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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. Post-translational modification of histone tails by methylation plays an important role in tumorigenesis. In this study, we investigated the nuclear expression of H3K4me3, H3K9me3 and H4K20me3 in early-stage c...

    Authors: Anne Benard, Inès J Goossens-Beumer, Anneke Q van Hoesel, Wouter de Graaf, Hamed Horati, Hein Putter, Eliane CM Zeestraten, Cornelis JH van de Velde and Peter JK Kuppen

    Citation: BMC Cancer 2014 14:531

    Content type: Research article

    Published on:

  2. Breast cancer is rarely diagnosed in very young women (35years old or younger), and it often presents with distinct clinical-pathological features related to a more aggressive phenotype and worse prognosis whe...

    Authors: Maria Peña-Chilet, Maria T Martínez, Jose A Pérez-Fidalgo, Lorena Peiró-Chova, Sara S Oltra, Eduardo Tormo, Elisa Alonso-Yuste, Beatriz Martinez-Delgado, Pilar Eroles, Joan Climent, Octavio Burgués, Jaime Ferrer-Lozano, Ana Bosch, Ana Lluch and Gloria Ribas

    Citation: BMC Cancer 2014 14:529

    Content type: Research article

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  3. Succinate dehydrogenase subunit B (SDHB) mutations are associated with aggressive pheochromocytoma (PHEO)/paraganglioma (PGL) behavior, often resulting in metastatic disease and fatal outcomes. These tumors are o...

    Authors: Jan Schovanek, Victoria Martucci, Robert Wesley, Tito Fojo, Jaydira del Rivero, Thanh Huynh, Karen Adams, Electron Kebebew, Zdenek Frysak, Constantine A Stratakis and Karel Pacak

    Citation: BMC Cancer 2014 14:523

    Content type: Research article

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  4. Since patients diagnosed with BRAF V600E and V600K mutated advanced melanoma show response to treatment with MAP kinase inhibitors, several sensitive methods have been developed to determine the V600 allele st...

    Authors: Julie Marchant, Alain Mange, Marion Larrieux, Valérie Costes and Jérôme Solassol

    Citation: BMC Cancer 2014 14:519

    Content type: Technical advance

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  5. Mucosal melanomas represent about 1% of all melanoma cases and classically have a worse prognosis than cutaneous melanomas. Due to the rarity of mucosal melanomas, only limited clinical studies with metastatic...

    Authors: Chung-Young Kim, Dae Won Kim, Kevin Kim, Jonathan Curry, Carlos Torres-Cabala and Sapna Patel

    Citation: BMC Cancer 2014 14:516

    Content type: Case report

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  6. Grade IV glioblastomas exist in two forms, primary (de novo) glioblastomas (pGBM) that arise without precursor lesions, and the less common secondary glioblastomas (sGBM) which develop from earlier lower grade le...

    Authors: Victoria K Hill, Thoraia Shinawi, Christopher J Ricketts, Dietmar Krex, Gabriele Schackert, Julien Bauer, Wenbin Wei, Garth Cruickshank, Eamonn R Maher and Farida Latif

    Citation: BMC Cancer 2014 14:506

    Content type: Research article

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  7. Growing evidence exists that the neoplastic stromal cell population (GCTSC) within giant cell tumors (GCT) originates from mesenchymal stem cells (MSC). In a previous study we identified a microRNA signature t...

    Authors: Burkhard Lehner, Pierre Kunz, Heiner Saehr and Joerg Fellenberg

    Citation: BMC Cancer 2014 14:495

    Content type: Research article

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  8. CHEK2 is a multi-cancer susceptibility gene whose common germline mutations are known to contribute to the risk of developing breast and prostate cancer.

    Authors: Gianluca Tedaldi, Rita Danesi, Valentina Zampiga, Michela Tebaldi, Lucia Bedei, Wainer Zoli, Dino Amadori, Fabio Falcini and Daniele Calistri

    Citation: BMC Cancer 2014 14:478

    Content type: Case report

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  9. Genome-wide linkage studies have identified the 9q22 chromosomal region as linked with colorectal cancer (CRC) predisposition. A candidate gene in this region is transforming growth factor β receptor 1 (TGFBR1...

    Authors: Jason P Ross, Linda J Lockett, Bruce Tabor, Ian W Saunders, Graeme P Young, Finlay Macrae, Ignacio Blanco, Gabriel Capella, Glenn S Brown, Trevor J Lockett and Garry N Hannan

    Citation: BMC Cancer 2014 14:475

    Content type: Research article

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  10. Genetic predisposition is the primary risk factor for familial breast cancer. For the majority of familial breast cancer, however, the genetic predispositions remain unknown. All newly identified predispositio...

    Authors: Hongxiu Wen, Yeong C Kim, Carrie Snyder, Fengxia Xiao, Elizabeth A Fleissner, Dina Becirovic, Jiangtao Luo, Bradley Downs, Simon Sherman, Kenneth H Cowan, Henry T Lynch and San Ming Wang

    Citation: BMC Cancer 2014 14:470

    Content type: Research article

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  11. Several epidemiological studies have previously investigated the association between the TP53 codon 72 polymorphism and oral squamous cell carcinoma (OSCC) susceptibility; however, current results are inconsisten...

    Authors: Xian-Tao Zeng, Wei Luo, Pei-Liang Geng, Yi Guo, Yu-Ming Niu and Wei-Dong Leng

    Citation: BMC Cancer 2014 14:469

    Content type: Research article

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  12. Recent work led to recognize sessile serrated adenomas (SSA) as precursor to many of the sporadic colorectal cancers with microsatellite instability (MSI). However, comprehensive analyses of DNA methylation in...

    Authors: Yuta Muto, Takafumi Maeda, Koichi Suzuki, Takaharu Kato, Fumiaki Watanabe, Hidenori Kamiyama, Masaaki Saito, Kei Koizumi, Yuichiro Miyaki, Fumio Konishi, Sergio Alonso, Manuel Perucho and Toshiki Rikiyama

    Citation: BMC Cancer 2014 14:466

    Content type: Research article

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  13. Mutations in NBN, the gene for Nijmegen Breakage Syndrome (NBS), are thought to predispose women to developing breast cancer, but a breast cancer cell line containing mutations in NBN has not yet been describe...

    Authors: Bianca Schröder-Heurich, Natalia Bogdanova, Britta Wieland, Xiaoxi Xie, Monika Noskowicz, Tjoung-Won Park-Simon, Peter Hillemanns, Hans Christiansen and Thilo Dörk

    Citation: BMC Cancer 2014 14:434

    Content type: Research article

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  14. Hypoxia is often encountered in solid tumors and known to contribute to aggressive tumor behavior, radiation- and chemotherapy resistance resulting in a poor prognosis for the cancer patient. MicroRNAs (miRNAs...

    Authors: Caroline MM Gits, Patricia F van Kuijk, Jonneke CWM de Rijck, Nikky Muskens, Moniek BE Jonkers, Wilfred F van IJcken, Ron HJ Mathijssen, Jaap Verweij, Stefan Sleijfer and Erik AC Wiemer

    Citation: BMC Cancer 2014 14:429

    Content type: Research article

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  15. A germline, variant in the BRCA1 3’UTR (rs8176318) was previously shown to predict breast and ovarian cancer risk in women from high-risk families, as well as increased risk of triple negative breast cancer. Here...

    Authors: Jemima J Dorairaj, David W Salzman, Deirdre Wall, Tiffany Rounds, Carina Preskill, Catherine AW Sullivan, Robert Lindner, Catherine Curran, Kim Lezon-Geyda, Terri McVeigh, Lyndsay Harris, John Newell, Michael J Kerin, Marie Wood, Nicola Miller and Joanne B Weidhaas

    Citation: BMC Cancer 2014 14:421

    Content type: Research article

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  16. NQO1 (NAD(P)H: quinone oxidoreductase-1), located on chromosome 16q22, functions primarily to protect normal cells from oxidant stress and electrophilic attack. Recent studies have revealed that NQO1 is expres...

    Authors: Yue Ma, Jienan Kong, Guanghai Yan, Xiangshan Ren, Dan Jin, Tiefeng Jin, Lijuan Lin and Zhenhua Lin

    Citation: BMC Cancer 2014 14:414

    Content type: Research article

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  17. To date only a handful of drugs are available for the treatment of melanoma. Among them vemurafenib, a BrafV600E specific inhibitor, showed promising results in terms of response rate and increase in median survi...

    Authors: Madhuri Bhandaru, Gholamreza Safaee Ardekani, Guohong Zhang, Magdalena Martinka, Kevin J McElwee, Gang Li and Anand Rotte

    Citation: BMC Cancer 2014 14:398

    Content type: Research article

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  18. The progression of low-risk del(5q) myelodysplastic syndrome to acute myeloid leukemia is increased when associated with mutations of TP53, or with additional chromosomal abnormalities. However, to date the progn...

    Authors: Alberto L’Abbate, Crocifissa Lo Cunsolo, Ettore Macrì, Paolo Iuzzolino, Cristina Mecucci, Claudio Doglioni, Michelina Coco, Lucia Anna Muscarella, Simona Salati, Enrico Tagliafico, Carla Minoia, Giacoma De Tullio, Attilio Guarini, Nicoletta Testoni, Claudio Agostinelli and Clelia Tiziana Storlazzi

    Citation: BMC Cancer 2014 14:396

    Content type: Case report

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  19. The hypermethylation of Alcohol dehydrogenase iron containing 1 (ADHFE1) was recently reported to be associated with colorectal cancer (CRC) differentiation. However, the effect of alcohol on ADHFE1 hypermethylat...

    Authors: Ji Wook Moon, Soo Kyung Lee, Yong Woo Lee, Jung Ok Lee, Nami Kim, Hye Jeong Lee, Jung Seon Seo, Jin Kim, Hyeon Soo Kim and Sun-Hwa Park

    Citation: BMC Cancer 2014 14:377

    Content type: Research article

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  20. There is a body of evidence that shows a link between tumorigenesis and ribosome biogenesis. The precursor of mature 18S, 28S and 5.8S ribosomal RNAs is transcribed from the ribosomal DNA gene (rDNA), which ex...

    Authors: Maria Giulia Bacalini, Annalisa Pacilli, Cristina Giuliani, Marianna Penzo, Davide Treré, Chiara Pirazzini, Stefano Salvioli, Claudio Franceschi, Lorenzo Montanaro and Paolo Garagnani

    Citation: BMC Cancer 2014 14:361

    Content type: Research article

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  21. IL-6 triggers oncogenic/angiogenic signals and the cytokine-dependent pro-cachexia cascade. The prognostic role of the functional IL-6 (promoter) rs1800795 and the IL-6R (receptor) rs8192284 single nucleotide pol...

    Authors: Annamaria Ruzzo, Vincenzo Catalano, Emanuele Canestrari, Elisa Giacomini, Daniele Santini, Giuseppe Tonini, Bruno Vincenzi, Giammaria Fiorentini, Mauro Magnani and Francesco Graziano

    Citation: BMC Cancer 2014 14:357

    Content type: Research article

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  22. The association between alpha-1 antitrypsin (AAT) deficiency and colorectal cancer (CRC) is currently controversial. The present study compares AAT serum concentrations and gene frequencies between a group of ...

    Authors: Sergio Pérez-Holanda, Ignacio Blanco, Manuel Menéndez and Luis Rodrigo

    Citation: BMC Cancer 2014 14:355

    Content type: Research article

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  23. Metastasis to the cervical (neck) lymph nodes is one of the most significant clinical factors responsible for death from oral squamous cell carcinoma (SCC). Therefore, the lymph nodes are frequently removed wh...

    Authors: Kenichiro Uchida, Ratna Veeramachaneni, Bing Huey, Aditi Bhattacharya, Brian L Schmidt and Donna G Albertson

    Citation: BMC Cancer 2014 14:353

    Content type: Research article

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  24. Esophageal cancer ranks eighth among frequent cancers worldwide. Our aim was to investigate whether and at which neoplastic stage promoter hypermethylation of CAV1 is involved in human esophageal carcinogenesis.

    Authors: Zhe Jin, Liang Wang, Ziyi Cao, Yulan Cheng, Yan Gao, Xianling Feng, Si Chen, Huimin Yu, Wenjing Wu, Zhenfu Zhao, Ming Dong, Xiaojing Zhang, Jie Liu, Xinmin Fan, Yuriko Mori and Stephen J Meltzer

    Citation: BMC Cancer 2014 14:345

    Content type: Research article

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  25. BRCA1 plays an essential role in maintaining genome stability. Inherited BRCA1 germline mutation (BRCA1+) is a determined genetic predisposition leading to high risk of breast cancer. While BRCA1+ induces breast ...

    Authors: Fengxia Xiao, Yeong C Kim, Carrie Snyder, Hongxiu Wen, Pei Xian Chen, Jiangtao Luo, Dina Becirovic, Bradley Downs, Kenneth H Cowan, Henry Lynch and San Ming Wang

    Citation: BMC Cancer 2014 14:342

    Content type: Research article

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  26. It is known that all tumors studied in sufficient number to draw conclusions show characteristic/specific chromosomal rearrangements, and the identification of these chromosomes and the genes rearranged behind...

    Authors: Francesca Micci, Lisbeth Haugom, Vera M Abeler, Ben Davidson, Claes G Tropé and Sverre Heim

    Citation: BMC Cancer 2014 14:315

    Content type: Research article

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  27. Mercaptopurine (6-MP) plays a pivotal role in treatment of childhood acute lymphoblastic leukemia (ALL); however, interindividual variability in toxicity of this drug due to genetic polymorphism in 6-MP metabo...

    Authors: Mauricio J Farfan, Carolina Salas, Cristina Canales, Felipe Silva, Milena Villarroel, Katherine Kopp, Juan P Torres, María E Santolaya and Jorge Morales

    Citation: BMC Cancer 2014 14:299

    Content type: Research article

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  28. Malignant ascites is often present at diagnostic in women with advanced ovarian cancer (OC) and its presence is associated with a worse outcome. Human peritoneal mesothelial cells (HPMCs) are key components of...

    Authors: Isabelle Matte, Denis Lane, Dimcho Bachvarov, Claudine Rancourt and Alain Piché

    Citation: BMC Cancer 2014 14:288

    Content type: Research article

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  29. The transcription factor GATA3 is a favorable prognostic indicator in estrogen receptor-α (ERα)-positive breast tumors in which it participates with ERα and FOXA1 in a complex transcriptional regulatory progra...

    Authors: Aleksandra B Adomas, Sara A Grimm, Christine Malone, Motoki Takaku, Jennifer K Sims and Paul A Wade

    Citation: BMC Cancer 2014 14:278

    Content type: Research article

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  30. Advanced squamous cervical cancer, one of the most commonly diagnosed cancers in women, still remains a major problem in oncology due to treatment failure and distant metastasis. Antitumor therapy failure is d...

    Authors: Ovidiu Balacescu, Loredana Balacescu, Oana Tudoran, Nicolae Todor, Meda Rus, Rares Buiga, Sergiu Susman, Bogdan Fetica, Laura Pop, Laura Maja, Simona Visan, Claudia Ordeanu, Ioana Berindan-Neagoe and Viorica Nagy

    Citation: BMC Cancer 2014 14:246

    Content type: Research article

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  31. Pleomorphic xanthoastrocytoma (PXA) is a rare WHO grade II tumor accounting for less than 1% of all astrocytomas. Malignant transformation into PXA with anaplastic features, is unusual and correlates with poor...

    Authors: Ramón Martínez, F Javier Carmona, Miguel Vizoso, Veit Rohde, Matthias Kirsch, Gabriele Schackert, Santiago Ropero, Werner Paulus, Alonso Barrantes, Antonio Gomez and Manel Esteller

    Citation: BMC Cancer 2014 14:213

    Content type: Research article

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  32. The epidermal growth factor receptor (EGFR) is differently expressed in breast cancer, and its presence may favor cancer progression. We hypothesized that two EGFR functional polymorphisms, a (CA)n repeat in intr...

    Authors: Marcelo Sobral Leite, Letícia Carlos Giacomin, Diogo Nascimento Piranda, Juliana Simões Festa-Vasconcellos, Vanessa Indio-do-Brasil, Sérgio Koifman, Rodrigo Soares de Moura-Neto, Marcelo Alex de Carvalho and Rosane Vianna-Jorge

    Citation: BMC Cancer 2014 14:190

    Content type: Research article

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  33. The aim of this study was to examine the association of non-random X chromosome inactivation (XCI) and loss of heterozygosity (LOH) at Xq25 with breast cancer development.

    Authors: Hui-Tzu Chen, Yao-Chung Wu, Shou-Tung Chen, Hsien-Chang Tsai and Yi-Chih Chien

    Citation: BMC Cancer 2014 14:144

    Content type: Research article

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  34. To evaluate the insulin receptor isoform mRNA expression status in non-small cell lung cancer (NSCLC) patients.

    Authors: Liyan Jiang, Wei Zhu, Katie Streicher, Chris Morehouse, Philip Brohawn, Xiaoxiao Ge, Zhengwei Dong, Xiaolu Yin, Guanshan Zhu, Yi Gu, Koustubh Ranade, Brandon W Higgs, Yihong Yao and Jiaqi Huang

    Citation: BMC Cancer 2014 14:131

    Content type: Research article

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  35. Acute leukemia in early age (EAL) is characterized by acquired genetic alterations such as MLL rearrangements (MLL-r). The aim of this case-controlled study was to investigate whether single nucleotide polymorphi...

    Authors: Mariana Emerenciano, Thayana Conceição Barbosa, Bruno Almeida Lopes, Caroline Barbieri Blunck, Alessandra Faro, Camilla Andrade, Claus Meyer, Rolf Marschalek and Maria S Pombo-de-Oliveira

    Citation: BMC Cancer 2014 14:127

    Content type: Research article

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  36. It remains presently unclear whether disease progression in colorectal carcinoma (CRC), from early, to invasive and metastatic forms, is associated to a gradual increase in genetic instability and to a scheme ...

    Authors: Béatrice Orsetti, Janick Selves, Caroline Bascoul-Mollevi, Laurence Lasorsa, Karine Gordien, Frédéric Bibeau, Blandine Massemin, François Paraf, Isabelle Soubeyran, Isabelle Hostein, Valérie Dapremont, Rosine Guimbaud, Christophe Cazaux, Michel Longy and Charles Theillet

    Citation: BMC Cancer 2014 14:121

    Content type: Research article

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  37. MicroRNAs(miRNAs) are small non-coding RNAs that participate in a variety of biologic processes, and dysregulation of miRNA is always associated with cancer development and progression. Aberrant expression of ...

    Authors: Guang-jun Zhang, He Zhou, Hua-xu Xiao, Yu Li and Tong Zhou

    Citation: BMC Cancer 2014 14:109

    Content type: Research article

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  38. GATA-5, a zinc-finger transcription factor and member of the GATA family proteins 1–6, is known to be involved in cellular differentiation. We recently found that tumor-specific hypermethylation of the GATA5 CpG ...

    Authors: Inga Peters, Natalia Dubrowinskaja, Michael Kogosov, Mahmoud Abbas, Jörg Hennenlotter, Christoph von Klot, Axel S Merseburger, Arnulf Stenzl, Ralph Scherer, Markus A Kuczyk and Jürgen Serth

    Citation: BMC Cancer 2014 14:101

    Content type: Research article

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  39. Preclinical and clinical studies have shown for decades that tumor cells demonstrate significantly enhanced sensitivity to “fever range” hyperthermia (increasing the intratumoral temperature to 42-45°C) than n...

    Authors: Clarissa Amaya, Vittal Kurisetty, Jessica Stiles, Alice M Nyakeriga, Arunkumar Arumugam, Rajkumar Lakshmanaswamy, Cristian E Botez, Dianne C Mitchell and Brad A Bryan

    Citation: BMC Cancer 2014 14:81

    Content type: Research article

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  40. Improved insight into the molecular characteristics of the different ovarian cancer subgroups is needed for developing a more individualized and optimized treatment regimen. The aim of this study was to a) ide...

    Authors: Bente Vilming Elgaaen, Ole Kristoffer Olstad, Kari Bente Foss Haug, Berit Brusletto, Leiv Sandvik, Anne Cathrine Staff, Kaare M Gautvik and Ben Davidson

    Citation: BMC Cancer 2014 14:80

    Content type: Research article

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  41. An early age at Breast Cancer (BC) onset may be a hallmark of inherited predisposition, but BRCA1/2 mutations are only found in a minority of younger BC patients. Among the others, a fraction may carry mutatio...

    Authors: Laura Maria Pradella, Cecilia Evangelisti, Claudia Ligorio, Claudio Ceccarelli, Iria Neri, Roberta Zuntini, Laura Benedetta Amato, Simona Ferrari, Alberto Maria Martelli, Giuseppe Gasparre and Daniela Turchetti

    Citation: BMC Cancer 2014 14:70

    Content type: Case report

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  42. Tumor expression of estrogen receptor (ER) is an important marker of prognosis, and is predictive of response to endocrine therapy in breast cancer. Several studies have observed that epigenetic events, such m...

    Authors: Joaquina Martínez-Galán, Blanca Torres-Torres, María Isabel Núñez, Jesús López-Peñalver, Rosario Del Moral, José Mariano Ruiz De Almodóvar, Salomón Menjón, Ángel Concha, Clara Chamorro, Sandra Ríos and Juan Ramón Delgado

    Citation: BMC Cancer 2014 14:59

    Content type: Research article

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  43. Methylentetrahydrofolate reductase (MTHFR) plays a major role in folate metabolism and consequently could be an important factor for the efficacy of a treatment with 5-fluorouracil. Our aim was to evaluate the...

    Authors: Susanne Blank, Sivaramakrishna Rachakonda, Gisela Keller, Wilko Weichert, Florian Lordick, Rupert Langer, Christoph Springfeld, Thomas Bruckner, Karen Becker, Rajiv Kumar and Katja Ott

    Citation: BMC Cancer 2014 14:58

    Content type: Research article

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  44. The development of colorectal cancer (CRC) is accompanied by extensive epigenetic changes, including frequent regional hypermethylation particularly of gene promoter regions. Specific genes, including SEPT9, VIM1

    Authors: Susan M Mitchell, Jason P Ross, Horace R Drew, Thu Ho, Glenn S Brown, Neil FW Saunders, Konsta R Duesing, Michael J Buckley, Rob Dunne, Iain Beetson, Keith N Rand, Aidan McEvoy, Melissa L Thomas, Rohan T Baker, David A Wattchow, Graeme P Young…

    Citation: BMC Cancer 2014 14:54

    Content type: Research article

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  45. Breast cancer is the most common malignancy that develops in women, responsible for the highest cancer-associated death rates. Triple negative breast cancers represent an important subtype that have an aggress...

    Authors: Kelly A Avery-Kiejda, Stephen G Braye, Andrea Mathe, John F Forbes and Rodney J Scott

    Citation: BMC Cancer 2014 14:51

    Content type: Research article

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  46. Hypoxia-induced genes are potential targets in cancer therapy. Responses to hypoxia have been extensively studied in vitro, however, they may differ in vivo due to the specific tumor microenvironment. In this stu...

    Authors: Katharina Leithner, Christoph Wohlkoenig, Elvira Stacher, Jörg Lindenmann, Nicole A Hofmann, Birgit Gallé, Christian Guelly, Franz Quehenberger, Philipp Stiegler, Freyja-Maria Smolle-Jüttner, Sjaak Philipsen, Helmut H Popper, Andelko Hrzenjak, Andrea Olschewski and Horst Olschewski

    Citation: BMC Cancer 2014 14:40

    Content type: Research article

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  47. Renal cell carcinoma (RCC) is marked by high mortality rate. To date, no robust risk stratification by clinical or molecular prognosticators of cancer-specific survival (CSS) has been established for early sta...

    Authors: Daniel Vergho, Susanne Kneitz, Andreas Rosenwald, Charlotte Scherer, Martin Spahn, Maximilian Burger, Hubertus Riedmiller and Burkhard Kneitz

    Citation: BMC Cancer 2014 14:25

    Content type: Research article

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  48. Primary small cell carcinoma of the esophagus (PSCCE) is a rare and aggressive tumor with poor prognosis. The aim of this study was to investigate the existence of EGFR, KRAS, PIK3CA and PTEN mutations in PSCCE.

    Authors: Zhimin Zhang, Hualiang Xiao, Fei Xie, Hui Zhang, Chuan Chen, He Xiao, Zhenzhou Yang, Dong Wang, Zengpeng Li and Ge Wang

    Citation: BMC Cancer 2014 14:19

    Content type: Research article

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