleotide, Article, Cystadenocarcinoma, Serous, Leukemia, Myeloid, Acute, Humans, Female, Genetic Predisposition to Disease, Age of Onset, Tumor Suppressor Protein p53, Sequence Deletion
Abstract

The identification of patients with inherited cancer susceptibility syndromes facilitates early diagnosis, prevention, and treatment. However, in many cases of suspected cancer susceptibility, the family history is unclear and genetic testing of common cancer susceptibility genes is unrevealing.To apply whole-genome sequencing to a patient without any significant family history of cancer but with suspected increased cancer susceptibility because of multiple primary tumors to identify rare or novel germline variants in cancer susceptibility genes. DESIGN, SETTING, AND PARTICIPANT: Skin (normal) and bone marrow (leukemia) DNA were obtained from a patient with early-onset breast and ovarian cancer (negative for BRCA1 and BRCA2 mutations) and therapy-related acute myeloid leukemia (t-AML) and analyzed with the following: whole-genome sequencing using paired-end reads, single-nucleotide polymorphism (SNP) genotyping, RNA expression profiling, and spectral karyotyping.Structural variants, copy number alterations, single-nucleotide variants, and small insertions and deletions (indels) were detected and validated using the described platforms. RESULTS; Whole-genome sequencing revealed a novel, heterozygous 3-kilobase deletion removing exons 7-9 of TP53 in the patient's normal skin DNA, which was homozygous in the leukemia DNA as a result of uniparental disomy. In addition, a total of 28 validated somatic single-nucleotide variations or indels in coding genes, 8 somatic structural variants, and 12 somatic copy number alterations were detected in the patient's leukemia genome.Whole-genome sequencing can identify novel, cryptic variants in cancer susceptibility genes in addition to providing unbiased information on the spectrum of mutations in a cancer genome.

Published
2011

10. A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer

Author

Haiman, Christopher A. Chen, Gary K. Vachon, Celine M. and Canzian, Federico Dunning, Alison Millikan, Robert C. Wang, Xianshu Ademuyiwa, Foluso Ahmed, Shahana Ambrosone, Christine B. Baglietto, Laura Balleine, Rosemary Bandera, Elisa V. Beckmann, Matthias W. Berg, Christine D. Bernstein, Leslie Blomqvist, Carl Blot, William J. Brauch, Hiltrud and Buring, Julie E. Carey, Lisa A. Carpenter, Jane E. and Chang-Claude, Jenny Chanock, Stephen J. Chasman, Daniel I. and Clarke, Christine L. Cox, Angela Cross, Simon S. Deming, Sandra L. Diasio, Robert B. Dimopoulos, Athanasios M. and Driver, W. Ryan Duennebier, Thomas Durcan, Lorraine Eccles, Diana Edlund, Christopher K. Ekici, Arif B. Fasching, Peter A. Feigelson, Heather S. Flesch-Janys, Dieter Fostira, Florentia Foersti, Asta Fountzilas, George Gerty, Susan M. and Giles, Graham G. Godwin, Andrew K. Goodfellow, Paul and Graham, Nikki Greco, Dario Hamann, Ute Hankinson, Susan E. and Hartmann, Arndt Hein, Rebecca Heinz, Judith Holbrook, Andrea Hoover, Robert N. Hu, Jennifer J. Hunter, David J. and Ingles, Sue A. Irwanto, Astrid Ivanovich, Jennifer John, Esther M. Johnson, Nicola Jukkola-Vuorinen, Arja Kaaks, Rudolf Ko, Yon-Dschun Kolonel, Laurence N. Konstantopoulou, Irene Kosma, Veli-Matti Kulkarni, Swati Lambrechts, Diether and Lee, Adam M. Le Marchand, Loic Lesnick, Timothy Liu, Jianjun Lindstrom, Sara Mannermaa, Arto Margolin, Sara and Martin, Nicholas G. Miron, Penelope Montgomery, Grant W. and Nevanlinna, Heli Nickels, Stephan Nyante, Sarah Olswold, Curtis Palmer, Julie Pathak, Harsh Pectasides, Dimitrios and Perou, Charles M. Peto, Julian Pharoah, Paul D. P. Pooler, Loreall C. Press, Michael F. Pylkas, Katri Rebbeck, Timothy R. Rodriguez-Gil, Jorge L. Rosenberg, Lynn Ross, Eric and Ruediger, Thomas Silva, Isabel dos Santos Sawyer, Elinor and Schmidt, Marjanka K. Schulz-Wendtland, Ruediger Schumacher, Fredrick Severi, Gianluca Sheng, Xin Signorello, Lisa B. and Sinn, Hans-Peter Stevens, Kristen N. Southey, Melissa C. and Tapper, William J. Tomlinson, Ian Hogervorst, Frans B. L. and Wauters, Els Weaver, JoEllen Wildiers, Hans Winqvist, Robert and Van Den Berg, David Wan, Peggy Xia, Lucy Y. Yannoukakos, Drakoulis Zheng, Wei Ziegler, Regina G. Siddiq, Afshan and Slager, Susan L. Stram, Daniel O. Easton, Douglas Kraft, Peter Henderson, Brian E. Couch, Fergus J. Gene Environm Interaction Breast C

Abstract

Estrogen receptor (ER)-negative breast cancer shows a higher incidence in women of African ancestry compared to women of European ancestry. In search of common risk alleles for ER-negative breast cancer, we combined genome-wide association study (GWAS) data from women of African ancestry (1,004 ER-negative cases and 2,745 controls) and European ancestry (1,718 ER-negative cases and 3,670 controls), with replication testing conducted in an additional 2,292 ER-negative cases and 16,901 controls of European ancestry. We identified a common risk variant for ER-negative breast cancer at the TERT-CLPTM1L locus on chromosome 5p15 (rs10069690: per-allele odds ratio (OR) = 1.18 per allele, P = 1.0 x 10(-10)). The variant was also significantly associated with triple-negative (ER-negative, progesterone receptor (PR)-negative and human epidermal growth factor-2 (HER2)-negative) breast cancer (OR = 1.25, P = 1.1 x 10(-9)), particularly in younger women (

Published
2011

11. Germline DICER1 Mutations in Familial Pleuropulmonary Blastoma

Author

Hill, D. Ashley, Ivanovich, J, Priest, John R., Gurnett, Christina A., Dehner, Louis P., Desruisseau, David, Jarzembowski, Jason A., Wikenheiser-Brokamp, Kathryn A., Suarez, Brian K., Whelan, Alison J., Williams, Gretchen, Bracamontes, Dawn, Messinger, Yoav, and Goodfellow, Paul J.

Subjects
DEAD-box RNA Helicases, Male, Ribonuclease III, Heterozygote, Lung Neoplasms, Humans, Female, Genetic Predisposition to Disease, Pulmonary Blastoma, Article, Epithelium, Germ-Line Mutation, Pedigree
Abstract

Pleuropulmonary blastoma (PPB) is a rare pediatric lung tumor that is often part of an inherited cancer syndrome. PPBs consist of mesenchymal cells that are susceptible to malignant transformation and cysts lined by epithelial cells. In a subset of patients, overgrowth of the cysts by mesenchymal cells leads to sarcoma formation. Here, we show that 11 multiplex PPB families harbor heterozygous germline mutations in DICER1, a gene encoding an endoribonuclease critical to the generation of small noncoding regulatory RNAs. Expression of DICER1 protein was undetectable in the epithelial component of PPB tumors but was retained in the malignant mesenchyme (sarcoma). We hypothesize that loss of DICER1 in the epithelium of the developing lung alters the regulation of diffusible factors that promote mesenchymal proliferation.

Published
2009

12. Reply to Vance et al

Author

Yee, Woon-Chee, Elliott, Jeffrey L., Kwon, Jennifer M., and Goodfellow, Paul

Subjects
Letters to the Editor
Published
1996

13. Art as a Distributed Ecosystem: mapping the limits of systems-based art

Author

Goodfellow, Paul and Dorsett, Chris

Subjects
W100
Abstract

My practice-based fine art research is shaped and informed by my transdisciplinary background and specifically my experience of ecology, geography and data visualisation. As a result I draw on the concepts of the 'ecosystem' and the 'information system' to consider how an artwork can be understood in ecological and informational terms, especially in relation to my own engagement with 'Systems Art', a mode of practice which shares a systems thinking foundation with these concepts.\ud \ud This research identifies three periods of systems thinking influencing culture, and this understanding has helped structure the thesis. Firstly, the holistic ecology movements of the mid-1960s which generated expanded expectations of the term ‘system’, secondly, the shift towards the ‘informational’ inherent in the critiques of linguistic and institutional systems of the 1980s, finally, our current ‘post-systems’ condition in which the pervading and infinitely complex nature of socio-environmental systems and their simulation is acknowledged.\ud \ud This three-fold journey is marked by incremental modifications to the definition of a system as the idea takes on greater extension through Latour's Actor-Network Theory and Deleuze and Guattari's Assemblage Theory. Later, the incomprehensibility of complex systems is conjured through references to Timothy Morton's concept of the Hyperobject and Object-Oriented Ontology's notion of ‘withdrawal'.\ud \ud The practical component of my research is a body of artwork, which is a product of my engagement with systems thinking, the natural environment, complex information, image processing and painting. Within the material production of two and three-dimensional artworks, the perspective I have gained is that of a researcher exploring the analogical potential of an extensively ‘distributed ecosystem'. If this perspective is persuasive, then artists interested in systems should be encouraged to not only map more expansive and complex boundaries for their work, but also articulate the unknowability of these complex systems as a knowable dimension of the distributed meaning of ‘Systems Art’.

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