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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. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. p27 is a cell cycle suppressor gene, whose protein is a negative regulator of cyclin/cdk complexes. p27 is also a potential target of retinoids in cancer prevention studies. In benign prostate hyperplasia (BPH...

    Authors: Winna Taylor, Amanda Mathias, Arshia Ali, Hengning Ke, Nikolay Stoynev, Anne Shilkaitis, Albert Green, Hiroaki Kiyokawa and Konstantin Christov

    Citation: BMC Cancer 2010 10:541

    Content type: Research article

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  26. Around 20% of breast cancers (BC) show ERBB2 gene amplification and overexpression of the ERBB2 tyrosine kinase receptor. They are associated with a poor prognosis but can benefit from targeted therapy. A better ...

    Authors: Fabrice Sircoulomb, Ismahane Bekhouche, Pascal Finetti, José Adélaïde, Azza Ben Hamida, Julien Bonansea, Stéphane Raynaud, Charlène Innocenti, Emmanuelle Charafe-Jauffret, Carole Tarpin, Farhat Ben Ayed, Patrice Viens, Jocelyne Jacquemier, François Bertucci, Daniel Birnbaum and Max Chaffanet

    Citation: BMC Cancer 2010 10:539

    Content type: Research article

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  27. Association between rectal or colon cancer risk and serine hydroxymethyltransferase 1 (SHMT1) C1420T or methylenetetrahydrofolate reductase (MTHFR) C677T polymorphisms was assessed. The serum total homocysteine (...

    Authors: Viktor Komlósi, Erika Hitre, Éva Pap, Vilmos Adleff, Andrea Réti, Éva Székely, Anna Bíró, Péter Rudnai, Bernadette Schoket, Judit Müller, Béla Tóth, Szabolcs Ottó, Miklós Kásler, Judit Kralovánszky and Barna Budai

    Citation: BMC Cancer 2010 10:525

    Content type: Research article

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  28. Genetic factors related to the regulation of apoptosis in schizophrenia patients may be involved in a reduced vulnerability to cancer. XRCC4 is one of the potential candidate genes associated with schizophreni...

    Authors: Yang Wang, Lei Wang, Xingwang Li, Baocheng Liu, Qingzhu Zhao, Peng Chen, Ti Wang, Tao Li, Jue Ji, Fengping Yang, Quan Wang, Jinfen Wang, Yanzeng Xiao, Yifeng Xu, Guoyin Feng, Zhihai Peng…

    Citation: BMC Cancer 2010 10:523

    Content type: Research article

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  29. As a key gene in the immunosurveillance of cell malignancy, Cytotoxic T-lymphocyte antigen 4 (CTLA-4 is an important negative regulator of T cell activation and proliferation. The CTLA-4 +49G > A polymorphism ...

    Authors: Jian Zheng, Xiao Yu, Lan Jiang, Mang Xiao, Bing Bai, Jiachun Lu and Yifeng Zhou

    Citation: BMC Cancer 2010 10:522

    Content type: Research article

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  30. Abnormalities of 11q23 involving the MLL gene are found in approximately 10% of human leukemias. To date, nearly 100 different chromosome bands have been described in rearrangements involving 11q23 and 64 fusion ...

    Authors: Nuno Cerveira, Claus Meyer, Joana Santos, Lurdes Torres, Susana Lisboa, Manuela Pinheiro, Susana Bizarro, Cecília Correia, Lucília Norton, Rolf Marschalek and Manuel R Teixeira

    Citation: BMC Cancer 2010 10:518

    Content type: Research article

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  31. Epigenetic inactivation of tumor suppressor genes (TSG) by promoter CpG island hypermethylation is a hallmark of cancer. To assay its extent in human lymphoma, methylation of 24 TSG was analyzed in lymphoma-de...

    Authors: Sonja Eberth, Björn Schneider, Andreas Rosenwald, Elena M Hartmann, Julia Romani, Margarete Zaborski, Reiner Siebert, Hans G Drexler and Hilmar Quentmeier

    Citation: BMC Cancer 2010 10:517

    Content type: Research article

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  32. Mutations in FLT3 result in activated tyrosine kinase activity, cell growth stimulation, and a poor prognosis among various subtypes of leukemia. The causes and timing of the mutations are not currently known. We...

    Authors: Patrick Chang, Michelle Kang, Anny Xiao, Jeffrey Chang, James Feusner, Patricia Buffler and Joseph Wiemels

    Citation: BMC Cancer 2010 10:513

    Content type: Research article

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  33. Hyaluronan accumulation correlates with the degree of malignancy in many solid tumor types, including malignant endometrial carcinomas. To elucidate the mechanism of hyaluronan accumulation, we examined the ex...

    Authors: Timo K Nykopp, Kirsi Rilla, Markku I Tammi, Raija H Tammi, Reijo Sironen, Kirsi Hämäläinen, Veli-Matti Kosma, Seppo Heinonen and Maarit Anttila

    Citation: BMC Cancer 2010 10:512

    Content type: Research article

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  34. The selection of patients according to key genetic characteristics may help to tailor chemotherapy and optimize the treatment in Castration-Resistant Prostate Cancer (CRPC) patients. Functional polymorphisms w...

    Authors: Ilaria Pastina, Elisa Giovannetti, Aldo Chioni, Tristan M Sissung, Francesco Crea, Cinzia Orlandini, Douglas K Price, Claudia Cianci, William D Figg, Sergio Ricci and Romano Danesi

    Citation: BMC Cancer 2010 10:511

    Content type: Research article

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  35. Osteosarcoma (OSA) spontaneously arises in the appendicular skeleton of large breed dogs and shares many physiological and molecular biological characteristics with human OSA. The standard treatment for OSA in...

    Authors: Liza E O'Donoghue, Andrey A Ptitsyn, Debra A Kamstock, Janet Siebert, Russell S Thomas and Dawn L Duval

    Citation: BMC Cancer 2010 10:506

    Content type: Research article

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  36. The cortical cytoskeleton network connects the actin cytoskeleton to various membrane proteins, influencing cell adhesion, polarity, migration and response to extracellular signals. Previous studies have sugge...

    Authors: Wolfgang A Schulz, Marc Ingenwerth, Carolle E Djuidje, Christiane Hader, Jörg Rahnenführer and Rainer Engers

    Citation: BMC Cancer 2010 10:505

    Content type: Research article

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  37. Fibronectin 1 (FN1) is a glycoprotein involved in cellular adhesion and migration processes. The aim of this study was to elucidate the role of FN1 in development of renal cell cancer (RCC) and to determine a pro...

    Authors: Sandra Waalkes, Faranaz Atschekzei, Mario W Kramer, Jörg Hennenlotter, Gesa Vetter, Jan U Becker, Arnulf Stenzl, Axel S Merseburger, Andres J Schrader, Markus A Kuczyk and Jürgen Serth

    Citation: BMC Cancer 2010 10:503

    Content type: Research article

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  38. The involvement of miRNAs in the regulation of fundamental cellular functions has placed them at the fore of ongoing investigations into the processes underlying carcinogenesis. MiRNA expression patterns have ...

    Authors: Aoife J Lowery, Nicola Miller, Roisin M Dwyer and Michael J Kerin

    Citation: BMC Cancer 2010 10:502

    Content type: Research article

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  39. BRCA1 gene inactivation causes chromosomal instability, leading to rapid accumulation of chromosomal rearrangements and mutations. The loss of BRCA1 function due to either germline/somatic mutation or epigenet...

    Authors: Manohar Pradhan, Björn Å Risberg, Claes G Tropé, Matt van de Rijn, C Blake Gilks and Cheng-Han Lee

    Citation: BMC Cancer 2010 10:493

    Content type: Research article

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  40. Members of the ErbB family of growth factor receptors are intricately linked with epithelial cell biology, development and tumourigenesis; however, the mechanisms involved in their downstream signalling are po...

    Authors: Jenny Worthington, Mariana Bertani, Hong-Lin Chan, Bertran Gerrits and John F Timms

    Citation: BMC Cancer 2010 10:490

    Content type: Research article

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  41. Cytochrome P450-based suicide gene therapy for cancer using prodrugs such as cyclophosphamide (CPA) increases anti-tumor activity, both directly and via a bystander killing mechanism. Bystander cell killing is es...

    Authors: Joshua C Doloff, Ting Su and David J Waxman

    Citation: BMC Cancer 2010 10:487

    Content type: Research article

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  42. Transcription factors and nuclear receptors constitute a link between exposure to heterocyclic amines and polycyclic aromatic hydrocarbons from meat and tobacco smoke and colorectal cancer (CRC) risk. The aim ...

    Authors: Vibeke Andersen, Jane Christensen, Kim Overvad, Anne Tjønneland and Ulla Vogel

    Citation: BMC Cancer 2010 10:484

    Content type: Research article

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  43. The cytokine-induced anti-apoptotic molecule (CIAPIN1) had been found to be a differentially-expressed gene involved in a variety of cancers, and it was also considered as a candidate tumour suppressor gene in...

    Authors: Hai Shi, Yi Zhou, Heliang Liu, Changsheng Chen, Shujun Li, Nanlin Li, Xiaohua Li, Xi Zhang, Hongwei Zhang, Weizhong Wang and Qingchuan Zhao

    Citation: BMC Cancer 2010 10:477

    Content type: Research article

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  44. Human neuroblastoma (NB) cell lines may present with either one of the so-called S-and N-subtypes. We have previously reported a strong correlation between protein expression levels of vimentin, an S-subtype m...

    Authors: Xénia Mergui, Marie-Line Puiffe, Dominique Valteau-Couanet, Marc Lipinski, Jean Bénard and Mounira Amor-Guéret

    Citation: BMC Cancer 2010 10:473

    Content type: Research article

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  45. Chondrosarcomas are malignant cartilage tumors that do not respond to traditional chemotherapy or radiation. The 5-year survival rate of histologic grade III chondrosarcoma is less than 30%. An animal model of...

    Authors: Christopher A Hamm, Jeff W Stevens, Hehuang Xie, Elio F Vanin, Jose A Morcuende, Hakeem Abdulkawy, Elisabeth A Seftor, Simone T Sredni, Jared M Bischof, Deli Wang, Sergey Malchenko, Maria de Fatima Bonaldo, Thomas L Casavant, Mary JC Hendrix and Marcelo B Soares

    Citation: BMC Cancer 2010 10:471

    Content type: Research article

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  46. Severe toxicity to 5-fluorouracil (5-FU) based chemotherapy in gastrointestinal cancer has been associated with constitutional genetic alterations of the dihydropyrimidine dehydrogenase gene (DPYD).

    Authors: Joana Savva-Bordalo, João Ramalho-Carvalho, Manuela Pinheiro, Vera L Costa, Ângelo Rodrigues, Paula C Dias, Isabel Veiga, Manuela Machado, Manuel R Teixeira, Rui Henrique and Carmen Jerónimo

    Citation: BMC Cancer 2010 10:470

    Content type: Research article

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  47. Glioblastoma multiforme (GBM) is refractory to conventional therapies. To overcome the problem of heterogeneity, more brain tumor markers are required for prognosis and targeted therapy. We have identified and...

    Authors: Chien-Tsun Kuan, Kenji Wakiya, James E Herndon II, Eric S Lipp, Charles N Pegram, Gregory J Riggins, Ahmed Rasheed, Scott E Szafranski, Roger E McLendon, Carol J Wikstrand and Darell D Bigner

    Citation: BMC Cancer 2010 10:468

    Content type: Research article

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  48. Prognostic factors in patients who are diagnosed with T4 breast carcinomas are widely awaited. We here evaluated the clinical role of some molecular alterations involved in tumorigenesis in a well-characterize...

    Authors: Bruno Massidda, MariaCristina Sini, Mario Budroni, Francesco Atzori, MariaCristina Deidda, Valeria Pusceddu, MariaTeresa Perra, Paola Sirigu, Antonio Cossu, Grazia Palomba, MariaTeresa Ionta and Giuseppe Palmieri

    Citation: BMC Cancer 2010 10:458

    Content type: Research article

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  49. Genomic gains and losses are a result of genomic instability in many types of cancers. BRCA1- and BRCA2-mutated breast cancers are associated with increased amounts of chromosomal aberrations, presumably due thei...

    Authors: Henne Holstege, Erik van Beers, Arno Velds, Xiaoling Liu, Simon A Joosse, Sjoerd Klarenbeek, Eva Schut, Ron Kerkhoven, Christiaan N Klijn, Lodewyk FA Wessels, Petra M Nederlof and Jos Jonkers

    Citation: BMC Cancer 2010 10:455

    Content type: Research article

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  50. Gliomas are the most common type of primary brain tumours, and in this group glioblastomas (GBMs) are the higher-grade gliomas with fast progression and unfortunate prognosis. Two major aspects of glioma biolo...

    Authors: Juan L Garcia, Maria Perez-Caro, Juan A Gomez-Moreta, Francisco Gonzalez, Javier Ortiz, Oscar Blanco, Magdalena Sancho, Jesus M Hernandez-Rivas, Rogelio Gonzalez-Sarmiento and Manuel Sanchez-Martin

    Citation: BMC Cancer 2010 10:454

    Content type: Research article

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