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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. Identification of predictive markers of response to treatment is a major objective in breast cancer. A major problem in clinical sampling is the variability of RNA templates, requiring accurate management of t...

    Authors: Patricia de Cremoux, Fabien Valet, David Gentien, Jacqueline Lehmann-Che, Véronique Scott, Carine Tran-Perennou, Catherine Barbaroux, Nicolas Servant, Sophie Vacher, Brigitte Sigal-Zafrani, Marie-Christine Mathieu, Philippe Bertheau, Jean-Marc Guinebretière, Bernard Asselain, Michel Marty and Frédérique Spyratos

    Citation: BMC Cancer 2011 11:215

    Content type: Research article

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  2. Osteosarcoma (OS) is a bone malignancy which occurs primarily in adolescents. Since it occurs during a period of rapid growth, genes important in bone formation and growth are plausible modifiers of risk. Gene...

    Authors: Lisa Mirabello, Kai Yu, Sonja I Berndt, Laurie Burdett, Zhaoming Wang, Salma Chowdhury, Kedest Teshome, Arinze Uzoka, Amy Hutchinson, Tom Grotmol, Chester Douglass, Richard B Hayes, Robert N Hoover and Sharon A Savage

    Citation: BMC Cancer 2011 11:209

    Content type: Research article

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  3. Metastatic melanoma represents a major clinical problem. Its incidence continues to rise in western countries and there are currently no curative treatments. While mutation of the P53 tumour suppressor gene is a ...

    Authors: Kelly A Avery-Kiejda, Nikola A Bowden, Amanda J Croft, Lyndee L Scurr, Carla F Kairupan, Katie A Ashton, Bente A Talseth-Palmer, Helen Rizos, Xu D Zhang, Rodney J Scott and Peter Hersey

    Citation: BMC Cancer 2011 11:203

    Content type: Research article

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  4. Histiocytic malignancies in both humans and dogs are rare and poorly understood. While canine histiocytic sarcoma (HS) is uncommon in the general domestic dog population, there is a strikingly high incidence i...

    Authors: Benoit Hedan, Rachael Thomas, Alison Motsinger-Reif, Jerome Abadie, Catherine Andre, John Cullen and Matthew Breen

    Citation: BMC Cancer 2011 11:201

    Content type: Research article

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  5. Recent data in esophageal cancer suggests the variant allele of a single-nucleotide polymorphism (SNP) in XRCC1 may be associated with resistance to radiochemotherapy. However, this SNP has not been assessed in a...

    Authors: Harry H Yoon, Paul J Catalano, Kathleen M Murphy, Todd C Skaar, Santosh Philips, Mark Powell, Elizabeth A Montgomery, Michael J Hafez, Steven M Offer, Geoffrey Liu, Stephen J Meltzer, Xifeng Wu, Arlene A Forastiere, Al B Benson, Lawrence R Kleinberg and Michael K Gibson

    Citation: BMC Cancer 2011 11:176

    Content type: Research article

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  6. The DNA repair gene Ku70, an important member of non-homologous end-joining repair system, is thought to play an important role in the repairing of DNA double strand breaks. It is known that defects in double str...

    Authors: Mei-Due Yang, Hwei-Chung Wang, Wen-Shin Chang, Chia-Wen Tsai and Da-Tian Bau

    Citation: BMC Cancer 2011 11:174

    Content type: Research article

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  7. MAP2K4 is a putative tumor and metastasis suppressor gene frequently found to be deleted in various cancer types. We aimed to conduct a comprehensive analysis of this gene to assess its involvement in ovarian ca...

    Authors: Sally J Davis, David YH Choong, Manasa Ramakrishna, Georgina L Ryland, Ian G Campbell and Kylie L Gorringe

    Citation: BMC Cancer 2011 11:173

    Content type: Research article

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  8. A subset of lung cancer patients harbour EGFR somatic mutations in their tumours and are candidates for treatment with EGFR tyrosine kinase inhibitors. In a few cases EGFR mutations have also been found in the ge...

    Authors: Irene Centeno, Pilar Blay, Iñigo Santamaría, Aurora Astudillo, Ana S Pitiot, Fernando G Osorio, Patricia González-Arriaga, Fernando Iglesias, Primitiva Menéndez, Adonina Tardón, Jose M Freije and Milagros Balbín

    Citation: BMC Cancer 2011 11:172

    Content type: Research article

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  9. Mesothelioma is an aggressive neoplasm with few effective treatments, one being cytoreductive surgery. We previously described a test, based on differential expression levels of four genes, to predict clinical...

    Authors: Gavin J Gordon, Raphael Bueno and David J Sugarbaker

    Citation: BMC Cancer 2011 11:169

    Content type: Research article

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  10. Aquaporins (AQPs) have been recognized to promote tumor progression, invasion, and metastasis and are therefore recognized as promising targets for novel anti-cancer therapies. Potentially relevant AQPs in dis...

    Authors: Arne Warth, Thomas Muley, Michael Meister, Esther Herpel, Anita Pathil, Hans Hoffmann, Philipp A Schnabel, Christian Bender, Andreas Buness, Peter Schirmacher and Ruprecht Kuner

    Citation: BMC Cancer 2011 11:161

    Content type: Research article

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  11. A cross-talk between different receptor tyrosine kinases (RTKs) plays an important role in the pathogenesis of human cancers.

    Authors: Chen-Yun Yeh, Shin-Mei Shin, Hsuan-Heng Yeh, Tsung-Jung Wu, Jyh-Wei Shin, Tsuey-Yu Chang, Giri Raghavaraju, Chung-Ta Lee, Jung-Hsien Chiang, Vincent S Tseng, Yuan-Chii G Lee, Cheng-Huang Shen, Nan-Haw Chow and Hsiao-Sheng Liu

    Citation: BMC Cancer 2011 11:139

    Content type: Research article

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  12. Mortality is high in patients with esophageal carcinoma as tumors are rarely detected before the disease has progressed to an advanced stage. Here, we sought to isolate cell-free DNA released into the plasma o...

    Authors: Immacolata Andolfo, Giuseppe Petrosino, Loredana Vecchione, Pasqualino De Antonellis, Mario Capasso, Donatella Montanaro, Marica Gemei, Giancarlo Troncone, Achille Iolascon, Michele Orditura, Fortunato Ciardiello, Fernando De Vita and Massimo Zollo

    Citation: BMC Cancer 2011 11:126

    Content type: Research article

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  13. The PTEN tumour suppressor gene and PIK3CA proto-oncogene encode proteins which contribute to regulation and propagation of signal transduction through the PI3K/AKT signalling pathway. This study investigates the...

    Authors: Adam Naguib, James C Cooke, Lisa Happerfield, Lucy Kerr, Laura J Gay, Robert N Luben, Richard Y Ball, Panagiota N Mitrou, Alison McTaggart and Mark J Arends

    Citation: BMC Cancer 2011 11:123

    Content type: Research article

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  14. Phosphatase of regenerating liver-3 (PRL-3) has deserved attention as a crucial molecule in the multiple steps of metastasis. In the present study, we examined the mechanisms regulating PRL-3 expression, and a...

    Authors: Akira Ooki, Keishi Yamashita, Shiro Kikuchi, Shinichi Sakuramoto, Natsuya Katada, Mina Waraya, Hiroshi Kawamata, Hiroshi Nishimiya, Kazunori Nakamura and Masahiko Watanabe

    Citation: BMC Cancer 2011 11:122

    Content type: Research article

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  15. Latexin, also known as endogenous carboxypeptidase inhibitor (CPI), has been found to inhibit mouse stem cell populations and lymphoma cell proliferation, demonstrating its potential role as a tumor suppressor...

    Authors: Yong Li, Zhuoma Basang, Huirong Ding, Zheming Lu, Tao Ning, Haoran Wei, Hong Cai and Yang Ke

    Citation: BMC Cancer 2011 11:121

    Content type: Research article

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  16. KLK15 over-expression is reported to be a significant predictor of reduced progression-free survival and overall survival in ovarian cancer. Our aim was to analyse the KLK15 gene for putative functional single n...

    Authors: Jyotsna Batra, Christina M Nagle, Tracy O'Mara, Melanie Higgins, Ying Dong, Olivia L Tan, Felicity Lose, Lene Marie Skeie, Srilakshmi Srinivasan, Kelly L Bolton, Honglin Song, Susan J Ramus, Simon A Gayther, Paul DP Pharoah, Mary-Anne Kedda, Amanda B Spurdle…

    Citation: BMC Cancer 2011 11:119

    Content type: Research article

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  17. The human apurinic/apyrimidinic endonuclease 1/Redox effector factor-1 (APE1/Ref-1) is implicated in tumor development and progression. Recently, the APE1/Ref-1 promoter -141T/G variant (rs1760944) has been repor...

    Authors: Keke Zhou, Dezhi Hu, Juan Lu, Weiwei Fan, Hongliang Liu, Hongyan Chen, Gong Chen, Qingyi Wei, Guhong Du, Ying Mao, Daru Lu and Liangfu Zhou

    Citation: BMC Cancer 2011 11:104

    Content type: Research article

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  18. DNA methylation in the SHOX2 locus was previously used to reliably detect lung cancer in a group of critical controls, including 'cytologically negative' samples with no visible tumor cell content, at a high spec...

    Authors: Katja U Schneider, Dimo Dietrich, Michael Fleischhacker, Gunda Leschber, Johannes Merk, Frank Schäper, Henk R Stapert, Erik R Vossenaar, Sabine Weickmann, Volker Liebenberg, Christoph Kneip, Anke Seegebarth, Fikret Erdogan, Gudrun Rappold and Bernd Schmidt

    Citation: BMC Cancer 2011 11:102

    Content type: Research article

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  19. The aim of this study was to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targ...

    Authors: Genni M Newnham, Matthew Conron, SueAnne McLachlan, Alexander Dobrovic, Hongdo Do, Jason Li, Kenneth Opeskin, Natalie Thompson, Gavin M Wright and David M Thomas

    Citation: BMC Cancer 2011 11:93

    Content type: Research article

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  20. Pregnane X receptor (PXR) is a key transcription factor that regulates drug metabolizing enzymes such as cytochrome P450 (CYP) 3A4, and plays important roles in intestinal first-pass metabolism. Although there...

    Authors: Wataru Habano, Toshie Gamo, Jun Terashima, Tamotsu Sugai, Koki Otsuka, Go Wakabayashi and Shogo Ozawa

    Citation: BMC Cancer 2011 11:81

    Content type: Research article

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  21. Cervical cancer is the most common cancer among Indian women. This cancer has well defined pre-cancerous stages and evolves over 10-15 years or more. This study was undertaken to identify differentially expres...

    Authors: Thangarajan Rajkumar, Kesavan Sabitha, Neelakantan Vijayalakshmi, Sundersingh Shirley, Mayil Vahanan Bose, Gopisetty Gopal and Ganesharaja Selvaluxmy

    Citation: BMC Cancer 2011 11:80

    Content type: Research article

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  22. One key step in gene expression is the biogenesis of mRNA ribonucleoparticle complexes (mRNPs). Formation of the mRNP requires the participation of a number of conserved factors such as the THO complex. THO in...

    Authors: María S Domínguez-Sánchez, Carmen Sáez, Miguel A Japón, Andrés Aguilera and Rosa Luna

    Citation: BMC Cancer 2011 11:77

    Content type: Research article

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  23. The genetics of advanced biliary tract cancers (BTC), which encompass intra- and extra-hepatic cholangiocarcinomas as well as gallbladder carcinomas, are heterogeneous and remain to be fully defined.

    Authors: Vikram Deshpande, Afamefuna Nduaguba, Stephanie M Zimmerman, Sarah M Kehoe, Laura E MacConaill, Gregory Y Lauwers, Cristina Ferrone, Nabeel Bardeesy, Andrew X Zhu and Aram F Hezel

    Citation: BMC Cancer 2011 11:60

    Content type: Research article

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  24. CD26 (dipeptidyl peptidase IV, DPPIV) is a 110 kDa surface glycoprotein expressed in most normal tissues, and is a potential novel therapeutic target for selected cancers. Our work evaluates the mechanism invo...

    Authors: Masako Abe, Pamela A Havre, Yasuyo Urasaki, Kei Ohnuma, Chikao Morimoto, Long H Dang and Nam H Dang

    Citation: BMC Cancer 2011 11:51

    Content type: Research article

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  25. FMS-like tyrosine kinase 3 (FLT3) is a commonly mutated protein in a variety of human acute leukemias. Mutations leading to constitutively active FLT3, including internal tandem duplications of the juxtamembra...

    Authors: Steven E Suter, George W Small, Eric L Seiser, Rachael Thomas, Matthew Breen and Kristy L Richards

    Citation: BMC Cancer 2011 11:38

    Content type: Research article

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  26. Neuroblastoma is a paediatric cancer which originates from precursor cells of the sympathetic nervous system and accounts for 15% of childhood cancer mortalities. With regards to the role of miRNAs in neurobla...

    Authors: Amanda Tivnan, Lorraine Tracey, Patrick G Buckley, Leah C Alcock, Andrew M Davidoff and Raymond L Stallings

    Citation: BMC Cancer 2011 11:33

    Content type: Research article

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  27. Activating mutations of the epidermal growth factor receptor (EGFR) confer sensitivity to the tyrosine kinase inhibitors (TKi), gefitinib and erlotinib. We analysed EGFR expression, EGFR mutation status and gene ...

    Authors: Caterina Peraldo-Neia, Giorgia Migliardi, Maurizia Mello-Grand, Filippo Montemurro, Raffaella Segir, Ymera Pignochino, Giuliana Cavalloni, Bruno Torchio, Luciano Mosso, Giovanna Chiorino and Massimo Aglietta

    Citation: BMC Cancer 2011 11:31

    Content type: Research article

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  28. The c-Myb transcription factor regulates differentiation and proliferation in hematopoietic cells, stem cells and epithelial cells. Although oncogenic versions of c-Myb were first associated with leukemias, ov...

    Authors: Anita M Quintana, Fan Liu, John P O'Rourke and Scott A Ness

    Citation: BMC Cancer 2011 11:30

    Content type: Research article

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  29. Polycomb Group (PcG) proteins are epigenetic silencers involved in maintaining cellular identity, and their deregulation can result in cancer. Expression of Mel-18 and Bmi-1 has been studied in tumor tissue, b...

    Authors: Margit LH Riis, Torben Lüders, Anne-Jorunn Nesbakken, Hilde S Vollan, Vessela Kristensen and Ida RK Bukholm

    Citation: BMC Cancer 2010 10:686

    Content type: Research article

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  30. The protein AGR2 is a putative member of the protein disulfide isomerase family and was first identified as a homolog of the Xenopus laevis gene XAG-2. AGR2 has been implicated in a number of human cancers. In pa...

    Authors: Erin L Maresh, Vei Mah, Mohammad Alavi, Steve Horvath, Lora Bagryanova, Emily S Liebeskind, Laura A Knutzen, Yong Zhou, David Chia, Alvin Y Liu and Lee Goodglick

    Citation: BMC Cancer 2010 10:680

    Content type: Research article

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  31. The presence of circulating tumor cells (CTC) in the peripheral blood of cancer patients has been described for various solid tumors and their clinical relevance has been shown. CTC detection based on the anal...

    Authors: Eva Obermayr, Fatima Sanchez-Cabo, Muy-Kheng M Tea, Christian F Singer, Michael Krainer, Michael B Fischer, Jalid Sehouli, Alexander Reinthaller, Reinhard Horvat, Georg Heinze, Dan Tong and Robert Zeillinger

    Citation: BMC Cancer 2010 10:666

    Content type: Research article

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  32. Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides no information about organ site of metastases. Patterns ...

    Authors: Sjoerd C Bruin, Christiaan Klijn, Gerrit-Jan Liefers, Linde M Braaf, Simon A Joosse, Eric H van Beers, Victor J Verwaal, Hans Morreau, Lodewyk F Wessels, Marie-Louise F van Velthuysen, Rob AEM Tollenaar and Laura J van't Veer

    Citation: BMC Cancer 2010 10:662

    Content type: Research article

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  33. Basal-like breast cancers (BLBC) are aggressive breast cancers for which, so far, no targeted therapy is available because they typically lack expression of hormone receptors and HER2. Phenotypic features of B...

    Authors: Henne Holstege, Hugo M Horlings, Arno Velds, Anita Langerød, Anne-Lise Børresen-Dale, Marc J van de Vijver, Petra M Nederlof and Jos Jonkers

    Citation: BMC Cancer 2010 10:654

    Content type: Research article

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  34. The etiology of hemangiosarcoma remains incompletely understood. Its common occurrence in dogs suggests predisposing factors favor its development in this species. These factors could represent a constellation...

    Authors: Beth A Tamburini, Tzu L Phang, Susan P Fosmire, Milcah C Scott, Susan C Trapp, Megan M Duckett, Sally R Robinson, Jill E Slansky, Leslie C Sharkey, Gary R Cutter, John W Wojcieszyn, Donald Bellgrau, Robert M Gemmill, Lawrence E Hunter and Jaime F Modiano

    Citation: BMC Cancer 2010 10:619

    Content type: Research article

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  35. Similar to human breast cancer mammary tumors of the female dog are commonly associated with a fatal outcome due to the development of distant metastases. However, the molecular defects leading to metastasis a...

    Authors: Robert Klopfleisch, Dido Lenze, Michael Hummel and Achim D Gruber

    Citation: BMC Cancer 2010 10:618

    Content type: Research article

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  36. Epigenetic silencing of tumor suppressor genes play important roles in NPC tumorgenesis. Tissue factor pathway inhibitor-2 (TFPI-2), is a protease inhibitor. Recently, TFPI-2 was suggested to be a tumor suppresso...

    Authors: Shumin Wang, Xue Xiao, Xiaoying Zhou, Tingting Huang, Chunping Du, Nana Yu, Yingxi Mo, Longde Lin, Jinyan Zhang, Ning Ma, Mariko Murata, Guangwu Huang and Zhe Zhang

    Citation: BMC Cancer 2010 10:617

    Content type: Research article

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  37. Elucidating the activation pattern of molecular pathways across a given tumour type is a key challenge necessary for understanding the heterogeneity in clinical response and for developing novel more effective...

    Authors: Andrew E Teschendorff, Sergio Gomez, Alex Arenas, Dorraya El-Ashry, Marcus Schmidt, Mathias Gehrmann and Carlos Caldas

    Citation: BMC Cancer 2010 10:604

    Content type: Research article

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  38. The genetic control of prostate cancer development is poorly understood. Large numbers of gene-expression datasets on different aspects of prostate tumorigenesis are available. We used these data to identify a...

    Authors: Ivan P Gorlov, Kanishka Sircar, Hongya Zhao, Sankar N Maity, Nora M Navone, Olga Y Gorlova, Patricia Troncoso, Curtis A Pettaway, Jin Young Byun and Christopher J Logothetis

    Citation: BMC Cancer 2010 10:599

    Content type: Research article

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  39. Several investigators have employed high throughput mitochondrial sequencing array (MitoChip) in clinical studies to search mtDNA for markers linked to cancers. In consequence, a host of somatic mtDNA mutation...

    Authors: Malliya Gounder Palanichamy and Ya-Ping Zhang

    Citation: BMC Cancer 2010 10:597

    Content type: Research article

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  40. The anti-infective agent Taurolidine (TRD) has been shown to have cell death inducing properties, but the mechanism of its action is largely unknown. The aim of this study was to identify potential common targ...

    Authors: Ansgar M Chromik, Stephan A Hahn, Adrien Daigeler, Annegret Flier, Daniel Bulut, Christina May, Kamran Harati, Jan Roschinsky, Dominique Sülberg, Dirk Weyhe, Ulrich Mittelkötter and Waldemar Uhl

    Citation: BMC Cancer 2010 10:595

    Content type: Research article

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  41. NORE1 (RASSF5) is a newly described member of the RASSF family with Ras effector function. NORE1 expression is frequently inactivated by aberrant promoter hypermethylation in many human cancers, suggesting that N...

    Authors: Chang Kyun Lee, Jin-Hee Lee, Min-Goo Lee, Seong-In Jeong, Tae-Kyu Ha, Min-Ju Kang, Byung-Kyu Ryu, Young Hwangbo, Jae-Jun Shim, Jae Young Jang, Kil Yeon Lee, Hyo Jong Kim and Sung-Gil Chi

    Citation: BMC Cancer 2010 10:577

    Content type: Research article

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  42. An estimated 12% of females in the United States will develop breast cancer in their lifetime. Although, there are advances in treatment options including surgery and chemotherapy, breast cancer is still the s...

    Authors: Jeffrey C Miecznikowski, Dan Wang, Song Liu, Lara Sucheston and David Gold

    Citation: BMC Cancer 2010 10:573

    Content type: Research article

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  43. Telomerase activation, a critical step in cell immortalization and oncogenesis, is partly regulated by alternative splicing. In this study, we aimed to use the Marek's disease virus (MDV) T-cell lymphoma model...

    Authors: Souheila Amor, Sylvie Remy, Ginette Dambrine, Yves Le Vern, Denis Rasschaert and Sylvie Laurent

    Citation: BMC Cancer 2010 10:571

    Content type: Research article

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  44. Numerous studies reported genomic alterations in colorectal human tumors but few focused on rectal tumors with the specification of preoperative-treated or untreated tumors. The goals of this study were to lis...

    Authors: Benoît Romain, Agnès Neuville, Nicolas Meyer, Cécile Brigand, Serge Rohr, Anne Schneider, Marie-Pierre Gaub and Dominique Guenot

    Citation: BMC Cancer 2010 10:561

    Content type: Research article

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  45. Gastrointestinal stromal tumors (GISTs) are common mesenchymal neoplasms in the gastrointestinal tract of humans and dogs. Little is known about the pathogenesis of these tumors. This study evaluated the role of

    Authors: Emmalena Gregory-Bryson, Elizabeth Bartlett, Matti Kiupel, Schantel Hayes and Vilma Yuzbasiyan-Gurkan

    Citation: BMC Cancer 2010 10:559

    Content type: Research article

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  46. Whether a systemic adjuvant treatment is needed is an area of controversy in patients with node-negative early breast cancer with tumor size of ≤1 cm, including T1mic.

    Authors: Ji Hyun Kwon, Yu Jung Kim, Keun-Wook Lee, Do-Youn Oh, So Yeon Park, Jee Hyun Kim, Eui Kyu Chie, Sung-Won Kim, Seock-Ah Im, In-Ah Kim, Tae-You Kim, In Ae Park, Dong-Young Noh, Yung-Jue Bang and Sung Whan Ha

    Citation: BMC Cancer 2010 10:557

    Content type: Research article

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  47. Early metastasis and infiltration are survival limiting characteristics of pancreatic ductal adenocarcinoma (PDAC). Thus, PDAC is likely to harbor alterations in metastasis suppressor genes that may provide no...

    Authors: Wolf A Mardin, Kostadin O Petrov, Andreas Enns, Norbert Senninger, Joerg Haier and Soeren T Mees

    Citation: BMC Cancer 2010 10:549

    Content type: Research article

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  48. Claudin-1 is a membrane protein of tight junctions, and is associated with the development of various cancers. However, the significance of claudin-1 expression in cancer cells is not well understood. Here, we...

    Authors: Harue Akasaka, Fuyuki Sato, Satoko Morohashi, Yunyan Wu, Yang Liu, Jun Kondo, Hiroki Odagiri, Kenichi Hakamada and Hiroshi Kijima

    Citation: BMC Cancer 2010 10:548

    Content type: Research article

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