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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 3 of 14

  1. Content type: Research article

    DNA damage repair is a complex process, which can trigger the development of cancer if disturbed. In this study, we hypothesize a role of variants in the ATM, H2AFX and MRE11 genes in determining breast cancer (B...

    Authors: Marta Podralska, Iwona Ziółkowska-Suchanek, Magdalena Żurawek, Agnieszka Dzikiewicz-Krawczyk, Ryszard Słomski, Jerzy Nowak, Agnieszka Stembalska, Karolina Pesz and Maria Mosor

    Citation: BMC Cancer 2018 18:452

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  2. Content type: Research article

    Several studies in the past have investigated the expression of micro RNAs (miRNAs) in saliva as potential biomarkers. Since miRNAs associated with extracellular vesicles (EVs) are known to be protected from e...

    Authors: Chiara Gai, Francesco Camussi, Roberto Broccoletti, Alessio Gambino, Marco Cabras, Luca Molinaro, Stefano Carossa, Giovanni Camussi and Paolo G. Arduino

    Citation: BMC Cancer 2018 18:439

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  4. Content type: Research article

    Precursor T-cell lymphoblastic lymphomas (T-LBL) are rare aggressive hematological malignancies that mainly develop in children. As in other cancers, the loss of cell cycle control plays a prominent role in th...

    Authors: Pilar López-Nieva, Pablo Fernández-Navarro, Concepción Vaquero-Lorenzo, María Villa-Morales, Osvaldo Graña-Castro, María Ángeles Cobos-Fernández, José Luis López-Lorenzo, Pilar Llamas, Laura González-Sanchez, Isabel Sastre, Marina Pollan, Marcos Malumbres, Javier Santos and José Fernández-Piqueras

    Citation: BMC Cancer 2018 18:430

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  5. Content type: Research article

    Robust and precise molecular prognostic predictors for luminal breast cancer are required. This study aimed to identify key methylation sites in luminal breast cancer, as well as precise molecular tools for pr...

    Authors: Bin Xiao, Lidan Chen, Yongli Ke, Jianfeng Hang, Ling Cao, Rong Zhang, Weiyun Zhang, Yang Liao, Yang Gao, Jianyun Chen, Li Li, Wenbo Hao, Zhaohui Sun and Linhai Li

    Citation: BMC Cancer 2018 18:405

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  6. Content type: Study protocol

    Genomic sequencing in cancer (both tumour and germline), and development of therapies targeted to tumour genetic status, hold great promise for improvement of patient outcomes. However, the imminent introducti...

    Authors: Megan Best, Ainsley J. Newson, Bettina Meiser, Ilona Juraskova, David Goldstein, Kathy Tucker, Mandy L. Ballinger, Dominique Hess, Timothy E. Schlub, Barbara Biesecker, Richard Vines, Kate Vines, David Thomas, Mary-Anne Young, Jacqueline Savard, Chris Jacobs…

    Citation: BMC Cancer 2018 18:389

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  7. Content type: Research article

    Gene expression can be employed for the discovery of prognostic gene or multigene signatures cancer. In this study, we assessed the prognostic value of a 35-gene expression signature selected by pathway and ma...

    Authors: Azeez A. Fatai and Junaid Gamieldien

    Citation: BMC Cancer 2018 18:377

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  8. Content type: Case report

    Epstein-Barr virus positive peripheral T cell lymphoma (EBV + PTCL) is a rare type of lymphoproliferative disorder which is always present in late adulthood. However, pediatric EBV + PTCL is extremely rare and...

    Authors: Zihang Chen, Limin Gao, Mi Wang, Yuan Tang, Sha Zhao and Weiping Liu

    Citation: BMC Cancer 2018 18:373

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  9. Content type: Research article

    Giant Cell Tumour of Bone (GCT) is a locally aggressive primary bone tumour that usually occurs at the epiphyses of the long bones of the appendicular skeleton with a tendency to recurrence. Recurrent somatic H3F...

    Authors: Federica Scotto di Carlo, Giuseppina Divisato, Maurizio Iacoangeli, Teresa Esposito and Fernando Gianfrancesco

    Citation: BMC Cancer 2018 18:358

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  10. Content type: Case report

    Chronic neutrophilic leukemia (CNL) is a rare myeloproliferative neoplasm (MPN) with less than 40 cases of patients being reported or clinically suspected meeting with 2008 World Health Organization (“WHO”) di...

    Authors: Xue Bin Wu, Wei Wei Wu, Yue Zhou, Xuan Wang, Jia Li and Yang Yu

    Citation: BMC Cancer 2018 18:343

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  11. Content type: Research article

    Next-generation sequencing (NGS) is an efficient and sensitive method to detect mutations from ctDNA. Many features and clinical conditions could significantly affect the concordance between ctDNA and correspo...

    Authors: Nong Yang, Yi Li, Zhidong Liu, Hao Qin, Duanming Du, Xinkai Cao, Xiaoqing Cao, Jun Li, Dongge Li, Bo Jiang, Lincan Duan, Haiyan Yang, Zhenghua Zhang, Hao Lin, Jianying Li, Zhenhua Yang…

    Citation: BMC Cancer 2018 18:319

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  12. Content type: Research article

    C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are...

    Authors: Junya Matsushita, Kazuyuki Okamura, Kazuhiko Nakabayashi, Takehiro Suzuki, Yu Horibe, Tomoko Kawai, Toshihiro Sakurai, Satoshi Yamashita, Yoshikazu Higami, Gaku Ichihara, Kenichiro Hata and Keiko Nohara

    Citation: BMC Cancer 2018 18:317

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  13. Content type: Research article

    It is unclear whether germline breast cancer susceptibility gene mutations affect breast cancer related outcomes. We wanted to evaluate mutation patterns in 20 breast cancer susceptibility genes and correlate ...

    Authors: Yong Alison Wang, Jhih-Wei Jian, Chen-Fang Hung, Hung-Pin Peng, Chi-Fan Yang, Hung-Chun Skye Cheng and An-Suei Yang

    Citation: BMC Cancer 2018 18:315

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  14. Content type: Research article

    Genetic determinants of breast cancer (BC) remained largely unknown in the majority of Moroccan patients. The purpose of this study was to explore the association of ERCC2 and MTHFR polymorphisms with genetic sus...

    Authors: Hanaa Hardi, Rahma Melki, Zouhour Boughaleb, Tijani El Harroudi, Souria Aissaoui and Noureddine Boukhatem

    Citation: BMC Cancer 2018 18:292

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  15. Content type: Research article

    Renal cell carcinoma (RCC) account for over 80% of renal malignancies. The most common type of RCC can be classified into three subtypes including clear cell, papillary and chromophobe. ccRCC (the Clear Cell R...

    Authors: Peng Wu, Jia-Li Liu, Shi-Mei Pei, Chang-Peng Wu, Kai Yang, Shu-Peng Wang and Song Wu

    Citation: BMC Cancer 2018 18:287

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  16. Content type: Case report

    The role of the hypoxia signaling pathway in the pathogenesis of pheochromocytoma/paraganglioma (PPGL)-polycythemia syndrome has been elucidated. Novel somatic mutations in hypoxia-inducible factor type 2A (HIF2A

    Authors: Ying Pang, Garima Gupta, Chunzhang Yang, Herui Wang, Thanh-Truc Huynh, Ziedulla Abdullaev, Svetlana D. Pack, Melanie J. Percy, Terence R. J. Lappin, Zhengping Zhuang and Karel Pacak

    Citation: BMC Cancer 2018 18:286

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  17. Content type: Research article

    Ribosomes, the organelles responsible for the translation of mRNA, are comprised of four rRNAs and ~ 80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some R...

    Authors: James M. Dolezal, Arie P. Dash and Edward V. Prochownik

    Citation: BMC Cancer 2018 18:275

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  18. Content type: Research article

    MYC overexpression is associated with poor prognosis in breast tumors (BCa). The objective of this study was to determine the prevalence of MYC amplification and associated markers in BCa tumors from African A...

    Authors: Tammey J. Naab, Anita Gautam, Luisel Ricks-Santi, Ashwini K. Esnakula, Yasmine M. Kanaan, Robert L. DeWitty, Girmay Asgedom, Khepher H. Makambi, Massih Abawi and Jan K. Blancato

    Citation: BMC Cancer 2018 18:274

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  19. Content type: Research article

    As hybrid RNAs, transcription-induced chimeras (TICs) may have tumor-promoting properties, and some specific chimeras have become important diagnostic markers and therapeutic targets for cancer.

    Authors: Ye Tao, Neil Gross, Xiaojiao Fan, Jianming Yang, Maikun Teng, Xu Li, Guojun Li, Yang Zhang and Zhigang Huang

    Citation: BMC Cancer 2018 18:248

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  20. Content type: Research article

    Since the first evidence suggesting existence of stem-like cancer cells, the process of cells reprogramming to the stem cell state remains as an attractive tool for cancer stemness research. Current knowledge ...

    Authors: Egle Strainiene, Mindaugas Binkis, Silvija Urnikyte, Vaidotas Stankevicius, Ausra Sasnauskiene, Gabrielis Kundrotas, Andrius Kazlauskas and Kestutis Suziedelis

    Citation: BMC Cancer 2018 18:222

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  22. Content type: Research article

    Acute myeloid leukemia (AML) is a heterogeneous group of hematopoietic malignancies due to sophisticated genetic mutations and epigenetic dysregulation. MicroRNAs (miRNAs), a class of small non-coding RNAs, ar...

    Authors: Laixi Bi, Bin Zhou, Haiying Li, Licai He, Chunjing Wang, Zhonggai Wang, Liqing Zhu, Mengqian Chen and Shenmeng Gao

    Citation: BMC Cancer 2018 18:182

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  23. Content type: Research article

    While a range of common genetic variants have been identified to be associated with risk of sporadic breast cancer in several Western studies, little is known about their role in South Asian populations. Our o...

    Authors: Nirmala Dushyanthi Sirisena, Adebowale Adeyemo, Anchala I. Kuruppu, Nilaksha Neththikumara, Nilakshi Samaranayake and Vajira H. W. Dissanayake

    Citation: BMC Cancer 2018 18:180

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  24. Content type: Research article

    Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied...

    Authors: Una Kjällquist, Rikard Erlandsson, Nicholas P. Tobin, Amjad Alkodsi, Ikram Ullah, Gustav Stålhammar, Eva Karlsson, Thomas Hatschek, Johan Hartman, Sten Linnarsson and Jonas Bergh

    Citation: BMC Cancer 2018 18:174

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  25. Content type: Research article

    Breast cancer risk for BRCA1 and BRCA2 pathogenic mutation carriers is modified by risk factors that cluster in families, including genetic modifiers of risk. We considered genetic modifiers of risk for carriers ...

    Authors: Tú Nguyen-Dumont, Zhi L. Teo, Fleur Hammet, Alexis Roberge, Maryam Mahmoodi, Helen Tsimiklis, Daniel J. Park, Bernard J. Pope, Andrew Lonie, Miroslav K. Kapuscinski, Khalid Mahmood, David E. Goldgar, Graham G. Giles, Ingrid Winship, John L. Hopper and Melissa C. Southey

    Citation: BMC Cancer 2018 18:165

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  26. Content type: Research article

    Pancreas ductal adenocarcinoma (PDAC) has the most dismal prognosis among all human cancers since it is highly resistant to chemotherapy, radiotherapy and immunotherapy. The anticipated consequence of all ther...

    Authors: Chunwan Lu, Dafeng Yang, Maria E. Sabbatini, Aaron H. Colby, Mark W. Grinstaff, Nicholas H. Oberlies, Cedric Pearce and Kebin Liu

    Citation: BMC Cancer 2018 18:149

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  27. Content type: Research article

    Increasing evidence shows that dysregulated long non-coding RNAs (lncRNAs) can serve as potential biomarkers for cancer prognosis. However, lncRNA signatures, as potential prognostic biomarkers for esophageal ...

    Authors: Guo-Wei Huang, Yu-Jie Xue, Zhi-Yong Wu, Xiu-E Xu, Jian-Yi Wu, Hui-Hui Cao, Ying Zhu, Jian-Zhong He, Chun-Quan Li, En-Min Li and Li-Yan Xu

    Citation: BMC Cancer 2018 18:147

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  28. Content type: Research article

    The heterogeneous behavior of patients with melanoma makes prognostication challenging. To address this, a gene expression profile (GEP) test to predict metastatic risk was previously developed. This study eva...

    Authors: Jonathan S. Zager, Brian R. Gastman, Sancy Leachman, Rene C. Gonzalez, Martin D. Fleming, Laura K. Ferris, Jonhan Ho, Alexander R. Miller, Robert W. Cook, Kyle R. Covington, Kristen Meldi-Plasseraud, Brooke Middlebrook, Lewis H. Kaminester, Anthony Greisinger, Sarah I. Estrada, David M. Pariser…

    Citation: BMC Cancer 2018 18:130

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  29. Content type: Research article

    MicroRNAs (miRNAs or miRs) are small molecules known to be involved in post-transcriptional gene expression. Many of them have been shown to influence risk for various diseases. Recent studies suggest that low...

    Authors: Aleksandra Butrym, Piotr Łacina, Kazimierz Kuliczkowski, Katarzyna Bogunia-Kubik and Grzegorz Mazur

    Citation: BMC Cancer 2018 18:107

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  30. Content type: Research article

    A unified analysis of DNA sequences from hundreds of tumors concluded that the driver mutations primarily occur in the earliest stages of cancer formation, with relatively few driver mutation events detected i...

    Authors: Karen Gomez, Sayaka Miura, Louise A. Huuki, Brianna S. Spell, Jeffrey P. Townsend and Sudhir Kumar

    Citation: BMC Cancer 2018 18:85

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  31. Content type: Research article

    Sessile serrated adenomas with BRAF mutation progress rapidly to cancer following the development of dysplasia (SSAD). Approximately 75% of SSADs methylate the mismatch repair gene MLH1, develop mismatch repair d...

    Authors: Lochlan J. Fennell, Saara Jamieson, Diane McKeone, Tracie Corish, Megan Rohdmann, Tori Furner, Mark Bettington, Cheng Liu, Futoshi Kawamata, Catherine Bond, Jolieke Van De Pols, Barbara Leggett and Vicki Whitehall

    Citation: BMC Cancer 2018 18:35

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  32. Content type: Research article

    Aberrant overexpression of PIWI/piRNA pathway proteins is shown for many types of tumors. Interestingly, these proteins are downregulated in testicular germ cell tumors (TGCTs) compared to normal testis tissue...

    Authors: Ildar V. Gainetdinov, Yulia V. Skvortsova, Sofia A. Kondratieva, Alexey Klimov, Alexey A. Tryakin and Tatyana L. Azhikina

    Citation: BMC Cancer 2018 18:20

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  33. Content type: Research article

    Prostate Cancer (PCa) is the second most prevalent cancer among U.S. males. In recent decades many men with low risk PCa have been over diagnosed and over treated. Given significant co-morbidities associated w...

    Authors: Katerina Pestova, Adam J. Koch, Charles P. Quesenberry, Jun Shan, Ying Zhang, Amethyst D. Leimpeter, Beth Blondin, Svetlana Sitailo, Lela Buckingham, Jing Du, Huixin Fei and Stephen K. Van Den Eeden

    Citation: BMC Cancer 2018 18:2

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  34. Content type: Research article

    Associations between polymorphisms of UDP-glucuronosyltransferases (UGTs) or efflux transporters (e.g., P-glycoprotein and MRP2) and different types of cancer have been described, whereas the role of influx tr...

    Authors: Sabrina Falkowski, Jean-Baptiste Woillard, Deborah Postil, Nicole Tubiana-Mathieu, Eric Terrebonne, Antoine Pariente, Denis Smith, Rosine Guimbaud, Claire Thalamas, Koukeb Rouguieg-Malki, Pierre Marquet and Nicolas Picard

    Citation: BMC Cancer 2017 17:901

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  35. Content type: Study protocol

    A wide range of studies has investigated the diagnostic proficiency of extracellular microRNAs (miRNAs) in hepatocellular cancer (HCC). HCC is expected to increase in Sub-Saharan Africa (SSA), due to endemic l...

    Authors: K. Sartorius, B. Sartorius, A. Kramvis, E. Singh, A. Turchinovich, B. Burwinkel, T. Madiba and C. A. Winkler

    Citation: BMC Cancer 2017 17:894

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  36. Content type: Research article

    EphA2 is a crucial oncogene in gastric cancer (GC) development and metastasis, this study aims to identify microRNAs that target it and serve as key regulators of gastric carcinogenesis.

    Authors: Jin Huang, Yijing He, Howard L. Mcleod, Yanchun Xie, Desheng Xiao, Huabin Hu, Pan Chen, Liangfang Shen, Shan Zeng, Xianli Yin, Jie Ge, Li Li, Lanhua Tang, Jian Ma and Zihua Chen

    Citation: BMC Cancer 2017 17:886

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  37. Content type: Research article

    Histones undergo extensive post-translational modifications and this epigenetic regulation plays an important role in modulating transcriptional programs capable of driving cancer progression. Acetylation of h...

    Authors: Shivashankar Damodaran, Nathan Damaschke, Joseph Gawdzik, Bing Yang, Cedric Shi, Glenn O. Allen, Wei Huang, John Denu and David Jarrard

    Citation: BMC Cancer 2017 17:874

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  38. Content type: Research article

    Hepatocellular carcinoma (HCC) is the leading cause of cancer mortality. Chemical and virus induction are two major risk factors, however, the potential molecular mechanisms of their differences remain elusive...

    Authors: Qin Tang, Qi Wang, Qiong Zhang, Sheng-Yan Lin, Yanhong Zhu, Xiangliang Yang and An-Yuan Guo

    Citation: BMC Cancer 2017 17:862

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  39. Content type: Research article

    The significance of PLK1 (polo-like kinase 1) has become increasingly essential as both a biomarker and a target for cancer treatment. Here, we aimed to determine the downstream genes of PLK1 and their effects...

    Authors: Zhe Zhang, Guojun Zhang, Zhipeng Gao, Shiguang Li, Zeliang Li, Jianbin Bi, Xiankui Liu, Zhenhua Li and Chuize Kong

    Citation: BMC Cancer 2017 17:861

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  40. Content type: Case report

    Colorectal carcinoma (CRC) is one of the most common causes of cancer-related deaths. The mean age of patients with CRC ranges from 49 to 60 years. Pediatric CRC is unusual, which often escapes early diagnosis...

    Authors: Yung-Sung Yeh, Yu-Tang Chang, Cheng-Jen Ma, Ching-Wen Huang, Hsiang-Lin Tsai, Yi-Ting Chen and Jaw-Yuan Wang

    Citation: BMC Cancer 2017 17:849

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  41. Content type: Research article

    A systematic review was conducted to assess the diagnostic test accuracy of polymerase chain reaction (PCR)-based microsatellite instability (MSI) testing for identifying Lynch syndrome in patients with colore...

    Authors: Helen Coelho, Tracey Jones-Hughes, Tristan Snowsill, Simon Briscoe, Nicola Huxley, Ian M. Frayling and Chris Hyde

    Citation: BMC Cancer 2017 17:836

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  43. Content type: Research article

    MicroRNAs (miRNAs) exhibit essential regulatory functions related to cell growth, apoptosis, development and differentiation. Dysregulated expression of miRNAs is associated with a wide variety of human diseas...

    Authors: Guanyu Wang, Fulu Dong, Zhiyao Xu, Sherven Sharma, Xiaotong Hu, Dafang Chen, Lumin Zhang, Jinping Zhang and Qinghua Dong

    Citation: BMC Cancer 2017 17:805

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  44. Content type: Research article

    Female breast cancer is frequently diagnosed at a later stage and the leading cause of cancer deaths world-wide. Levels of cell-free circulating microRNAs (miRNAs) can potentially be used as biomarkers to meas...

    Authors: Amal Qattan, Haya Intabli, Wafa Alkhayal, Chafica Eltabache, Taher Tweigieri and Suad Bin Amer

    Citation: BMC Cancer 2017 17:799

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  45. Content type: Research article

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-...

    Authors: Mingshan Liu, Yang Liu, Jiabo Di, Zhe Su, Hong Yang, Beihai Jiang, Zaozao Wang, Meng Zhuang, Fan Bai and Xiangqian Su

    Citation: BMC Cancer 2017 17:787

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  46. Content type: Research article

    ESR1 mutations have attracted attention as a potentially important marker and treatment target in endocrine therapy-resistant breast cancer patients. The E380Q mutation, which is one o...

    Authors: Takashi Takeshita, Yutaka Yamamoto, Mutsuko Yamamoto-Ibusuki, Aiko Sueta, Mai Tomiguchi, Keiichi Murakami, Yoko Omoto and Hirotaka Iwase

    Citation: BMC Cancer 2017 17:786

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  47. Content type: Research article

    Gastric cancer (GC) is one of the most frequently diagnosed digestive tract cancers and carries a high risk of mortality. Acetaldehyde (AA), a carcinogenic intermediate of ethanol metabolism contributes to the...

    Authors: Sudakshina Ghosh, Biswabandhu Bankura, Soumee Ghosh, Makhan Lal Saha, Arup Kumar Pattanayak, Souvik Ghatak, Manalee Guha, Senthil Kumar Nachimuthu, Chinmoy Kumar Panda, Suvendu Maji, Subrata Chakraborty, Biswanath Maity and Madhusudan Das

    Citation: BMC Cancer 2017 17:782

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  48. Content type: Research article

    Expression of caveolin-1 (Cav-1) is frequently altered in many human cancers and both tumor suppression and promotion functions of Cav-1 have been suggested based on its expression status. However, it remains ...

    Authors: Byung-Kyu Ryu, Min-Goo Lee, Nam-Hoon Kim, Kil Yeon Lee, Shin-Ju Oh, Jung-Rock Moon, Hyo Jong Kim and Sung-Gil Chi

    Citation: BMC Cancer 2017 17:766

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  49. Content type: Research article

    The association of genes XRCC1, TP53 and MDM2 with breast cancer (BC) has never been tested in Kyrgyz population. We, therefore, aimed to identify an association of alleles and genotypes of polymorphic markers Ar...

    Authors: Jainagul Isakova, Elnura Talaibekova, Nazira Aldasheva, Denis Vinnikov and Almaz Aldashev

    Citation: BMC Cancer 2017 17:758

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  50. Content type: Research article

    To better predict the likelihood of response to chemotherapy, we have conducted a study comparing the gene expression patterns of primary tumours with their corresponding response to systemic chemotherapy in t...

    Authors: Cemile Dilara Savci-Heijink, Hans Halfwerk, Jan Koster and Marc Joan Van de Vijver

    Citation: BMC Cancer 2017 17:755

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