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Genetics, genomics and epigenetics

Section edited by Ian Cree

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.

Page 4 of 13

  1. Content type: Research article

    There are several indications that the composition of the tumor stroma can contribute to the malignancy of a tumor. Here we utilized expression data sets to identify metagenes that may serve as surrogate marke...

    Authors: Sofia Winslow, Kajsa Ericson Lindquist, Anders Edsjö and Christer Larsson

    Citation: BMC Cancer 2016 16:841

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  2. Content type: Research article

    Human epidermal growth factor receptor (HER)-2 is a driver gene in non-small cell lung cancer (NSCLC). The present study evaluated the mutation rate of HER-2 within the wild-type epidermal growth factor receptor ...

    Authors: Xuefei Li, Chao Zhao, Chunxia Su, Shengxiang Ren, Xiaoxia Chen and Caicun Zhou

    Citation: BMC Cancer 2016 16:828

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  3. Content type: Research article

    Triple-negative breast cancer (TNBC) with a BRCA1-like molecular signature has been demonstrated to remarkably respond to platinum-based chemotherapy and might be suited for a future treatment with poly(ADP-ri...

    Authors: Eva Gross, Harm van Tinteren, Zhou Li, Sandra Raab, Christina Meul, Stefanie Avril, Nadja Laddach, Michaela Aubele, Corinna Propping, Apostolos Gkazepis, Manfred Schmitt, Alfons Meindl, Petra M. Nederlof, Marion Kiechle and Esther H. Lips

    Citation: BMC Cancer 2016 16:811

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  4. Content type: Research article

    Genes in inflammatory pathways play a pivotal role in the development of colorectal cancer. We conducted a two-stage case-control study and aimed at screening the colorectal cancer-associated genetic variation...

    Authors: Chunxiao Xu, Dan Zhou, Feixia Pan, Yi Liu, Dandan zhang, Aifen Lin, Xiaoping Miao, Yaqin Ni, Duo Lv, Shuai Zhang, Xiaobo Li, Yimin Zhu and Maode Lai

    Citation: BMC Cancer 2016 16:807

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  5. Content type: Research article

    This study addresses involvement of major 5-fluorouracil (5-FU) pathway genes in the prognosis of colorectal carcinoma patients.

    Authors: T. Kunicka, P. Prochazka, I. Krus, P. Bendova, M. Protivova, S. Susova, V. Hlavac, V. Liska, P. Novak, M. Schneiderova, P. Pitule, J. Bruha, O. Vycital, P. Vodicka and P. Soucek

    Citation: BMC Cancer 2016 16:795

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  6. Content type: Research article

    The extracellular matrix (ECM), one of the key components of tumor microenvironment, has a tremendous impact on cancer development and highly influences tumor cell features. ECM affects vital cellular function...

    Authors: Vaidotas Stankevicius, Gintautas Vasauskas, Danute Bulotiene, Stase Butkyte, Sonata Jarmalaite, Ricardas Rotomskis and Kestutis Suziedelis

    Citation: BMC Cancer 2016 16:789

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  7. Content type: Research article

    Single nucleotide polymorphisms (SNPs) involved in the estrogen pathway and SNPs in the estrogen receptor alpha gene (ESR1 6q25) have been linked to breast cancer development, and mammographic density is an estab...

    Authors: F. N. Fjeldheim, H. Frydenberg, V. G. Flote, A. McTiernan, A-S Furberg, P. T. Ellison, E. S. Barrett, T. Wilsgaard, G. Jasienska, G. Ursin, E. A. Wist and I. Thune

    Citation: BMC Cancer 2016 16:776

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  8. Content type: Research article

    Non-muscle-invasive bladder cancer (NMIBC) is a high incidence form of bladder cancer (BCa), where genetic and epigenetic alterations occur frequently. We assessed the performance of associating a FGFR3 mutation ...

    Authors: Jean-Pierre Roperch, Bernard Grandchamp, François Desgrandchamps, Pierre Mongiat-Artus, Vincent Ravery, Idir Ouzaid, Morgan Roupret, Véronique Phe, Calin Ciofu, Florence Tubach, Olivier Cussenot and Roberto Incitti

    Citation: BMC Cancer 2016 16:704

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  9. Content type: Research article

    In breast cancer, the epithelial to mesenchyme transition (EMT) is associated to tumour dissemination, drug resistance and high relapse risks. It is partly controlled by epigenetic modifications such as histon...

    Authors: Jean-Marc Gregoire, Laurence Fleury, Clara Salazar-Cardozo, Frédéric Alby, Véronique Masson, Paola Barbara Arimondo and Frédéric Ausseil

    Citation: BMC Cancer 2016 16:700

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  10. Content type: Research article

    Oral tongue squamous cell carcinoma (OTSCC) is one of the most aggressive forms of head and neck/oral cancer (HNOC), and is a complex disease with extensive genetic and epigenetic defects, including microRNA d...

    Authors: Qianting He, Zujian Chen, Qian Dong, Leitao Zhang, Dan Chen, Aditi Patel, Ajay Koya, Xianghong Luan, Robert J. Cabay, Yang Dai, Anxun Wang and Xiaofeng Zhou

    Citation: BMC Cancer 2016 16:685

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  11. Content type: Research article

    Vitamin D receptor (VDR) gene polymorphisms affect the risk of prostate cancer. However, studies investigating the relationship between VDR gene polymorphisms (Cdx2 and ApaI) and prostate cancer risk are equivoca...

    Authors: Kewei Wang, Guosheng Wu, Jinping Li and Wentao Song

    Citation: BMC Cancer 2016 16:674

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  12. Content type: Research article

    Nasopharyngeal carcinoma (NPC) is a type of head-neck cancer with a distinguishable geographic and racial distribution worldwide. Increasing evidence supports that the accumulation of additional genetic and ep...

    Authors: Pei-Yu Huang, Ting-Ting Zeng, Xiaojiao Ban, Meng-Qing Li, Bao-Zhu Zhang, Ying-Hui Zhu, Wen-Feng Hua, Hai-Qiang Mai, Li Zhang, Xin-Yuan Guan and Yan Li

    Citation: BMC Cancer 2016 16:669

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  13. Content type: Research article

    Cancer is increasingly understood to arise in the context of dynamically evolving genomes with continuously generated variants subject to selective pressures. Diverse mutations have been identified in papillar...

    Authors: Jill C. Rubinstein, Taylor C. Brown, Emily R. Christison-Lagay, Yawei Zhang, John W. Kunstman, C. Christofer Juhlin, Carol Nelson-Williams, Gerald Goh, Courtney E. Quinn, Glenda G. Callender, Robert Udelsman, Richard P. Lifton, Reju Korah and Tobias Carling

    Citation: BMC Cancer 2016 16:646

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  14. Content type: Research article

    Traditional prognostic indicators of breast cancer, i.e. lymph node diffusion, tumor size, grading and estrogen receptor expression, are inadequate predictors of metastatic relapse. Thus, additional prognostic...

    Authors: Emanuela Guerra, Alessia Cimadamore, Pasquale Simeone, Giovanna Vacca, Rossano Lattanzio, Gerardo Botti, Valentina Gatta, Marco D’Aurora, Barbara Simionati, Mauro Piantelli and Saverio Alberti

    Citation: BMC Cancer 2016 16:649

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  15. Content type: Research article

    Pancreatic cancer is poorly characterized at genetic and non-genetic levels. The current study evaluates in a large cohort of patients the prognostic relevance of molecular subtypes and key transcription facto...

    Authors: Rekin’s Janky, Maria Mercedes Binda, Joke Allemeersch, Anke Van den broeck, Olivier Govaere, Johannes V. Swinnen, Tania Roskams, Stein Aerts and Baki Topal

    Citation: BMC Cancer 2016 16:632

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  16. Content type: Case report

    Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8 % cases). The patient reported here is only the eighth case of MNTI presenting in an ...

    Authors: David J. Barnes, Edward Hookway, Nick Athanasou, Takeshi Kashima, Udo Oppermann, Simon Hughes, Daniel Swan, Dietrich Lueerssen, John Anson and A. Bassim Hassan

    Citation: BMC Cancer 2016 16:629

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  17. Content type: Research article

    The single hotspot mutation AKT1 [G49A:E17K] has been described in several cancers, with the highest incidence observed in breast cancer. However, its precise role in disease etiology remains unknown.

    Authors: Marion Rudolph, Tobias Anzeneder, Anke Schulz, Georg Beckmann, Annette T. Byrne, Michael Jeffers, Carol Pena, Oliver Politz, Karl Köchert, Richardus Vonk and Joachim Reischl

    Citation: BMC Cancer 2016 16:622

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  18. Content type: Research article

    The minor allele of two caspase 8 polymorphisms, namely CASP8 -652 6N InsDel (rs3834129) and CASP8 Asp302His (rs1045485), were repeatedly associated with reduced breast cancer susceptibility. Contrarily, the pres...

    Authors: J. D. Kuhlmann, A. Bankfalvi, K. W. Schmid, R. Callies, R. Kimmig, P. Wimberger, W. Siffert and H. S. Bachmann

    Citation: BMC Cancer 2016 16:618

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  19. Content type: Research article

    The screening of ROS proto-oncogene 1, receptor tyrosine kinase(ROS1) fusion rearrangement might be potentially beneficial for an effective therapy against non-small cell lung cancer (NSCLC). However, the thre...

    Authors: Jieyu Wu, Yunen Lin, Xinming He, Haihong Yang, Ping He, Xinge Fu, Guangqiu Li and Xia Gu

    Citation: BMC Cancer 2016 16:599

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  20. Content type: Research article

    In South and Southeast Asian, the majority of buccal squamous cell carcinoma (BSCC) can arise from oral submucous fibrosis (OSF). BSCCs develop in OSF that are often not completely resected, causing local rela...

    Authors: Wen Liu, Lijuan Zeng, Ning Li, Fei Wang, Canhua Jiang, Feng Guo, Xinqun Chen, Tong Su, Chunjiao Xu, Shanshan Zhang and Changyun Fang

    Citation: BMC Cancer 2016 16:584

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  21. Content type: Research article

    Long noncoding RNAs (lncRNAs) play crucial roles in tumorigenesis, and lncRNA taurine-upregulated gene 1 (TUG1) has been proven to be associated with several human cancers. However, the mechanisms of TUG1-involve...

    Authors: Pei-Chin Lin, Hsien-Da Huang, Chun-Chi Chang, Ya-Sian Chang, Ju-Chen Yen, Chien-Chih Lee, Wen-Hsin Chang, Ta-Chih Liu and Jan-Gowth Chang

    Citation: BMC Cancer 2016 16:583

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  22. Content type: Research article

    KRAS mutation testing is mandatory in the management of metastatic colorectal cancer prior to treatment with anti-EGFR antibodies as patients whose tumors express mutant KRAS do not benefit from these agents. Alt...

    Authors: Elisabeth Mack, Kathleen Stabla, Jorge Riera-Knorrenschild, Roland Moll, Andreas Neubauer and Cornelia Brendel

    Citation: BMC Cancer 2016 16:585

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  23. Content type: Technical advance

    Imatinib-resistant chronic myeloid leukemia (CML) patients receiving second-line tyrosine kinase inhibitor (TKI) therapy with dasatinib or nilotinib have a higher risk of disease relapse and progression and no...

    Authors: Simona Soverini, Caterina De Benedittis, Fausto Castagnetti, Gabriele Gugliotta, Manuela Mancini, Luana Bavaro, Katerina Machova Polakova, Jana Linhartova, Alessandra Iurlo, Domenico Russo, Fabrizio Pane, Giuseppe Saglio, Gianantonio Rosti, Michele Cavo, Michele Baccarani and Giovanni Martinelli

    Citation: BMC Cancer 2016 16:572

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  24. Content type: Research article

    SLC52A3 was recently identified as a susceptibility gene for esophageal squamous cell carcinoma (ESCC). However, associations between the single nucleotide polymorphisms (SNPs) rs13042...

    Authors: Hua-Zhen Tan, Zhi-Yong Wu, Jian-Yi Wu, Lin Long, Ji-Wei Jiao, Yu-Hui Peng, Yi-Wei Xu, Shan-Shan Li, Wei Wang, Jian-Jun Zhang, En-Min Li and Li-Yan Xu

    Citation: BMC Cancer 2016 16:560

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  25. Content type: Research article

    Long-term prognostic significance of loss of heterozygosity on chromosome 9p21 for localized renal cell carcinoma following surgery remains unreported. The study assessed the frequency of deletions of differen...

    Authors: Ismail El-Mokadem, Alison Lim, Thomas Kidd, Katherine Garret, Norman Pratt, David Batty, Stewart Fleming and Ghulam Nabi

    Citation: BMC Cancer 2016 16:546

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  26. Content type: Research article

    Despite the clinical significance of liver metastases, the difference between molecular and cellular changes in primary colorectal cancers (CRC) and matched liver metastases is poorly understood.

    Authors: Ja-Rang Lee, Chae Hwa Kwon, Yuri Choi, Hye Ji Park, Hyun Sung Kim, Hong-Jae Jo, Nahmgun Oh and Do Youn Park

    Citation: BMC Cancer 2016 16:539

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  27. Content type: Research article

    Colorectal cancer (CRC) is closely linked to Wnt signalling, with 94 % of cases exhibiting a Wnt related mutation. ROR2 is a receptor tyrosine kinase that is thought to repress β-catenin dependent Wnt signalli...

    Authors: Sean S. Q. Ma, Sameer Srivastava, Estelle Llamosas, Nicholas J. Hawkins, Luke B. Hesson, Robyn L. Ward and Caroline E. Ford

    Citation: BMC Cancer 2016 16:508

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  28. Content type: Research article

    Numerous case–control studies have been performed to investigate the association between three cyclooxygenase-2 (COX-2) polymorphisms (rs20417 (−765G > C), rs689466 (−1195G > A), and rs5275 (8473 T > C)) and t...

    Authors: Wei-Dong Leng, Xiu-Jie Wen, Joey S. W. Kwong, Wei Huang, Jian-Gang Chen and Xian-Tao Zeng

    Citation: BMC Cancer 2016 16:457

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  29. Content type: Research article

    We aimed to evaluate the correlation between p16ink4a-overexpression and high risk (hr)HPV-DNA in vulvar squamous cell carcinoma (vSCC) tumors as well as the impact of both biomarkers on the prognosis of vSCC pat...

    Authors: Jacek J. Sznurkowski, Anton Żawrocki and Wojciech Biernat

    Citation: BMC Cancer 2016 16:465

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  30. Content type: Research article

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-activated transcription factor that belongs to the nuclear hormone receptor superfamily. PPARγ is essential in adipocyte differentiation fro...

    Authors: Akihiko Takeuchi, Norio Yamamoto, Toshiharu Shirai, Katsuhiro Hayashi, Shinji Miwa, Seiichi Munesue, Yasuhiko Yamamoto and Hiroyuki Tsuchiya

    Citation: BMC Cancer 2016 16:442

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  31. Content type: Research article

    The 5-year overall survival rates for head and neck cancer (HNC) relies on distant metastasis. Importantly, the epithelial-mesenchymal transition (EMT) is believed to be an initial step of metastasis. However,...

    Authors: Li-Hsuen Chen, Wen-Lin Hsu, Yen-Ju Tseng, Dai-Wei Liu and Ching-Feng Weng

    Citation: BMC Cancer 2016 16:431

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    The Erratum to this article has been published in BMC Cancer 2016 16:595

  32. Content type: Technical advance

    MammaTyper is a novel CE-marked in vitro diagnostic RT-qPCR assay which assigns routinely processed breast cancer specimens into the molecular subtypes Luminal A-like, Luminal B-like (HER2 positive or negative),

    Authors: Mark Laible, Kornelia Schlombs, Katharina Kaiser, Elke Veltrup, Stefanie Herlein, Sotiris Lakis, Robert Stöhr, Sebastian Eidt, Arndt Hartmann, Ralph M. Wirtz and Ugur Sahin

    Citation: BMC Cancer 2016 16:398

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  33. Content type: Research article

    Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) mutations that activate the PI3K/AKT signaling pathway have been observed in several types of carcinoma and have been associated...

    Authors: Kazuto Harada, Yoshifumi Baba, Hironobu Shigaki, Takatsugu Ishimoto, Keisuke Miyake, Keisuke Kosumi, Ryuma Tokunaga, Daisuke Izumi, Mayuko Ohuchi, Kenichi Nakamura, Yuki Kiyozumi, Junji Kurashige, Masaaki Iwatsuki, Yuji Miyamoto, Yasuo Sakamoto, Naoya Yoshida…

    Citation: BMC Cancer 2016 16:400

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  34. Content type: Research article

    Better insights into the molecular changes involved in virus-associated and -independent head and neck cancer may advance our knowledge of HNC carcinogenesis and identify critical disease biomarkers. Here we a...

    Authors: Zuzana Vojtechova, Ivan Sabol, Martina Salakova, Jana Smahelova, Jiri Zavadil, Lubomir Turek, Marek Grega, Jan Klozar, Bohumir Prochazka and Ruth Tachezy

    Citation: BMC Cancer 2016 16:382

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  35. Content type: Research article

    African American (AA) colon cancer patients have a worse prognosis than Caucasian (CA) colon cancer patients, however, reasons for this disparity are not well understood. To determine if tumor biology might co...

    Authors: Rangaswamy Govindarajan, James Posey, Calvin Y. Chao, Ruixiao Lu, Trafina Jadhav, Ahmed Y. Javed, Awais Javed, Fade A. Mahmoud, Raymond U. Osarogiagbon and Upender Manne

    Citation: BMC Cancer 2016 16:368

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  36. Content type: Research article

    We adapted Bayesian statistical learning strategies to the prognosis field to investigate if genome-wide common SNP improve the prediction ability of clinico-pathological prognosticators and applied it to non-...

    Authors: E. López de Maturana, A. Picornell, A. Masson-Lecomte, M. Kogevinas, M. Márquez, A. Carrato, A. Tardón, J. Lloreta, M. García-Closas, D. Silverman, N. Rothman, S. Chanock, F. X. Real, M. E. Goddard and N. Malats

    Citation: BMC Cancer 2016 16:351

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  37. Content type: Research article

    Cholangiocarcinoma is characterized by late diagnosis and a poor survival rate. MicroRNAs have been involved in the pathogenesis of different cancer types, including cholangiocarcinoma. Our aim was to identify...

    Authors: Tiziana Palumbo, George A. Poultsides, Grigorios Kouraklis, Theodore Liakakos, Alexandra Drakaki, George Peros, Maria Hatziapostolou and Dimitrios Iliopoulos

    Citation: BMC Cancer 2016 16:353

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  38. Content type: Research article

    Early detection of oral squamous cell carcinomas (OSCCs) is urgently needed to improve the prognosis and quality of life (QOL) of patients. Oral leukoplakias (OLs), known as the most common premalignant lesion...

    Authors: Masanobu Abe, Satoshi Yamashita, Yoshiyuki Mori, Takahiro Abe, Hideto Saijo, Kazuto Hoshi, Toshikazu Ushijima and Tsuyoshi Takato

    Citation: BMC Cancer 2016 16:350

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  39. Content type: Research article

    Alterations in the host cellular immune response allow persistent infections with High-Risk Human Papillomavirus (HR-HPV) and development of premalignant cervical lesions and cervical cancer (CC). Variations o...

    Authors: K. Torres-Poveda, A. I. Burguete-García, M. Bahena-Román, R. Méndez-Martínez, M. A. Zurita-Díaz, G. López-Estrada, K. Delgado-Romero, O. Peralta-Zaragoza, V. H. Bermúdez-Morales, D. Cantú, A. García-Carrancá and V. Madrid-Marina

    Citation: BMC Cancer 2016 16:330

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  40. Content type: Research article

    Chemokines are well known inflammatory factors critical for tumor development in diverse tissues, including lung cancer. Chemokine (C-C motif) Ligand 2 (CCL2) was one of such chemokines important for both prim...

    Authors: Xu Li, Fangcai Lin and Hong Zhou

    Citation: BMC Cancer 2016 16:298

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  41. Content type: Research article

    The influence of the tumor microenvironment and tumor-stromal interactions on the heterogeneity of response within breast cancer subtypes have just begun to be explored. This study focuses on patients with est...

    Authors: Alexander S. Brodsky, Jinjun Xiong, Dongfang Yang, Christoph Schorl, Mary Anne Fenton, Theresa A. Graves, William M. Sikov, Murray B. Resnick and Yihong Wang

    Citation: BMC Cancer 2016 16:274

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  42. Content type: Research article

    The incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection. Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the cop...

    Authors: B. M. Shivakumar, Sanjiban Chakrabarty, Harish Rotti, Venu Seenappa, Lakshmi Rao, Vasudevan Geetha, B. V. Tantry, Hema Kini, Rajesh Dharamsi, C. Ganesh Pai and Kapaettu Satyamoorthy

    Citation: BMC Cancer 2016 16:271

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  43. Content type: Research article

    Interrogate the impact of IKZF1 deletion on therapy-outcomes of adults with common B-cell acute lymphoblastic leukemia.

    Authors: Qiu-Mei Yao, Kai-Yan Liu, Robert Peter Gale, Bin Jiang, Yan-Rong Liu, Qian Jiang, Hao Jiang, Xiao-Hui Zhang, Mei-Jie Zhang, Shan-Shan Chen, Xiao-Jun Huang, Lan-Ping Xu and Guo-Rui Ruan

    Citation: BMC Cancer 2016 16:269

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  44. Content type: Research article

    Endocrine resistance is a major obstacle to optimal treatment effect in breast cancer. Some genetic markers have been proposed to predict response to aromatase inhibitors (AIs) but the data is insufficient. Th...

    Authors: Maria Simonsson, Srinivas Veerla, Andrea Markkula, Carsten Rose, Christian Ingvar and Helena Jernström

    Citation: BMC Cancer 2016 16:256

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  45. Content type: Research article

    Post-transcriptional regulation by microRNAs is recognized as one of the major pathways for the control of cellular homeostasis. Less well understood is the transcriptional and epigenetic regulation of genes e...

    Authors: Erandi Ayala-Ortega, Rodrigo Arzate-Mejía, Rosario Pérez-Molina, Edgar González-Buendía, Karin Meier, Georgina Guerrero and Félix Recillas-Targa

    Citation: BMC Cancer 2016 16:226

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  46. Content type: Research article

    A large number of epigenetic alterations has been found to be implicated in the etiology of gastric cancer. We have studied the DNA methylation status of 27 500 gene promoter regions in 24 gastric adenocarcino...

    Authors: Lars Lohne Eftang, Jovana Klajic, Vessela N. Kristensen, Jörg Tost, Qin Ying Esbensen, Gustav Peter Blom, Ida Rashida Khan Bukholm and Geir Bukholm

    Citation: BMC Cancer 2016 16:225

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  47. Content type: Research article

    Array CGH analysis of breast tumors has contributed to the identification of different genomic profiles in these tumors. Loss of DNA repair by BRCA1 functional deficiency in breast cancer has been proposed as ...

    Authors: Carolina Alvarez, Andrés Aravena, Teresa Tapia, Ester Rozenblum, Luisa Solís, Alejandro Corvalán, Mauricio Camus, Manuel Alvarez, David Munroe, Alejandro Maass and Pilar Carvallo

    Citation: BMC Cancer 2016 16:219

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  48. Content type: Research article

    To investigate whether genetic variants of the HBV receptor gene NTCP are associated with HBV infection in the Han Chinese population.

    Authors: Jingmin Yang, Yuan Yang, Mingying Xia, Lianghui Wang, Weiping Zhou, Yajun Yang, Yueming Jiang, Hongyang Wang, Ji Qian, Li Jin and Xiaofeng Wang

    Citation: BMC Cancer 2016 16:211

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  49. Content type: Research article

    Changes in the number of alleles of a chromosome may have an impact upon gene expression. Loss of heterozygosity (LOH) indicates that one allele of a gene has been lost, and knowing the exact copy number of th...

    Authors: Peter Zauber, Stephen Marotta and Marlene Sabbath-Solitare

    Citation: BMC Cancer 2016 16:213

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