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Genetics, genomics and epigenetics

This section considers articles on all aspects of genome-scale analysis, functional genomics, genetic association studies, pharmacogenomics and epigenetics in relation to cancer biology, diagnosis and therapy.

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  1. Toll-like receptors (TLR) are key innate immunity receptors participating in an immune response. Growing evidence suggests that mutations of TLR2/TLR9 gene are associated with the progress of cancers. The pres...

    Authors: Xie Junjie, Jiang Songyao, Shi Minmin, Song Yanyan, Shen Baiyong, Deng Xiaxing, Jin Jiabin, Zhan Xi and Chen Hao

    Citation: BMC Cancer 2012 12:57

    Content type: Research article

    Published on:

  2. The phosphoinositide 3-kinase (PI3K)/Akt pathway plays a fundamental role in cell proliferation and survival in human tumorigenesis, including gastric cancer. PIK3CA mutations and amplification are two major caus...

    Authors: Jing Shi, Demao Yao, Wei Liu, Na Wang, Hongjun Lv, Guanjun Zhang, Meiju Ji, Li Xu, Nongyue He, Bingyin Shi and Peng Hou

    Citation: BMC Cancer 2012 12:50

    Content type: Research article

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  3. In cancer cells, transcriptional gene silencing has been associated with genetic and epigenetic defects. The disruption of DNA methylation patterns and covalent histone marks has been associated with cancer de...

    Authors: Ernesto Soto-Reyes, Rodrigo González-Barrios, Fernanda Cisneros-Soberanis, Roberto Herrera-Goepfert, Víctor Pérez, David Cantú, Diddier Prada, Clementina Castro, Félix Recillas-Targa and Luis A Herrera

    Citation: BMC Cancer 2012 12:40

    Content type: Research article

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  4. RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients.

    Authors: Mikkel Noerholm, Leonora Balaj, Tobias Limperg, Afshin Salehi, Lin Dan Zhu, Fred H Hochberg, Xandra O Breakefield, Bob S Carter and Johan Skog

    Citation: BMC Cancer 2012 12:22

    Content type: Research article

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  5. The newly discovered metastasis-associated in colon cancer-1 (MACC1) gene is a key regulator of the HGF/MET pathway. Deregulation of HGF/MET signaling is reported as a prognostic marker for tumorigenesis, earl...

    Authors: Alois H Lang, Simone Geller-Rhomberg, Thomas Winder, Nicole Stark, Klaus Gasser, Bernd Hartmann, Bertram Kohler, Ina Grizelj, Heinz Drexel and Axel Muendlein

    Citation: BMC Cancer 2012 12:20

    Content type: Research article

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  6. In colorectal carcinoma, extensive gene promoter hypermethylation is called the CpG island methylator phenotype (CIMP). Explaining why studies on CIMP and survival yield conflicting results is essential. Most ...

    Authors: Benjamin Tournier, Caroline Chapusot, Emilie Courcet, Laurent Martin, Côme Lepage, Jean Faivre and Françoise Piard

    Citation: BMC Cancer 2012 12:12

    Content type: Research article

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  7. The association between the TERT rs2736100 single nucleotide polymorphism (SNP) and cancer risk has been studied by many researchers, but the results remain inconclusive. To further explore this association, we p...

    Authors: Peng Zou, Aihua Gu, Guixiang Ji, Lin Zhao, Peng Zhao and Ailin Lu

    Citation: BMC Cancer 2012 12:7

    Content type: Research article

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  8. Leukemia is a heterogeneous disease commonly associated with recurrent chromosomal translocations that involve tyrosine kinases including BCR-ABL, TEL-PDGFRB and TEL-JAK2. Most studies on the activated tyrosin...

    Authors: Hani Kim, Lisa C Gillis, Jordan D Jarvis, Stuart Yang, Kai Huang, Sandy Der and Dwayne L Barber

    Citation: BMC Cancer 2011 11:528

    Content type: Research article

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  9. APE1 (apurinic/apyrimidinic endonuclease 1) is an important DNA repair protein in the base excision repair pathway. Polymorphisms in APE1 have been implicated in susceptibility to cancer; however, results from th...

    Authors: Bin Zhou, Hailin Shan, Ying Su, Kai Xia, Xiaxia Shao, Weidong Mao and Qing Shao

    Citation: BMC Cancer 2011 11:521

    Content type: Research article

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  10. The availability of well-annotated prostate tissue samples through biobanks is key for research. Whereas fresh-frozen tissue is well suited for a broad spectrum of molecular analyses, its storage and handling ...

    Authors: Martin Braun, Roopika Menon, Pavel Nikolov, Robert Kirsten, Karen Petersen, David Schilling, Christina Schott, Sibylle Gündisch, Falko Fend, Karl-Friedrich Becker and Sven Perner

    Citation: BMC Cancer 2011 11:511

    Content type: Research article

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  11. TMPRSS2-ERG gene fusions occur in about 50% of all prostate cancer cases and represent promising markers for molecular subtyping. Although TMPRSS2-ERG fusion seems to be a critical event in prostate cancer, the ...

    Authors: Jan C Brase, Marc Johannes, Heiko Mannsperger, Maria Fälth, Jennifer Metzger, Lukasz A Kacprzyk, Tatjana Andrasiuk, Stephan Gade, Michael Meister, Hüseyin Sirma, Guido Sauter, Ronald Simon, Thorsten Schlomm, Tim Beißbarth, Ulrike Korf, Ruprecht Kuner…

    Citation: BMC Cancer 2011 11:507

    Content type: Research article

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  12. The prognosis of hepatocellular carcinoma (HCC) varies following surgical resection and the large variation remains largely unexplained. Studies have revealed the ability of clinicopathologic parameters and ge...

    Authors: Ke Hao, John Lamb, Chunsheng Zhang, Tao Xie, Kai Wang, Bin Zhang, Eugene Chudin, Nikki P Lee, Mao Mao, Hua Zhong, Danielle Greenawalt, Mark D Ferguson, Irene O Ng, Pak C Sham, Ronnie T Poon, Cliona Molony…

    Citation: BMC Cancer 2011 11:481

    Content type: Research article

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  13. Epigenetic regulation is an important mechanism leading to cancer initiation and promotion. Histone acetylation by histone deacetylases (HDACs) represents an important part of it. The development of HDAC inhib...

    Authors: Nicolas Samartzis, Patrick Imesch, Konstantin J Dedes, Eleftherios P Samartzis, André Fedier, Daniel Fink, Rosmarie Caduff and Mathias K Fehr

    Citation: BMC Cancer 2011 11:463

    Content type: Research article

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  14. Hepatitis B virus (HBV) is a major cause of hepatocarcinogenesis.

    Authors: Masashi Tatsukawa, Akinobu Takaki, Hidenori Shiraha, Kazuko Koike, Yoshiaki Iwasaki, Haruhiko Kobashi, Shin-Ichi Fujioka, Kohsaku Sakaguchi and Kazuhide Yamamoto

    Citation: BMC Cancer 2011 11:458

    Content type: Research article

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  15. Metastatic progression due to development or enrichment of therapy-resistant tumor cells is eventually lethal. Molecular characterization of such chemotherapy resistant tumor cell clones may identify markers r...

    Authors: Geir Olav Hjortland, Leonardo A Meza-Zepeda, Klaus Beiske, Anne H Ree, Siri Tveito, Hanne Hoifodt, Per J Bohler, Knut H Hole, Ola Myklebost, Oystein Fodstad, Sigbjorn Smeland and Eivind Hovig

    Citation: BMC Cancer 2011 11:455

    Content type: Case report

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  16. Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC), w...

    Authors: Stefan Enroth, Alvaro Rada-Iglesisas, Robin Andersson, Ola Wallerman, Alkwin Wanders, Lars Påhlman, Jan Komorowski and Claes Wadelius

    Citation: BMC Cancer 2011 11:450

    Content type: Research article

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  17. The mucosae of the oral cavity are different at the histological level but appear all equally exposed to common genotoxic agents. As a result of this exposure, changes in the mucosal epithelia may develop givi...

    Authors: Patrizio Castagnola, Davide Malacarne, Paola Scaruffi, Massimo Maffei, Alessandra Donadini, Emanuela Di Nallo, Simona Coco, Gian Paolo Tonini, Monica Pentenero, Sergio Gandolfo and Walter Giaretti

    Citation: BMC Cancer 2011 11:445

    Content type: Research article

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  18. In cancer research the selection and definitions of survival endpoints are important and yet they are not used consistently. The aim of this study was to compare different survival endpoints in patients with p...

    Authors: Helgi Birgisson, Ulrik Wallin, Lars Holmberg and Bengt Glimelius

    Citation: BMC Cancer 2011 11:438

    Content type: Research article

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  19. Oral Squamous Cell Carcinoma (OSCC) is a major cause of cancer death worldwide, which is mainly due to recurrence leading to treatment failure and patient death. Histological status of surgical margins is a cu...

    Authors: Patricia P Reis, Levi Waldron, Bayardo Perez-Ordonez, Melania Pintilie, Natalie Naranjo Galloni, Yali Xuan, Nilva K Cervigne, Giles C Warner, Antti A Makitie, Colleen Simpson, David Goldstein, Dale Brown, Ralph Gilbert, Patrick Gullane, Jonathan Irish, Igor Jurisica…

    Citation: BMC Cancer 2011 11:437

    Content type: Research article

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  20. The CD44 cell adhesion molecule is aberrantly expressed in many breast tumors and has been implicated in the metastatic process as well as in the putative cancer stem cell (CSC) compartment. We aimed to invest...

    Authors: Eleonor Olsson, Gabriella Honeth, Pär-Ola Bendahl, Lao H Saal, Sofia Gruvberger-Saal, Markus Ringnér, Johan Vallon-Christersson, Göran Jönsson, Karolina Holm, Kristina Lövgren, Mårten Fernö, Dorthe Grabau, Åke Borg and Cecilia Hegardt

    Citation: BMC Cancer 2011 11:418

    Content type: Research article

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  21. Cancer/testis antigens are considered potential targets for immunotherapy due to their tumor-associated expression pattern. Although recent studies have demonstrated high expression of CT45 in classical Hodgki...

    Authors: Riguel J Inaoka, Achim A Jungbluth, Otávio CG Baiocchi, Mariane CG Assis, Nicole C Hanson, Denise Frosina, Jodie Tassello, Adriana B Bortoluzzo, Antonio C Alves and Gisele WB Colleoni

    Citation: BMC Cancer 2011 11:416

    Content type: Research article

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  22. Osteosarcoma is the most common primary bone malignancy in childhood and adolescence. However, it is very rare in children under 5 years of age. Although studies in young children are limited in number, they a...

    Authors: Maud AM Guillon, Pierre MJ Mary, Laurence Brugière, Perrine Marec-Bérard, Hélène D Pacquement, Claudine Schmitt, Jean-Marc Guinebretière and Marie-Dominique P Tabone

    Citation: BMC Cancer 2011 11:407

    Content type: Research article

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  23. The neural transcription factor SOX11 has been described as a prognostic marker in epithelial ovarian cancers (EOC), however its role in individual histological subtypes and tumour grade requires further clari...

    Authors: Sandra Sernbo, Elin Gustavsson, Donal J Brennan, William M Gallagher, Elton Rexhepaj, Frida Rydnert, Karin Jirström, Carl AK Borrebaeck and Sara Ek

    Citation: BMC Cancer 2011 11:405

    Content type: Research article

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  24. Development of the hepatitis B virus (HBV) rtA181T/sW172* mutant could occur during prolonged lamivudine (LAM) therapy, conferring cross resistance to adefovir. Recent studies demonstrated an increased oncogen...

    Authors: Chau-Ting Yeh, Tiffany Chen, Chao-Wei Hsu, Yi-Cheng Chen, Ming-Wei Lai, Kung-Hao Liang and Tse-Ching Chen

    Citation: BMC Cancer 2011 11:398

    Content type: Research article

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  25. 14-3-3ơ is an intracellular, phosphoserine binding protein and proposed to be involved in tumorigenesis. However, the expression dynamics of 14-3-3ơ and its clinicopathological/prognostic significance in human...

    Authors: Wei-hua Zhou, Fang Tang, Jie Xu, Xing Wu, Zhi-ying Feng, Hai-gang Li, Dong-jun Lin, Chun-kui Shao and Quentin Liu

    Citation: BMC Cancer 2011 11:397

    Content type: Research article

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  26. Lung cancer is the leading cause of cancer-related deaths worldwide. Early detection is considered critical for lung cancer treatment. MicroRNAs (miRNAs) have shown promise as diagnostic and prognostic indicat...

    Authors: Wangyu Zhu, XiaoGuang Liu, JianYing He, DongDong Chen, YanYan Hunag and Yong Kui Zhang

    Citation: BMC Cancer 2011 11:393

    Content type: Research article

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  27. Inducible costimulator (ICOS), a costimulatory molecular of the CD28 family, provides positive signal to enhance T cell proliferation. Its abnormal expression can disturb the immune response and entail an increa...

    Authors: Fengyan Xu, Dalin Li, Qiujin Zhang, Zhenkun Fu, Jie Zhang, Weiguang Yuan, Shuang Chen, Da Pang and Dianjun Li

    Citation: BMC Cancer 2011 11:392

    Content type: Research article

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  28. Uveal melanoma (UM) is a rare eye tumor. There are two classes of UM, which can be discriminated by the chromosome 3 status or global mRNA expression profile. Metastatic progression is predominantly originated...

    Authors: Lisa C Neumann, Andreas Weinhäusel, Stefanie Thomas, Bernhard Horsthemke, Dietmar R Lohmann and Michael Zeschnigk

    Citation: BMC Cancer 2011 11:380

    Content type: Research article

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  29. According to the very limited cancer registry, incidence and mortality rates for female breast cancer in China are regarded to be increasing especially in the metropolitan areas. Representative data on the bre...

    Authors: Jing Li, Bao-Ning Zhang, Jin-Hu Fan, Yi Pang, Pin Zhang, Shu-Lian Wang, Shan Zheng, Bin Zhang, Hong-Jian Yang, Xiao-Ming Xie, Zhong-Hua Tang, Hui Li, Jia-Yuan Li, Jian-Jun He and You-Lin Qiao

    Citation: BMC Cancer 2011 11:364

    Content type: Research article

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  30. RASSF1A gene silencing by DNA methylation has been suggested as a major event in pancreatic endocrine tumor (PET) but RASSF1A expression has never been studied. The RASSF1 locus contains two CpG islands (A and C

    Authors: Giorgio Malpeli, Eliana Amato, Mario Dandrea, Caterina Fumagalli, Valentina Debattisti, Letizia Boninsegna, Giuseppe Pelosi, Massimo Falconi and Aldo Scarpa

    Citation: BMC Cancer 2011 11:351

    Content type: Research article

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  31. Colorectal cancer (CRC) is the second leading cause of cancer death in developed countries. Familial aggregation in CRC is also important outside syndromic forms and, in this case, a polygenic model with sever...

    Authors: Anna Abulí, Ceres Fernández-Rozadilla, Virginia Alonso-Espinaco, Jenifer Muñoz, Victoria Gonzalo, Xavier Bessa, Dolors González, Joan Clofent, Joaquin Cubiella, Juan D Morillas, Joaquim Rigau, Mercedes Latorre, Fernando Fernández-Bañares, Elena Peña, Sabino Riestra, Artemio Payá…

    Citation: BMC Cancer 2011 11:339

    Content type: Research article

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  32. High serum levels of estradiol are associated with increased risk of postmenopausal breast cancer. Little is known about the gene expression in normal breast tissue in relation to levels of circulating serum e...

    Authors: Vilde D Haakensen, Trine Bjøro, Torben Lüders, Margit Riis, Ida K Bukholm, Vessela N Kristensen, Melissa A Troester, Marit M Homen, Giske Ursin, Anne-Lise Børresen-Dale and Åslaug Helland

    Citation: BMC Cancer 2011 11:332

    Content type: Research article

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  33. Several predisposition loci for hereditary prostate cancer (HPC) have been suggested, including HPCX1 at Xq27-q28, but due to the complex structure of the region, the susceptibility gene has not yet been identifi...

    Authors: Henna Mattila, Martin Schindler, Jarkko Isotalo, Tarja Ikonen, Mauno Vihinen, Hannu Oja, Teuvo LJ Tammela, Tiina Wahlfors and Johanna Schleutker

    Citation: BMC Cancer 2011 11:327

    Content type: Research article

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  34. CD133 is known to be a cancer stem cell (CSC) marker. However, recent studies have revealed that CD133 is not restricted to CSC but to be expressed not only in human normal tissues but also in some cancers and...

    Authors: Linni Fan, Furong He, Hongxiang Liu, Jin Zhu, Yixiong Liu, Zhiyong Yin, Lu Wang, Ying Guo, Zhe Wang, Qingguo Yan and Gaosheng Huang

    Citation: BMC Cancer 2011 11:320

    Content type: Research article

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  35. Ovarian cancer is the most deadly gynecological cancer with a very poor prognosis. Xenograft mouse models have proven to be one very useful tool in testing candidate therapeutic agents and gene function in vivo. ...

    Authors: Ashley Stuckey, Andrew Fischer, Daniel H Miller, Sara Hillenmeyer, Kyu K Kim, Anna Ritz, Rakesh K Singh, Benjamin J Raphael, Laurent Brard and Alexander S Brodsky

    Citation: BMC Cancer 2011 11:308

    Content type: Research article

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  36. MUTYH-associated polyposis (MAP) is an autosomal recessive form of intestinal polyposis predisposing to colorectal carcinoma. High resolution melting analysis (HRMA) is a mutation scanning method that allows det...

    Authors: Rossella Tricarico, Francesca Crucianelli, Antonio Alvau, Claudio Orlando, Roberta Sestini, Francesco Tonelli, Rosa Valanzano and Maurizio Genuardi

    Citation: BMC Cancer 2011 11:305

    Content type: Technical advance

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  37. To evaluate the association between polymorphisms involved in DNA repair and oxidative stress genes and mean dose to whole breast on acute skin reactions (erythema) in breast cancer (BC) patients following sin...

    Authors: Elisabetta Falvo, Lidia Strigari, Gennaro Citro, Carolina Giordano, Stefano Arcangeli, Antonella Soriani, Daniela D'Alessio, Paola Muti, Giovanni Blandino, Isabella Sperduti and Paola Pinnarò

    Citation: BMC Cancer 2011 11:291

    Content type: Research article

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  38. Since a substantial percentage of ovarian cancers express gonadotropin receptors and are responsive to the relatively high concentrations of pituitary gonadotropins during the postmenopausal years, it has been...

    Authors: Juan Cui, Brooke M Miner, Joanna B Eldredge, Susanne W Warrenfeltz, Phuongan Dam, Ying Xu and David Puett

    Citation: BMC Cancer 2011 11:280

    Content type: Research article

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  39. Inter-individual variation in DNA repair capacity is thought to modulate breast cancer risk. The phenotypic mutagen sensitivity assay (MSA) measures DNA strand breaks in lymphocytes; women with familial and sp...

    Authors: Luisel J Ricks-Santi, Lara E Sucheston, Yang Yang, Jo L Freudenheim, Claudine J Isaacs, Marc D Schwartz, Ramona G Dumitrescu, Catalin Marian, Jing Nie, Dominica Vito, Stephen B Edge and Peter G Shields

    Citation: BMC Cancer 2011 11:278

    Content type: Research article

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  40. Raf-1 kinase inhibitor protein (RKIP) has been reported to negatively regulate signal kinases of major survival pathways. RKIP activity is modulated in part by phosphorylation on Serine 153 by protein kinase C...

    Authors: Sara Huerta-Yepez, Nam K Yoon, Angeles Hernandez-Cueto, Vei Mah, Clara M Rivera-Pazos, Devasis Chatterjee, Mario I Vega, Erin L Maresh, Steve Horvath, David Chia, Benjamin Bonavida and Lee Goodglick

    Citation: BMC Cancer 2011 11:259

    Content type: Research article

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  41. Phospholipase C epsilon 1 (PLCE1) (an effector of Ras) belonging to the phospholipase family plays crucial roles in carcinogenesis and progression of several cancers, including squamous cell carcinoma of the h...

    Authors: Hongxia Ma, Li-E Wang, Zhensheng Liu, Erich M Sturgis and Qingyi Wei

    Citation: BMC Cancer 2011 11:258

    Content type: Research article

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  42. Molecular predictors of bevacizumab efficacy in colorectal cancer have not been identified yet. Specific VEGF polymorphisms may affect gene transcription and therefore indirectly influence the efficacy of bevaciz...

    Authors: Fotios Loupakis, Annamaria Ruzzo, Lisa Salvatore, Chiara Cremolini, Gianluca Masi, Paolo Frumento, Marta Schirripa, Vincenzo Catalano, Nadia Galluccio, Emanuele Canestrari, Bruno Vincenzi, Daniele Santini, Katia Bencardino, Vincenzo Ricci, Mariangela Manzoni, Marco Danova…

    Citation: BMC Cancer 2011 11:247

    Content type: Research article

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  43. Clear cell renal cell carcinoma (ccRCC) is characterized by recurrent copy number alterations (CNAs) and loss of heterozygosity (LOH), which may have potential diagnostic and prognostic applications. Here, we ...

    Authors: Ingrid Cifola, Cristina Bianchi, Eleonora Mangano, Silvia Bombelli, Fabio Frascati, Ester Fasoli, Stefano Ferrero, Vitalba Di Stefano, Maria A Zipeto, Fulvio Magni, Stefano Signorini, Cristina Battaglia and Roberto A Perego

    Citation: BMC Cancer 2011 11:244

    Content type: Research article

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  44. Heterozygosity of TP53 missense mutations is related to the phenomenon of the dominant-negative effect (DNE). To estimate the importance of the DNE of TP53 mutations, we analysed the percentage of cancer cases sh...

    Authors: Ewelina Stoczynska-Fidelus, Malgorzata Szybka, Sylwester Piaskowski, Michal Bienkowski, Krystyna Hulas-Bigoszewska, Mateusz Banaszczyk, Izabela Zawlik, Dorota Jesionek-Kupnicka, Radzislaw Kordek, Pawel P Liberski and Piotr Rieske

    Citation: BMC Cancer 2011 11:243

    Content type: Research article

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  45. Increased cyclooxygenase activity promotes progression of colorectal cancer, but the mechanisms behind COX-2 induction remain elusive. This study was therefore aimed to define external cell signaling and trans...

    Authors: Annika Gustafsson Asting, Helena Carén, Marianne Andersson, Christina Lönnroth, Kristina Lagerstedt and Kent Lundholm

    Citation: BMC Cancer 2011 11:238

    Content type: Research article

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  46. Long-term gene silencing throughout cell division is generally achieved by DNA methylation and other epigenetic processes. Aberrant DNA methylation is now widely recognized to be associated with cancer and oth...

    Authors: Mercedes Dávalos-Salas, Mayra Furlan-Magaril, Edgar González-Buendía, Christian Valdes-Quezada, Erandi Ayala-Ortega and Félix Recillas-Targa

    Citation: BMC Cancer 2011 11:232

    Content type: Research article

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  47. N-methyl-D-aspartate receptors (NMDAR) act as tumor suppressors of digestive malignancies. The expression and genetic methylation patterns of NMDAR2B in non-small cell lung cancer (NSCLC) are unknown.

    Authors: Hajime Tamura, Makoto Suzuki, Yasumitsu Moriya, Hidehisa Hoshino, Tatsuro Okamoto, Shigetoshi Yoshida and Ichiro Yoshino

    Citation: BMC Cancer 2011 11:220

    Content type: Research article

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