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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. Colorectal cancer (CRC) is one of the most common and comprehensively studied malignancies. Hypoxic conditions during formation of CRC may support the development of more aggressive cancers. Hypoxia inducible ...

    Authors: Agnieszka A Rawluszko, Katarzyna E Bujnicka, Karolina Horbacka, Piotr Krokowicz and Paweł P Jagodziński

    Citation: BMC Cancer 2013 13:526

    Content type: Research article

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  2. Breast cancer is the most common type of cancer and the second leading cause of cancer-death among women in Poland. The known high-risk mutations account for 25% of familial aggregation cases and 5% of total b...

    Authors: Joanna K Ledwoń, Ewa E Hennig, Natalia Maryan, Krzysztof Goryca, Dorota Nowakowska, Anna Niwińska and Jerzy Ostrowski

    Citation: BMC Cancer 2013 13:510

    Content type: Research article

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  3. Genetic aberrations are required for the progression of HPV-induced cervical precancers. A prerequisite for clonal expansion of cancer cells is unlimited proliferative capacity. In a cell culture model for cer...

    Authors: Melanie Liesenfeld, Sandy Mosig, Harald Funke, Lars Jansen, Ingo B Runnebaum, Matthias Dürst and Claudia Backsch

    Citation: BMC Cancer 2013 13:507

    Content type: Research article

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  4. Small intestinal neuroendocrine tumors (SI-NETs) are typically slow-growing tumors that have metastasized already at the time of diagnosis. The purpose of the present study was to further refine and define reg...

    Authors: Jamileh Hashemi, Omid Fotouhi, Luqman Sulaiman, Magnus Kjellman, Anders Höög, Jan Zedenius and Catharina Larsson

    Citation: BMC Cancer 2013 13:505

    Content type: Research article

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  5. MTO1 and MRPL41 are nuclear-encoded mitochondrial genes encoding a mitochondrial tRNA-modifying enzyme and a mitochondrial ribosomal protein, respectively. Although both genes have been known to have potential...

    Authors: Tae Woo Kim, Byungtak Kim, Ju Hee Kim, Seongeun Kang, Sung-Bin Park, Gookjoo Jeong, Han-Sung Kang and Sun Jung Kim

    Citation: BMC Cancer 2013 13:502

    Content type: Research article

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  6. Platinum-based chemotherapy has long been used in the treatment of a variety of cancers and functions by inducing DNA damage. ERCC1 and ERCC4 are involved in the removal of this damage and have previously been...

    Authors: David Hersi Smith, Ib Jarle Christensen, Niels Frank Jensen, Bo Markussen, Sven Müller, Hans Jørgen Nielsen, Nils Brünner and Kirsten Vang Nielsen

    Citation: BMC Cancer 2013 13:489

    Content type: Research article

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  7. Most currently known breast cancer predisposition genes play a role in DNA repair by homologous recombination. Recent studies conducted on RAD51 paralogs, involved in the same DNA repair pathway, have identified ...

    Authors: Lisa Golmard, Virginie Caux-Moncoutier, Grégoire Davy, Essam Al Ageeli, Brigitte Poirot, Carole Tirapo, Dorothée Michaux, Catherine Barbaroux, Catherine Dubois d’Enghien, André Nicolas, Laurent Castéra, Xavier Sastre-Garau, Marc-Henri Stern, Claude Houdayer and Dominique Stoppa-Lyonnet

    Citation: BMC Cancer 2013 13:484

    Content type: Research article

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  8. MiR-106a is frequently down-regulated in various types of human cancer. However the underlying mechanism of miR-106a involved in glioma remains elusive.

    Authors: Dong-Wei Dai, Qiong Lu, Lai-Xing Wang, Wen-Yuan Zhao, Yi-Qun Cao, Ya-Nan Li, Guo-Sheng Han, Jian-Min Liu and Zhi-Jian Yue

    Citation: BMC Cancer 2013 13:478

    Content type: Research article

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  9. Long-term estrogen deprivation models are widely employed in an in vitro setting to recapitulate the hormonal milieu of breast cancer patients treated with endocrine therapy. Despite the wealth information we hav...

    Authors: Jelena Milosevic, Johanna Klinge, Anna-Lena Borg, Theodoros Foukakis, Jonas Bergh and Nicholas P Tobin

    Citation: BMC Cancer 2013 13:473

    Content type: Research article

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  10. Distinguishing between multiple primary lung cancers and metastatic tumors is often difficult when the tumor histology is same. Since genomic instability is a common feature of cancer, we hypothesized that ind...

    Authors: Cheng Shen, Huan Xu, Lunxu Liu, Yubin Zhou, Dali Chen, Heng Du, Zhaojie Han and Guowei Che

    Citation: BMC Cancer 2013 13:467

    Content type: Research article

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  11. MT1G inactivation mediated by promoter methylation has been reported in thyroid cancer. However, the role of MT1G in thyroid carcinogenesis remains unclear. The aim of this study is to examine the biological fun...

    Authors: Jiao Fu, Hongjun Lv, Haixia Guan, Xiaoying Ma, Meiju Ji, Nongyue He, Bingyin Shi and Peng Hou

    Citation: BMC Cancer 2013 13:462

    Content type: Research article

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  12. The MRE11, RAD50, and NBN genes encode proteins of the MRE11-RAD50-NBN (MRN) complex involved in cellular response to DNA damage and the maintenance of genome stability. In our previous study we showed that the g...

    Authors: Maria Mosor, Iwona Ziółkowska-Suchanek, Karina Nowicka, Agnieszka Dzikiewicz-Krawczyk, Danuta Januszkiewicz–Lewandowska and Jerzy Nowak

    Citation: BMC Cancer 2013 13:457

    Content type: Research article

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  13. Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylat...

    Authors: Jovana Klajic, Thomas Fleischer, Emelyne Dejeux, Hege Edvardsen, Fredrik Warnberg, Ida Bukholm, Per Eystein Lønning, Hiroko Solvang, Anne-Lise Børresen-Dale, Jörg Tost and Vessela N Kristensen

    Citation: BMC Cancer 2013 13:456

    Content type: Research article

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  14. Retrospective analyses in the West suggest that mutations in KRAS codons 61 and 146, BRAF, NRAS, and PIK3CA are negative predictive factors for cetuximab treatment in colorectal cancer patients. We developed a no...

    Authors: Hideaki Bando, Takayuki Yoshino, Eiji Shinozaki, Tomohiro Nishina, Kentaro Yamazaki, Kensei Yamaguchi, Satoshi Yuki, Shinya Kajiura, Satoshi Fujii, Takeharu Yamanaka, Katsuya Tsuchihara and Atsushi Ohtsu

    Citation: BMC Cancer 2013 13:405

    Content type: Technical advance

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  15. The septin 9 gene (SEPT9) codes for a GTP-binding protein associated with filamentous structures and cytoskeleton formation. SEPT9 plays a role in multiple cancers as either an oncogene or a tumor suppressor g...

    Authors: Reinhold Wasserkort, Alexandra Kalmar, Gabor Valcz, Sandor Spisak, Manuel Krispin, Kinga Toth, Zsolt Tulassay, Andrew Z Sledziewski and Bela Molnar

    Citation: BMC Cancer 2013 13:398

    Content type: Research article

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  16. Global hypomethylation of repetitive DNA sequences is believed to occur early in tumorigenesis. There is a great interest in identifying factors that contribute to global DNA hypomethylation and associated can...

    Authors: Maki Inoue-Choi, Heather H Nelson, Kim Robien, Erland Arning, Teodoro Bottiglieri, Woon-Puay Koh and Jian-Min Yuan

    Citation: BMC Cancer 2013 13:389

    Content type: Research article

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  17. Paediatric low-grade gliomas (LGGs) encompass a heterogeneous set of tumours of different histologies, site of lesion, age and gender distribution, growth potential, morphological features, tendency to progres...

    Authors: Samantha Mascelli, Annalisa Barla, Alessandro Raso, Sofia Mosci, Paolo Nozza, Roberto Biassoni, Giovanni Morana, Martin Huber, Cristian Mircean, Daniel Fasulo, Karin Noy, Gayle Wittemberg, Sara Pignatelli, Gianluca Piatelli, Armando Cama, Maria Luisa Garré…

    Citation: BMC Cancer 2013 13:387

    Content type: Research article

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  18. Cancer stem cell model hypothesizes existence of a small proportion of tumor cells capable of sustaining tumor formation, self-renewal and differentiation. In breast cancer, these cells were found to be associ...

    Authors: Marija Balic, Daniela Schwarzenbacher, Stefanie Stanzer, Ellen Heitzer, Martina Auer, Jochen B Geigl, Richard J Cote, Ram H Datar and Nadia Dandachi

    Citation: BMC Cancer 2013 13:358

    Content type: Research article

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  19. Mutation(s) of the JAK2 gene (V617F) has been described in a significant proportion of Philadelphia negative Myeloproliferative Neoplasms (MPN) patients and its detection is now a cornerstone in the diagnostic al...

    Authors: Enrico Bracco, Valentina Rosso, Anna Serra, Francesca Carnuccio, Valentina Gaidano, Paolo Nicoli, Pellegrino Musto, Giuseppe Saglio, Francesco Frassoni and Daniela Cilloni

    Citation: BMC Cancer 2013 13:348

    Content type: Research article

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  20. The influence of variants at the 9p21 locus on melanoma risk has been reported through investigation of CDKN2A variants through candidate gene approach as well as by genome wide association studies (GWAS).

    Authors: Livia Maccioni, Panduranga Sivaramakrishna Rachakonda, Justo Lorenzo Bermejo, Dolores Planelles, Celia Requena, Kari Hemminki, Eduardo Nagore and Rajiv Kumar

    Citation: BMC Cancer 2013 13:325

    Content type: Research article

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  21. Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during norm...

    Authors: James F Amatruda, Julie A Ross, Brock Christensen, Nicholas J Fustino, Kenneth S Chen, Anthony J Hooten, Heather Nelson, Jacquelyn K Kuriger, Dinesh Rakheja, A Lindsay Frazier and Jenny N Poynter

    Citation: BMC Cancer 2013 13:313

    Content type: Research article

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  22. Gene expression profiling (GEP) is increasingly used in the rapidly evolving field of personalized medicine. We sought to evaluate the association between GEP-assessed of breast cancer recurrence risk and pati...

    Authors: Valesca P Retèl, Catharina GM Groothuis-Oudshoorn, Neil K Aaronson, Noel T Brewer, Emiel JT Rutgers and Wim H van Harten

    Citation: BMC Cancer 2013 13:295

    Content type: Research article

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  23. MicroRNAs (miRNAs) are short, non-coding RNA molecules that act as regulators of gene expression. Circulating blood miRNAs offer great potential as cancer biomarkers. The objective of this study was to correla...

    Authors: Fung Lin Yong, Chee Wei Law and Chee Woon Wang

    Citation: BMC Cancer 2013 13:280

    Content type: Research article

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  24. Early detection and risk assessment are crucial for treating urothelial cancer (UC), which is characterized by a high recurrence rate, and necessitates frequent and invasive monitoring. We aimed to establish d...

    Authors: Yoshitomo Chihara, Yae Kanai, Hiroyuki Fujimoto, Kokichi Sugano, Kiyotaka Kawashima, Gangning Liang, Peter A Jones, Kiyohide Fujimoto, Hiroki Kuniyasu and Yoshihiko Hirao

    Citation: BMC Cancer 2013 13:275

    Content type: Technical advance

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  25. NOTCH1 PEST domain mutations in chronic lymphocytic leukemia have recently been shown to be of prognostic relevance. Both NOTCH1 and NOTCH2 are constitutively activated in B-cell CLL but not expressed in normal ...

    Authors: Kerstin Willander, Ravi Kumar Dutta, Jonas Ungerbäck, Rebeqa Gunnarsson, Gunnar Juliusson, Mats Fredrikson, Mats Linderholm and Peter Söderkvist

    Citation: BMC Cancer 2013 13:274

    Content type: Research article

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  26. Long interspersed nuclear element-1 (LINE-1 or L1), the most abundant and only autonomously active family of non-LTR retrotransposons in the human genome, expressed not only in the germ lines but also in somat...

    Authors: Gangshi Wang, Jie Gao, Haili Huang, Yu Tian, Liyan Xue, Weihua Wang, Weidi You, Hongwei Lian, Xiaojian Duan, Benyan Wu and Mengwei Wang

    Citation: BMC Cancer 2013 13:265

    Content type: Research article

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  27. The role of tumor suppressor gene RASSF1A in the esophageal and gastric cardia carcinogenesis is still inconclusive. In this study, the polymorphism, promoter methylation and gene expression of RASSF1A were chara...

    Authors: Sheng Li Zhou, Juan Cui, Zong Min Fan, Xue Min Li, Ji Lin Li, Bao Chi Liu, Dong Yun Zhang, Hong Yan Liu, Xue Ke Zhao, Xin Song, Ran Wang, Ze Chen Yan, Hui Xing Yi and Li Dong Wang

    Citation: BMC Cancer 2013 13:259

    Content type: Research article

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  28. High-grade (WHO grade III and IV) astrocytomas are aggressive malignant brain tumors affecting humans with a high risk of recurrence in both children and adults. To date, limited information is available on th...

    Authors: Sara Tomaselli, Federica Galeano, Luca Massimi, Concezio Di Rocco, Libero Lauriola, Angela Mastronuzzi, Franco Locatelli and Angela Gallo

    Citation: BMC Cancer 2013 13:255

    Content type: Research article

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  29. The prevalence of BRCA1 and BRCA2 mutations in Spain is heterogeneous and varies according to geographical origin of studied families. The contribution of these mutations to hereditary breast and ovarian cancer h...

    Authors: Pilar Blay, Iñigo Santamaría, Ana S Pitiot, María Luque, Marta G Alvarado, Ana Lastra, Yolanda Fernández, Ángeles Paredes, José MP Freije and Milagros Balbín

    Citation: BMC Cancer 2013 13:243

    Content type: Research article

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  30. Glioblastoma (GBM) is the most malignant brain tumor. Many abnormal secretion and expression of cytokines have been found in GBM, initially speculated that the occurrence of GBM may be involved in these abnorm...

    Authors: Tianbo Jin, Xiaolan Li, Jiayi Zhang, Hong Wang, Tingting Geng, Gang Li, Guodong Gao and Chao Chen

    Citation: BMC Cancer 2013 13:236

    Content type: Research article

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  31. Genetic variations in DNA double-strand break repair genes can influence the ability of a cell to repair damaged DNA and alter an individual’s susceptibility to cancer. We studied whether polymorphisms in DNA ...

    Authors: Peng Zhao, Peng Zou, Lin Zhao, Wei Yan, Chunsheng Kang, Tao Jiang and Yongping You

    Citation: BMC Cancer 2013 13:234

    Content type: Research article

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  32. Aggressive neuroblastoma remains a significant cause of childhood cancer death despite current intensive multimodal treatment protocols. The purpose of the present work was to characterize the genetic and clin...

    Authors: Cihan Cetinkaya, Tommy Martinsson, Johanna Sandgren, Catarina Träger, Per Kogner, Jan Dumanski, Teresita Díaz de Ståhl and Fredrik Hedborg

    Citation: BMC Cancer 2013 13:231

    Content type: Research article

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  33. The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease...

    Authors: Giada V Zapparoli, Robert N Jorissen, Chelsee A Hewitt, Michelle McBean, David A Westerman and Alexander Dobrovic

    Citation: BMC Cancer 2013 13:206

    Content type: Technical advance

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  34. Conventional treatment for locally advanced rectal cancer usually combines neoadjuvant radiochemotherapy and surgery. Until recently, there have been limited predictive factors (clinical or biological) for rec...

    Authors: Olfa Derbel, Qing Wang, Françoise Desseigne, Michel Rivoire, Pierre Meeus, Patrice Peyrat, Mattia Stella, Isabelle Martel-Lafay, Anne-Isabelle Lemaistre and Christelle de La Fouchardière

    Citation: BMC Cancer 2013 13:200

    Content type: Research article

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  35. The acyclic retinoid, peretinoin, has been shown to be effective for suppressing hepatocellular carcinoma (HCC) recurrence after definitive treatment in a small-scale randomized clinical trial. However, little...

    Authors: Masao Honda, Taro Yamashita, Tatsuya Yamashita, Kuniaki Arai, Yoshio Sakai, Akito Sakai, Mikiko Nakamura, Eishiro Mizukoshi and Shuichi Kaneko

    Citation: BMC Cancer 2013 13:191

    Content type: Research article

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  36. Adrenocortical carcinomas (ACCs) are among the most common childhood cancers occurring in infants affected with the Li-Fraumeni and Li- Fraumeni-like (LFS/LFL) syndromes, which are caused by dominant germline ...

    Authors: Juliana Giacomazzi, Simone Selistre, Juliana Duarte, Jorge Pinto Ribeiro, Paulo JC Vieira, Gabriel de Souza Macedo, Cristina Rossi, Mauro Czepielewski, Cristina Brinkmann Oliveira Netto, Pierre Hainaut and Patricia Ashton-Prolla

    Citation: BMC Cancer 2013 13:187

    Content type: Case report

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  37. Ultra-conserved regions (UCRs) are segments of the genome (≥ 200 bp) that exhibit 100% DNA sequence conservation between human, mouse and rat. Transcribed UCRs (T-UCRs) have been shown to be differentially exp...

    Authors: Karen M Watters, Kenneth Bryan, Niamh H Foley, Maria Meehan and Raymond L Stallings

    Citation: BMC Cancer 2013 13:184

    Content type: Research article

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  38. The EGFR 3′ untranslated region (UTR) harbors a polyadenine repeat which is polymorphic (A13/A14) and undergoes somatic deletions in microsatellite instability (MSI) colorectal cancer (CRC). These mutations could...

    Authors: Nasrin Sarafan-Vasseur, David Sefrioui, David Tougeron, Aude Lamy, France Blanchard, Florence Le Pessot, Frédéric Di Fiore, Pierre Michel, Stéphane Bézieau, Jean-Baptiste Latouche, Thierry Frebourg and Richard Sesboüé

    Citation: BMC Cancer 2013 13:183

    Content type: Research article

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  39. The immune system is a key player in fighting cancer. Thus, we sought to identify a molecular ‘immune response signature’ indicating the presence of epithelial ovarian cancer (EOC) and to combine this with a s...

    Authors: Dietmar Pils, Dan Tong, Gudrun Hager, Eva Obermayr, Stefanie Aust, Georg Heinze, Maria Kohl, Eva Schuster, Andrea Wolf, Jalid Sehouli, Ioana Braicu, Ignace Vergote, Toon Van Gorp, Sven Mahner, Nicole Concin, Paul Speiser…

    Citation: BMC Cancer 2013 13:178

    Content type: Research article

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  40. KRAS is an EGFR effector in the RAS/RAF/ERK cascade that is mutated in about 40% of metastatic colorectal cancer (mCRC). Activating mutations in codons 12 and 13 of the KRAS gene are the only established negative...

    Authors: Joana G Guedes, Isabel Veiga, Patrícia Rocha, Pedro Pinto, Carla Pinto, Manuela Pinheiro, Ana Peixoto, Maria Fragoso, Ana Raimundo, Paula Ferreira, Manuela Machado, Nuno Sousa, Paula Lopes, António Araújo, Joana Macedo, Fernando Alves…

    Citation: BMC Cancer 2013 13:169

    Content type: Research article

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  41. Cancer stem cells (CSCs) are notorious for their capacity of tumor progression, metastasis or resistance to chemo-radiotherapy. However, the undisputed role of cancer stem marker, CD133, in colorectal cancers ...

    Authors: Khalilullah Mia-Jan, So Young Jung, Ik-Yong Kim, Sung Soo Oh, EunHee Choi, Sei Jin Chang, Tae Young Kang and Mee-Yon Cho

    Citation: BMC Cancer 2013 13:166

    Content type: Research article

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  42. Few high penetrance genes are known in Malignant Melanoma (MM), however, the involvement of low-penetrance genes such as MC1R, OCA2, ASIP, SLC45A2 and TYR has been observed. Lately, genome-wide association studie...

    Authors: Maria Peña-Chilet, Maite Blanquer-Maceiras, Maider Ibarrola-Villava, Conrado Martinez-Cadenas, Manuel Martin-Gonzalez, Cristina Gomez-Fernandez, Matias Mayor, Juan Antonio Aviles, Ana Lluch and Gloria Ribas

    Citation: BMC Cancer 2013 13:160

    Content type: Research article

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  43. L1CAM was originally identified as an adhesion molecule involved in neural development. In many human carcinomas L1CAM is over-expressed and is associated with a bad prognosis. We previously reported that L1CA...

    Authors: Uwe Schirmer, Heidi Fiegl, Marco Pfeifer, Alain G Zeimet, Elisabeth Müller-Holzner, Peter K Bode, Verena Tischler and Peter Altevogt

    Citation: BMC Cancer 2013 13:156

    Content type: Research article

    Published on:

    The Correction to this article has been published in BMC Cancer 2018 18:1047

  44. The insulin-like growth factor-1 (IGF-1) plays an important role in growth of prostate cancer (PCa) cells and facilitating the development and progression of PCa. This study aimed to evaluate the association o...

    Authors: Norihiko Tsuchiya, Shintaro Narita, Takamitsu Inoue, Mitsuru Saito, Kazuyuki Numakura, Mingguo Huang, Shingo Hatakeyama, Shigeru Satoh, Seiichi Saito, Chikara Ohyama, Yoichi Arai, Osamu Ogawa and Tomonori Habuchi

    Citation: BMC Cancer 2013 13:150

    Content type: Research article

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  45. The Cancer/Testis Antigens (CTAs) are a heterogeneous group of proteins whose expression is typically restricted to the testis. However, they are aberrantly expressed in most cancers that have been examined to...

    Authors: Robert Kim, Prakash Kulkarni and Sridhar Hannenhalli

    Citation: BMC Cancer 2013 13:144

    Content type: Research article

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  46. The aberrant methylation of CpG islands in the promoter is associated with colorectal cancer (CRC) carcinogenesis. In our previous study, the promoter of alcohol dehydrogenase, iron containing, 1 (ADHFE1) was mos...

    Authors: Chung Hyun Tae, Kyung Ju Ryu, Seok-Hyung Kim, Hee Cheol Kim, Ho-Kyung Chun, Byung-Hoon Min, Dong Kyung Chang, Poong-Lyul Rhee, Jae J Kim, Jong Chul Rhee and Young-Ho Kim

    Citation: BMC Cancer 2013 13:142

    Content type: Research article

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