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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. Human epidermal growth factor receptor-2 (HER2) overexpression and gene amplification are currently established by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. This stud...

    Authors: Thomas v O Hansen, Jonas Vikesaa, Sine S Buhl, Henrik H Rossing, Vera Timmermans-Wielenga and Finn C Nielsen

    Citation: BMC Cancer 2015 15:35

    Content type: Research article

    Published on:

  2. Germline mutations in PALB2 have been identified in approximately 1% of familial breast cancer (BC) in several populations. Nevertheless its contribution in the South-American population is unknown. The goal of t...

    Authors: Yessica Leyton, Patricio Gonzalez-Hormazabal, Rafael Blanco, Teresa Bravo, Ricardo Fernandez-Ramires, Sebastian Morales, Natalia Landeros, Jose M Reyes, Octavio Peralta, Julio C Tapia, Fernando Gomez, Enrique Waugh, Gladys Ibañez, Janara Pakomio, Gilberto Grau and Lilian Jara

    Citation: BMC Cancer 2015 15:30

    Content type: Research article

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  3. The number of predictive biomarkers that will be necessary to assess in clinical practice will increase with the availability of drugs that target specific molecular alterations. Therefore, diagnostic laborato...

    Authors: Bastiaan BJ Tops, Nicola Normanno, Henriette Kurth, Eliana Amato, Andrea Mafficini, Nora Rieber, Delphine Le Corre, Anna Maria Rachiglio, Anne Reiman, Orla Sheils, Christoph Noppen, Ludovic Lacroix, Ian A Cree, Aldo Scarpa, Marjolijn JL Ligtenberg and Pierre Laurent-Puig

    Citation: BMC Cancer 2015 15:26

    Content type: Research article

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  4. PRDM5 is an epigenetic regulator that has been recognized as an important tumour suppressor gene. Silencing of PRDM5 by promoter hypermethylation has been demonstrated in several cancer types and PRDM5 loss resul...

    Authors: Catherine E Bond, Mark L Bettington, Sally-Ann Pearson, Diane M McKeone, Barbara A Leggett and Vicki LJ Whitehall

    Citation: BMC Cancer 2015 15:20

    Content type: Research article

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  5. EphA5 is a member of the Eph/ephrin family and plays a critical role in the regulation of carcinogenesis. A significant reduction of EphA5 transcripts in high-grade prostate cancer tissue was shown using a tra...

    Authors: Shibao Li, Yingfeng Zhu, Chunguang Ma, Zhenhua Qiu, Xinju Zhang, Zhihua Kang, Zhiyuan Wu, Hua Wang, Xiao Xu, Hu Zhang, Guoqiang Ren, Jianmin Tang, Xiangyu Li and Ming Guan

    Citation: BMC Cancer 2015 15:18

    Content type: Research article

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  7. Evidence from cachectic cancer patients and animal models of cancer cachexia supports the involvement of Forkhead box O (FoxO) transcription factors in driving cancer-induced skeletal muscle wasting. However, ...

    Authors: Sarah M Judge, Chia-Ling Wu, Adam W Beharry, Brandon M Roberts, Leonardo F Ferreira, Susan C Kandarian and Andrew R Judge

    Citation: BMC Cancer 2014 14:997

    Content type: Research article

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  8. It is well established that genetic and epigenetic alterations are common events in prostate cancer, which may lead to aberrant expression of critical genes. The importance of epigenetic mechanisms in prostate...

    Authors: Marjolaine Ngollo, Andre Lebert, Aslihan Dagdemir, Gaelle Judes, Seher Karsli-Ceppioglu, Marine Daures, Jean-Louis Kemeny, Frederique Penault-Llorca, Jean-Paul Boiteux, Yves-Jean Bignon, Laurent Guy and Dominique Bernard-Gallon

    Citation: BMC Cancer 2014 14:994

    Content type: Research article

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  9. Ovarian low-grade serous carcinoma (LGSC) has fewer mutations than ovarian high-grade serous carcinoma (HGSC) and a less aggressive clinical course. However, an overwhelming majority of LGSC patients do not re...

    Authors: Alicia A Tone, Melissa K McConechy, Winnie Yang, Jiarui Ding, Stephen Yip, Esther Kong, Kwong-Kwok Wong, David M Gershenson, Helen Mackay, Sohrab Shah, Blake Gilks, Anna V Tinker, Blaise Clarke, Jessica N McAlpine and David Huntsman

    Citation: BMC Cancer 2014 14:982

    Content type: Research article

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  10. Uveal melanoma is a tumour arising from melanocytes of the eye, and 30 per cent of these patients develop liver metastases. Exosomes are small RNA containing nano-vesicles released by most cells, including mal...

    Authors: Maria Eldh, Roger Olofsson Bagge, Cecilia Lässer, Joar Svanvik, Margareta Sjöstrand, Jan Mattsson, Per Lindnér, Dong-Sic Choi, Yong Song Gho and Jan Lötvall

    Citation: BMC Cancer 2014 14:962

    Content type: Research article

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  11. Breast cancer is a complex multifactorial genetic disease. Among other factors, race and, to an even greater extent, viruses are known to influence the development of this heterogeneous disease. It has been re...

    Authors: Alberto Cedro-Tanda, Alejandro Córdova-Solis, Teresa Juárez-Cedillo, Emmanuel Pina-Jiménez, Marta E Hernández-Caballero, Christian Moctezuma-Meza, Germán Castelazo-Rico, Alejandro Gómez-Delgado, Alejandro Cruz Monsalvo-Reyes, Fabio A Salamanca-Gómez, Diego J Arenas-Aranda and Normand García-Hernández

    Citation: BMC Cancer 2014 14:942

    Content type: Research article

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  12. Long non-coding RNAs have been shown to have critical regulatory roles in cancer biology. However, the contributions of lncRNAs to gastric cancer remain largely unknown.

    Authors: Yuehua Han, Jun Ye, Dang Wu, Pin Wu, Zhigang Chen, Jian Chen, Shunliang Gao and Jian Huang

    Citation: BMC Cancer 2014 14:932

    Content type: Research article

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  13. PREDICT (http://​www.​predict.​nhs.​uk) is a prognostication and treatment benefit tool for early breast cancer (EBC). The aim of this study was to incorpo...

    Authors: Gordon C Wishart, Emad Rakha, Andrew Green, Ian Ellis, Hamid Raza Ali, Elena Provenzano, Fiona M Blows, Carlos Caldas and Paul DP Pharoah

    Citation: BMC Cancer 2014 14:908

    Content type: Research article

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  15. Posttranslational protein modifications are known to modulate key biological processes like proliferation and apoptosis. Accumulating evidence shows that ST6GAL1, an enzyme that catalyzes the transfer of siali...

    Authors: Pia Antony, Michael Rose, Axel Heidenreich, Ruth Knüchel, Nadine T Gaisa and Edgar Dahl

    Citation: BMC Cancer 2014 14:901

    Content type: Research article

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  16. There is emerging evidence that Wnt pathway activity may increase during the progression from colorectal adenoma to carcinoma and that this increase is potentially an important step towards the invasive stage....

    Authors: Ana-Luisa Silva, Sarah N Dawson, Mark J Arends, Kiran Guttula, Nigel Hall, Ewen A Cameron, Tim H-M Huang, James D Brenton, Simon Tavaré, Mariann Bienz and Ashraf EK Ibrahim

    Citation: BMC Cancer 2014 14:891

    Content type: Research article

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  17. Upregulator of cell proliferation 4 (URG4) has been implicated in the oncogenesis of certain cancers. However, the correlation between URG4 expression and clinicopathological significance in human cancer remai...

    Authors: Lan Zhang, He Huang, Longjuan Zhang, Teng Hou, Shu Wu, Qidan Huang, Libing Song and Jihong Liu

    Citation: BMC Cancer 2014 14:885

    Content type: Research article

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  18. Endometrial cancer (EC) is the 8th leading cause of cancer death amongst American women. Most ECs are endometrioid, serous, or clear cell carcinomas, or an admixture of histologies. Serous and clear ECs are clini...

    Authors: Meghan L Rudd, Hassan Mohamed, Jessica C Price, Andrea J O’Hara, Matthieu Le Gallo, Mary Ellen Urick, Pedro Cruz, Suiyuan Zhang, Nancy F Hansen, Andrew K Godwin, Dennis C Sgroi, Tyra G Wolfsberg, James C Mullikin, Maria J Merino and Daphne W Bell

    Citation: BMC Cancer 2014 14:884

    Content type: Research article

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  19. Polymorphisms in angiogenesis-related genes and metabolic syndrome (MetS) risk factors play important roles in cancer development. Moreover, recent studies have reported associations between a number of 3′-UTR...

    Authors: Young Joo Jeon, Jong Woo Kim, Hye Mi Park, Hyo Geun Jang, Jung O Kim, Jisu Oh, So Young Chong, Sung Won Kwon, Eo Jin Kim, Doyeun Oh and Nam Keun Kim

    Citation: BMC Cancer 2014 14:881

    Content type: Research article

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  20. The clinical behaviour of colon cancer is heterogeneous. Five-year overall survival is 50-65% with all stages included. Recurring somatic chromosomal alterations have been identified and some have shown potent...

    Authors: Markus Mayrhofer, Hanna Göransson Kultima, Helgi Birgisson, Magnus Sundström, Lucy Mathot, Karolina Edlund, Björn Viklund, Tobias Sjöblom, Johan Botling, Patrick Micke, Lars Påhlman, Bengt Glimelius and Anders Isaksson

    Citation: BMC Cancer 2014 14:872

    Content type: Research article

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  22. Alterations in the redox balance are involved in the origin, promotion and progression of cancer. Inter-individual differences in the oxidative stress regulation can explain a part of the variability in cancer...

    Authors: Patricia Rodrigues, Griselda de Marco, Jessica Furriol, Maria Luisa Mansego, Mónica Pineda-Alonso, Anna Gonzalez-Neira, Juan Carlos Martin-Escudero, Javier Benitez, Ana Lluch, Felipe J Chaves and Pilar Eroles

    Citation: BMC Cancer 2014 14:861

    Content type: Research article

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  23. Prostate cancer is one of the leading causes of cancer death amongst men in economically advanced countries. The disease is characterized by a greatly varying clinical course, where some patients harbor non- o...

    Authors: Martin Mørck Mortensen, Søren Høyer, Torben Falck Ørntoft, Karina Dalsgaard Sørensen, Lars Dyrskjøt and Michael Borre

    Citation: BMC Cancer 2014 14:859

    Content type: Research article

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  24. Chromosomal instability in exfoliated urothelial cells has been associated with the development of bladder cancer. Here, we analyzed the accumulation of copy number variations (CNVs) using fluorescence in situ...

    Authors: Nadine Bonberg, Beate Pesch, Thomas Behrens, Georg Johnen, Dirk Taeger, Katarzyna Gawrych, Christian Schwentner, Harald Wellhäußer, Matthias Kluckert, Gabriele Leng, Michael Nasterlack, Christoph Oberlinner, Arnulf Stenzl and Thomas Brüning

    Citation: BMC Cancer 2014 14:854

    Content type: Research article

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  25. One of the hallmarks of cancer is the occurrence of high levels of chromosomal rearrangements as a result of inaccurate repair of double-strand breaks (DSB). Germline mutations in BRCA and RAD51 genes, involved i...

    Authors: Ana Paula Carneiro Brandalize, Lavínia Schüler-Faccini, Jean-Sébastien Hoffmann, Maira Caleffi, Christophe Cazaux and Patricia Ashton-Prolla

    Citation: BMC Cancer 2014 14:850

    Content type: Research article

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  26. The procoagulant state in cancer increases the thrombotic risk, but also supports tumor progression. To investigate the molecular mechanisms controlling cancer and hemostasis, we conducted a case-control study...

    Authors: Mari Tinholt, Marte Kathrine Viken, Anders Erik Dahm, Hans Kristian Moen Vollan, Kristine Kleivi Sahlberg, Øystein Garred, Anne-Lise Børresen-Dale, Anne Flem Jacobsen, Vessela Kristensen, Ida Bukholm, Rolf Kåresen, Ellen Schlichting, Grethe Skretting, Benedicte Alexandra Lie, Per Morten Sandset and Nina Iversen

    Citation: BMC Cancer 2014 14:845

    Content type: Research article

    Published on:

  27. Current knowledge about the molecular properties and prognostic markers of upper tract urothelial carcinoma (UTUC) is sparse and often based on bladder urothelial carcinoma (UC), which is thought to share comm...

    Authors: Song Wu, Jiahao Chen, Pei Dong, Shiqiang Zhang, Yingying He, Liang Sun, Jialou Zhu, Yanbing Cheng, Xianxin Li, Aifa Tang, Yi Huang, Yaoting Gui, Chunxiao Liu, Guosheng Yang, Fangjian Zhou, Zhiming Cai…

    Citation: BMC Cancer 2014 14:836

    Content type: Research article

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  28. The translocations of the anaplastic lymphoma kinase (ALK) gene with the echinoderm microtubule-associated protein-like 4 (EML4) gene on chromosome 2p have been identified in non-small-cell lung cancers (NSCLCs) ...

    Authors: Yongjun Guo, Jie Ma, Xiaodong Lyu, Hai Liu, Bing Wei, Jiuzhou Zhao, Shuang Fu, Lu Ding and Jihong Zhang

    Citation: BMC Cancer 2014 14:834

    Content type: Research article

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  29. MicroRNA-21 (miR-21) has been suggested to play a significant role in the prognosis of carcinoma. The recognition of novel biomarkers for the prediction of cancer outcomes is urgently required. However, the po...

    Authors: Wenjia Wang, Jinhui Li, Wei Zhu, Chen Gao, RuiJingfang Jiang, Wenxue Li, Qiansheng Hu and Bo Zhang

    Citation: BMC Cancer 2014 14:819

    Content type: Research article

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  30. Radiotherapy is a chosen treatment option for prostate cancer patients and while some tumours respond well, up to 50% of patients may experience tumour recurrence. Identification of functionally relevant predi...

    Authors: Arabella Young, Rachael Berry, Adele F Holloway, Nicholas B Blackburn, Joanne L Dickinson, Marketa Skala, Jessica L Phillips and Kate H Brettingham-Moore

    Citation: BMC Cancer 2014 14:808

    Content type: Research article

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  31. Cigarette smoke is associated with the majority of lung cancers: however, 25% of lung cancer patients are non-smokers, and half of all newly diagnosed lung cancer patients are former smokers. Lung tumors exhib...

    Authors: Emily A Vucic, Kelsie L Thu, Larissa A Pikor, Katey SS Enfield, John Yee, John C English, Calum E MacAulay, Stephen Lam, Igor Jurisica and Wan L Lam

    Citation: BMC Cancer 2014 14:778

    Content type: Research article

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  32. The CpG island methylator phenotype (CIMP) of clear cell renal cell carcinomas (ccRCCs) is characterized by accumulation of DNA methylation at CpG islands and poorer patient outcome. The aim of this study was ...

    Authors: Ying Tian, Eri Arai, Masahiro Gotoh, Motokiyo Komiyama, Hiroyuki Fujimoto and Yae Kanai

    Citation: BMC Cancer 2014 14:772

    Content type: Research article

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  33. Mutations in the activation segment of the v-raf murine sarcoma viral oncogene homolog B (BRAF) gene are present in approximately 50% of melanomas. The selective BRAF inhibitor vemurafenib has demonstrated signif...

    Authors: Stéphanie Trudel, Norbert Odolczyk, Julie Dremaux, Jérôme Toffin, Aline Regnier, Henri Sevestre, Piotr Zielenkiewicz, Jean-Philippe Arnault and Brigitte Gubler

    Citation: BMC Cancer 2014 14:727

    Content type: Case report

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  34. Glioblastoma is a highly malignant brain tumor for which no cure is available. To identify new therapeutic targets, we performed a mutation analysis of kinase genes in glioblastoma.

    Authors: Fonnet E Bleeker, Simona Lamba, Carlo Zanon, Remco J Molenaar, Theo JM Hulsebos, Dirk Troost, Angela A van Tilborg, W Peter Vandertop, Sieger Leenstra, Cornelis JF van Noorden and Alberto Bardelli

    Citation: BMC Cancer 2014 14:718

    Content type: Research article

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  35. Acute promyelocytic leukemia (APL) is characterized by the reciprocal translocation t(15;17), which fuses PML with retinoic acid receptor alpha (RARα). Although PML-RARα is crucially important for pathogenesis...

    Authors: Chengwu Zeng, Yan Xu, Ling Xu, Xibao Yu, Jingjing Cheng, Lijian Yang, Shaohua Chen and Yangqiu Li

    Citation: BMC Cancer 2014 14:693

    Content type: Research article

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  36. About 10-15% of adult gastrointestinal stromal tumors (GIST) and the vast majority of pediatric GIST do not harbour KIT or platelet-derived growth factor receptor alpha (PDGFRA) mutations (J Clin Oncol 22:3813–38...

    Authors: Margherita Nannini, Annalisa Astolfi, Milena Urbini, Valentina Indio, Donatella Santini, Michael C Heinrich, Christopher L Corless, Claudio Ceccarelli, Maristella Saponara, Anna Mandrioli, Cristian Lolli, Giorgio Ercolani, Giovanni Brandi, Guido Biasco and Maria A Pantaleo

    Citation: BMC Cancer 2014 14:685

    Content type: Research article

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  37. Oral tongue squamous cell carcinomas (TSCC) are a unique subset of head and neck cancers with a distinct demographic profile, where up to half of the cases are never smokers. A small proportion of patients wit...

    Authors: Daniel SW Tan, Weining Wang, Hui Sun Leong, Pui Hoon Sew, Dawn P Lau, Fui Teen Chong, Sai Sakktee Krisna, Tony KH Lim and N Gopalakrishna Iyer

    Citation: BMC Cancer 2014 14:679

    Content type: Research article

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  38. Previously we have suggested that cancer cells develop a mechanism(s) which allows for either: silencing of the wild-type TP53 transcription, degradation of the wild-type TP53 mRNA, or selective overproduction of...

    Authors: Marta Winiecka-Klimek, Malgorzata Szybka, Piotr Rieske, Sylwester Piaskowski, Michal Bienkowski, Maciej Walczak, Marcin Pacholczyk, Michal Rostkowski, Jolanta Zieba, Mateusz Banaszczyk, Krystyna Hulas-Bigoszewska, Joanna Peciak, Rafal Pawliczak and Ewelina Stoczynska-Fidelus

    Citation: BMC Cancer 2014 14:669

    Content type: Research article

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  39. Hamartomatous polyposis syndromes (HPS) are inherited conditions associated with high cancer risk. They include the Peutz-Jeghers and the PTEN hamartoma tumor syndromes, which are caused by mutations in the LKB1 ...

    Authors: Giovanna Forte, Valentina Grossi, Valentina Celestini, Giuseppe Lucisano, Marco Scardapane, Dora Varvara, Margherita Patruno, Rosanna Bagnulo, Daria Loconte, Laura Giunti, Antonio Petracca, Sabrina Giglio, Maurizio Genuardi, Fabio Pellegrini, Nicoletta Resta and Cristiano Simone

    Citation: BMC Cancer 2014 14:661

    Content type: Research article

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  40. A large body of genetic research has focused on the potential role that mitochondrial DNA (mtDNA) variants might play on the predisposition to common and complex (multi-factorial) diseases. It has been argued ...

    Authors: Antonio Salas, Manuel García-Magariños, Ian Logan and Hans-Jürgen Bandelt

    Citation: BMC Cancer 2014 14:659

    Content type: Research article

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  41. Prostate cancer has a variable clinical behaviour with frequently unpredictable outcome. DNA methylation plays an important role in determining the biology of cancer but prognostic information is scanty. We as...

    Authors: Nataša Vasiljević, Amar S Ahmad, Mangesh A Thorat, Gabrielle Fisher, Daniel M Berney, Henrik Møller, Christopher S Foster, Jack Cuzick and Attila T Lorincz

    Citation: BMC Cancer 2014 14:655

    Content type: Research article

    Published on:

  42. Several studies on the use of erythropoietin (Epo) to treat anaemia in patients undergoing cancer treatment have shown adverse effects on tumour control and survival. Experimental studies indicate that this co...

    Authors: Gustaf Lindgren, Lars Ekblad, Johan Vallon-Christersson, Elisabeth Kjellén, Maria Gebre-Medhin and Johan Wennerberg

    Citation: BMC Cancer 2014 14:648

    Content type: Research article

    Published on:

  43. The existence of two distinct groups of tumors with different clinical characteristic is a remarkable feature of transitional cell carcinomas (TCCs) of the bladder. More than 70% are low-grade (LG) non-infiltr...

    Authors: Donatella Conconi, Elena Panzeri, Serena Redaelli, Giorgio Bovo, Paolo Viganò, Guido Strada, Leda Dalprà and Angela Bentivegna

    Citation: BMC Cancer 2014 14:646

    Content type: Research article

    Published on:

  44. Large genomic rearrangements (LGRs) in the BRCA1/2 genes are frequently observed in breast cancer patients who are negative for BRCA1/2 small mutations. Here, we examined 221 familial breast cancer patients from ...

    Authors: Moon-Woo Seong, Sung Im Cho, Kyu Hyung Kim, Il Yong Chung, Eunyoung Kang, Jong Won Lee, Sue K Park, Min Hyuk Lee, Doo Ho Choi, Cha Kyong Yom, Woo-Chul Noh, Myung Chul Chang, Sung Sup Park and Sung-Won Kim

    Citation: BMC Cancer 2014 14:645

    Content type: Research article

    Published on:

  45. Although several single-nucleotide polymorphisms in microRNA (miRNA) genes have been associated with primary hepatocellular carcinoma, published findings regarding this relationship are inconsistent and inconc...

    Authors: Jia-Hui Qi, Jin Wang, Jinyun Chen, Fan Shen, Jing-Tao Huang, Subrata Sen, Xin Zhou and Song-Mei Liu

    Citation: BMC Cancer 2014 14:643

    Content type: Research article

    Published on:

  46. O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation is reported to be a prognostic and predictive factor of alkylating chemotherapy for glioblastoma patients. Methylation specific PCR (MSP) has bee...

    Authors: Manabu Kanemoto, Mitsuaki Shirahata, Akiyo Nakauma, Katsumi Nakanishi, Kazuya Taniguchi, Yoji Kukita, Yoshiki Arakawa, Susumu Miyamoto and Kikuya Kato

    Citation: BMC Cancer 2014 14:641

    Content type: Research article

    Published on:

  47. The standard treatment for non-metastatic muscle-invasive bladder cancer (stages T2–T4a) is radical cystectomy with lymphadenectomy. However, patients undergoing cystectomy show metastatic spread in 25% of cas...

    Authors: Jens Reumert Laurberg, Jørgen Bjerggaard Jensen, Troels Schepeler, Michael Borre, Torben F Ørntoft and Lars Dyrskjøt

    Citation: BMC Cancer 2014 14:638

    Content type: Research article

    Published on:

  48. Aggressive fibromatosis (AF) is a rare fibroblastic proliferative disease with a locally aggressive behavior and no distant metastasis, characterized by driver mutations in CTNNB1 or the APC gene. When progressiv...

    Authors: Armelle Dufresne, Laurent Alberti, Mehdi Brahmi, Sarah Kabani, Héloïse Philippon, David Pérol and Jean Yves Blay

    Citation: BMC Cancer 2014 14:632

    Content type: Research article

    Published on:

  49. Glypican 3 (GPC3) is a member of the family of glypican heparan sulfate proteoglycans (HSPGs). The GPC3 gene may play a role in controlling cell migration, negatively regulating cell growth and inducing apoptosis...

    Authors: Marina Curado Valsechi, Ana Beatriz Bortolozo Oliveira, André Luis Giacometti Conceição, Bruna Stuqui, Natalia Maria Candido, Paola Jocelan Scarin Provazzi, Luiza Ferreira de Araújo, Wilson Araújo Silva Jr, Marilia de Freitas Calmon and Paula Rahal

    Citation: BMC Cancer 2014 14:631

    Content type: Research article

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  50. Breast cancer is a heterogeneous disease with a highly variable clinical outcome in which both genetic and epigenetic changes have critical roles. We investigated tumor expression levels of histone-modifying e...

    Authors: Remco S Derr, Anneke Q van Hoesel, Anne Benard, Inès J Goossens-Beumer, Anita Sajet, N Geeske Dekker-Ensink, Esther M de Kruijf, Esther Bastiaannet, Vincent THBM Smit, Cornelis JH van de Velde and Peter JK Kuppen

    Citation: BMC Cancer 2014 14:604

    Content type: Research article

    Published on:

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