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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 1 of 14

  1. Content type: Research article

    MicroRNAs (miRNA) and other small RNAs are frequently dysregulated in cancer and are promising biomarkers for colon cancer. Here we profile human, virus and bacteria small RNAs in normal and tumor tissue from ...

    Authors: Robin Mjelle, Wenche Sjursen, Liv Thommesen, Pål Sætrom and Eva Hofsli

    Citation: BMC Cancer 2019 19:161

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  2. Content type: Research article

    Chemotherapy-induced alopecia has been well documented as a cause of distress to patients undergoing cancer treatment. Almost all traditional chemotherapeutic agents cause severe alopecia. Despite advances in ...

    Authors: Young-Cheol Lim, Hyeongi Kim, Sang Moo Lim and Jin Su Kim

    Citation: BMC Cancer 2019 19:149

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  3. Content type: Research article

    Differentiating between cancer patients who will experience metastasis within a short time and who will be long-term survivors without metastasis is a critical aim in healthcare. The microsatellite instability...

    Authors: Michelle E. Penney, Patrick S. Parfrey, Sevtap Savas and Yildiz E. Yilmaz

    Citation: BMC Cancer 2019 19:133

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  4. Content type: Research article

    Serum exosomal microRNAs (miRNAs) have been suggested as novel biomarkers for various diseases, especially gastric cancer (GC). But circulating biomarkers for Chronic atrophic gastritis (CAG) which is defined ...

    Authors: Hong Liu, Pei-wu Li, Wei-qin Yang, Hong Mi, Jing-lin Pan, Yuan-cheng Huang, Zheng-kun Hou, Qiu-ke Hou, Qi Luo and Feng-bin Liu

    Citation: BMC Cancer 2019 19:129

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  5. Content type: Research article

    The CD133 transmembrane protein is a well-recognized stem cell marker that has been used to isolate putative cancer stem cell populations from gastric cancers (GCs). However, the molecular features or biomarke...

    Authors: Tae-Min Kim, Yoon Ho Ko, Shin Jung Ha and Han Hong Lee

    Citation: BMC Cancer 2019 19:119

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  6. Content type: Research article

    Heterozygous germline TP53 gene mutations result in Li-Fraumeni Syndrome (LFS). Breast cancer (BC) is the most frequent tumor in young women with LFS. An important issue related to BC in the Mexican population is...

    Authors: Lenny N. Gallardo-Alvarado, María Teresa Tusié-Luna, María Isabel Tussié-Luna, José Díaz-Chávez, Yayoi X. Segura, Enrique Bargallo-Rocha, Cynthia Villarreal, Luis A. Herrera-Montalvo, Enrique M. Herrera-Medina and David F. Cantu-de Leon

    Citation: BMC Cancer 2019 19:118

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  7. Content type: Research article

    Significant numbers of variants detected in cancer patients are often left labeled only as variants of unknown significance (VUS). In order to expand precision medicine to a wider population, we need to extend...

    Authors: Takahiko Koyama, Kahn Rhrissorrakrai and Laxmi Parida

    Citation: BMC Cancer 2019 19:114

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  8. Content type: Research article

    Genetic polymorphisms in genes involved in pain modulation have been reported to be associated to opioid efficacy and safety in different clinical settings.

    Authors: Ersilia Lucenteforte, Alfredo Vannacci, Giada Crescioli, Niccolò Lombardi, Laura Vagnoli, Laura Giunti, Valentina Cetica, Maria Luisa Coniglio, Alessandra Pugi, Roberto Bonaiuti, Maurizio Aricò, Sabrina Giglio, Andrea Messeri, Roberto Barale, Lisa Giovannelli, Alessandro Mugelli…

    Citation: BMC Cancer 2019 19:113

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  9. Content type: Research article

    Low-grade squamous intraepithelial lesion/cervical intraepithelial neoplasia grade 1 (LSIL/CIN1) preceded by colposcopy guided biopsy is recommended conservative follow-up, although some of these lesions are a...

    Authors: Jing Ye, Xiao-dong Cheng, Bei Cheng, Yi-fan Cheng, Xiao-Jing Chen and Wei-guo Lu

    Citation: BMC Cancer 2019 19:112

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  10. Content type: Research article

    MiRNAs that are potential biomarkers for predicting prognosis for acute myeloid leukemia (AML) have been identified. However, comprehensive analyses investigating the association between miRNA expression profi...

    Authors: Yao Xue, Yuqiu Ge, Meiyun Kang, Cong Wu, Yaping Wang, Liucheng Rong and Yongjun Fang

    Citation: BMC Cancer 2019 19:109

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  11. Content type: Research article

    Visceral adipose tissue (VAT) has been identified as the essential fat depot for pathogenetic theories that associateobesity and colon cancer. LINE-1 hypomethylation has been mostly detected in tumor colon tis...

    Authors: Daniel Castellano-Castillo, Sonsoles Morcillo, Ana B. Crujeiras, Lidia Sánchez-Alcoholado, Mercedes Clemente-Postigo, Esperanza Torres, Francisco José Tinahones and Manuel Macias-Gonzalez

    Citation: BMC Cancer 2019 19:93

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  12. Content type: Research article

    Diffuse gastric cancer (DGC) is associated with the reduction or absence of the expression of the cell adhesion protein E-cadherin (encoded by the CDH1 gene). Molecular characteristics are less well described for...

    Authors: Andrea Rebeca Bustos-Carpinteyro, Carla Oliveira, Abel Sousa, Patricia Oliveira, Hugo Pinheiro, Joana Carvalho, María Teresa Magaña-Torres, María Guadalupe Flores-Miramontes, Adriana Aguilar-Lemarroy, Luis Felipe Jave-Suárez, Jorge Peregrina-Sandoval, José Alfonso Cruz-Ramos and Josefina Yoaly Sánchez-López

    Citation: BMC Cancer 2019 19:69

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  13. Content type: Research article

    Precise diagnosis of the tissue origin for metastatic cancer of unknown primary (CUP) is essential for deciding the treatment scheme to improve patients’ prognoses, since the treatment for the metastases is th...

    Authors: Mengyao Li, Hongdong Li, Guini Hong, Zhongjie Tang, Guanghao Liu, Xiaofang Lin, Mingzhang Lin, Lishuang Qi and Zheng Guo

    Citation: BMC Cancer 2019 19:67

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  14. Content type: Research article

    Clear cell renal cell carcinoma (ccRCC) is the most common subtype among renal cancer and is associated with poor prognosis if metastasized. Up to one third of patients with local disease at diagnosis will dev...

    Authors: Emma Andersson Evelönn, Mattias Landfors, Zahra Haider, Linda Köhn, Börje Ljungberg, Göran Roos and Sofie Degerman

    Citation: BMC Cancer 2019 19:65

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  15. Content type: Research article

    HER2 (ERBB2 or HER2/neu) is a tyrosine-kinase increasing cell proliferation. Overexpression/amplification of HER2 is correlated with worse prognosis in solid malignancies. Consequently, HER2 targeting is estab...

    Authors: Patrick Sven Plum, Florian Gebauer, Max Krämer, Hakan Alakus, Felix Berlth, Seung-Hun Chon, Lars Schiffmann, Thomas Zander, Reinhard Büttner, Arnulf Heinrich Hölscher, Christiane Josephine Bruns, Alexander Quaas and Heike Loeser

    Citation: BMC Cancer 2019 19:38

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  16. Content type: Research article

    Cervical cancer is the 4th highest cause of female reproductive tract malignancies. Multiple loci have been identified as important determinant factors for tumor susceptibility. In this report, we aimed to exp...

    Authors: Gui-Cen Liu, Yun-Fei Zhou, Xiao-Chao Su and Jun Zhang

    Citation: BMC Cancer 2019 19:24

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  17. Content type: Research article

    BRCA1/2 pathogenic (P) and likely pathogenic (LP) germline variants are frequent among patients with ovarian carcinoma. However, these variants have not been extensively characterized in patients with ovarian can...

    Authors: Deborah Porto Cotrim, Adriana Regina Gonçalves Ribeiro, Daniele Paixão, Diogo Cordeiro de Queiroz Soares, Rima Jbili, Natasha Carvalho Pandolfi, Camila Cezana, Carine de Cássia Mauro, Henrique Mantoan, Graziele Bovolim, Louise de Brot, Giovana Tardin Torrezan, Dirce Maria Carraro, Glauco Baiocchi, Maria Nirvana da Cruz Formiga and Alexandre A. B. A. da Costa

    Citation: BMC Cancer 2019 19:4

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  18. Content type: Research article

    Breast cancer is the most common cancer in women worldwide. Around 50% of breast cancer familial risk has been so far explained by known susceptibility alleles with variable levels of risk and prevalence. The ...

    Authors: Yosr Hamdi, Mariem Ben Rekaya, Shan Jingxuan, Majdi Nagara, Olfa Messaoud, Amel Benammar Elgaaied, Ridha Mrad, Lotfi Chouchane, Mohamed Samir Boubaker, Sonia Abdelhak, Hamouda Boussen and Lilia Romdhane

    Citation: BMC Cancer 2018 18:1295

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  19. Content type: Research article

    Gastric cancer (GC) ranks the second in mortality rate among all cancers. Metastases account for most of the deaths in GC patients. Yet our understanding of GC and its metastasis mechanism is still very limited.

    Authors: Jie Zhang, Weiqing Qiu, Hua Liu, Changlin Qian, Dujuan Liu, Hailong Wang, Ni Hu, Y. Tom Tang, Jianhua Sun and Zhiyong Shen

    Citation: BMC Cancer 2018 18:1270

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  20. Content type: Research article

    Broad copy number aberrations (BCNAs) represent a common form of genome instability in colorectal cancer (CRC). CRCs show large variations in their level of aneuploidy: microsatellite-instable (MSI) tumors are...

    Authors: Vincenza Barresi, Giacomo Cinnirella, Giovanna Valenti, Giorgia Spampinato, Nicolò Musso, Sergio Castorina and Daniele F. Condorelli

    Citation: BMC Cancer 2018 18:1265

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  21. Content type: Research article

    Ocular melanoma is a rare but often deadly malignancy that arises in the uvea (commonest primary site), conjunctiva or the orbit. Primary orbital melanoma (POM) is exceedingly rare, with approximately 60 cases...

    Authors: Anna M. Rose, Rong Luo, Utsav K. Radia, Helen Kalirai, Sophie Thornton, Philip J. Luthert, Channa N. Jayasena, David H. Verity, Sarah E. Coupland and Geoffrey E. Rose

    Citation: BMC Cancer 2018 18:1262

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  22. Content type: Research article

    Genetic alterations in pediatric primary brain tumors can be used as diagnostic and prognostic markers and are the basis for the development of new target therapies that, ideally, would be associated with lowe...

    Authors: Laura Frazão, Maria do Carmo Martins, Vasco Moura Nunes, José Pimentel, Claudia Faria, José Miguéns, Amets Sagarribay, Mário Matos, Duarte Salgado, Sofia Nunes, Manuela Mafra and Lúcia Roque

    Citation: BMC Cancer 2018 18:1259

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  23. Content type: Research article

    SKA1, an important mitosis protein, has been indicated in the initiation and progression of several malignancies. However, its clinical significance in hepatocellular carcinoma (HCC) remain to be elucidated.

    Authors: Yibing Chen, Jingjing Zhao, Zhihui Jiao, Weiwei Wang, Dandan Wang, Xiaohe Yu, Zhiyong Shi, Naijian Ge, Qiuzhong Pan, Jianchuan Xia, Wancheng Niu, Ruihua Zhao, Xiaofei Zhang and Wei Du

    Citation: BMC Cancer 2018 18:1240

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  24. Content type: Research article

    The gene desert on human chromosomal band 8q24 harbors multiple genetic variants associated with common cancers, including breast cancer. The locus, including the gene desert and its flanking genes, MYC, PVT1 and...

    Authors: Collin Homer-Bouthiette, Yang Zhao, Lauren B. Shunkwiler, Benjamine Van Peel, Elizabeth Garrett-Mayer, Rachael C. Baird, Anna I. Rissman, Stephen T. Guest, Stephen P. Ethier, Manorama C. John, Patricia A. Powers, Jill D. Haag, Michael N. Gould and Bart M. G. Smits

    Citation: BMC Cancer 2018 18:1233

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  25. Content type: Research article

    A subset of lung adenocarcinoma with EGFR-tyrosine kinase inhibitor sensitizing mutations (mEGFR) is common in non-smokers and women, suggesting that mutational stressors other than smoking are involved.

    Authors: Eun Young Kim, Arum Kim, Gaeun Lee, Hangsuck Lee and Yoon Soo Chang

    Citation: BMC Cancer 2018 18:1221

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  26. Content type: Research article

    Analysis of high microsatellite instability (MSI-H) phenotype in colorectal carcinoma (CRC) is important for evaluating prognosis and choosing a proper adjuvant therapy. Although the conventional MSI analysis ...

    Authors: Mi Jang, Yujin Kwon, Hoguen Kim, Hyunki Kim, Byung Soh Min, Yehyun Park, Tae Il Kim, Sung Pil Hong and Won Kyu Kim

    Citation: BMC Cancer 2018 18:1218

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  27. Content type: Research article

    To explore the diagnostic value of FAM19A4 methylation in high-risk human papilloma virus (hrHPV)-positive cervical samples from Chinese women for estimating cervical cancer or its precancerous lesions.

    Authors: Qiaowen Bu, Sanfeng Wang, Jian Ma, Xiangcheng Zhou, Guiying Hu, Hua Deng, Xiaoli Sun, Xiaoshan Hong, Hengying Wu, Liang Zhang and Xiping Luo

    Citation: BMC Cancer 2018 18:1182

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  28. Content type: Research article

    Germline mutations in BAP1 have been associated with BAP1-Tumor Predisposition Syndrome (BAP1-TPDS), a predisposition to multiple tumors within a family that includes uveal melanoma (UM), cutaneous melanoma, mali...

    Authors: K. G. Ewens, E. Lalonde, J. Richards-Yutz, C. L. Shields and A. Ganguly

    Citation: BMC Cancer 2018 18:1172

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  29. Content type: Research article

    Hepatocellular carcinoma (HCC) is a malignant tumor that threatens global human health. High PKM2 expression is widely reported in multiple cancers, especially in HCC. This study aimed to explore the effects o...

    Authors: Wen-Wen Lv, Dahai Liu, Xing-Cun Liu, Tie-Nan Feng, Lei Li, Bi-Yun Qian and Wen-Xing Li

    Citation: BMC Cancer 2018 18:1150

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  30. Content type: Research article

    Epigenetic plays an important role in colorectal neoplasia process. There is a need to determine sound biomarkers of colorectal cancer (CRC) progression with clinical and therapeutic implications. Therefore, w...

    Authors: Hassan Ashktorab, Hamed Rahi, Mehdi Nouraie, Babak Shokrani, Edward Lee, Tahmineh Haydari, Adeyinka O. Laiyemo, Peter Siegel and Hassan Brim

    Citation: BMC Cancer 2018 18:1068

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  31. Content type: Research article

    Several genetic and epigenetic alterations are related to the development and progression of Gastric Cancer (GC), one of those being the deregulated microRNA (miRNA) expression profile. miRNAs are small noncod...

    Authors: Leandro Magalhães, Luciana Gonçalves Quintana, Dielly Catrina Favacho Lopes, Amanda Ferreira Vidal, Adenilson Leão Pereira, Lara Carolina D’Araujo Pinto, João de Jesus Viana Pinheiro, André Salim Khayat, Luiz Ricardo Goulart, Rommel Burbano, Paulo Pimentel de Assumpção and Ândrea Ribeiro-dos-Santos

    Citation: BMC Cancer 2018 18:1055

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  32. Content type: Research article

    Primary mucosal melanoma (MM) is a rare subtype of melanoma that arises from melanocytes in the mucosa. MM has not been well profiled for mutations and its etiology is not well understood, rendering current tr...

    Authors: Yuuki Iida, Matthew P. Salomon, Keisuke Hata, Kevin Tran, Shuichi Ohe, Chester F. Griffiths, Sandy C. Hsu, Nellie Nelson and Dave S. B. Hoon

    Citation: BMC Cancer 2018 18:1054

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  33. Content type: Research article

    Tumor suppressor gene p16 promoter hypermethylation has been widely studied in colorectal cancer (CRC), yet its clinicopathological significance remains controversial. The methylation alterations of other regions...

    Authors: Xiaoxia Ye, Mingming Mo, Simin Xu, Qingjin Yang, Minhua Wu, Junjie Zhang, Bin Chen, Jian Li, Yu Zhong, Qionglin Huang and Chun Cai

    Citation: BMC Cancer 2018 18:1023

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  34. Content type: Research article

    Clonal VDJ rearrangement of B/T cell receptors (B/TCRs) occurring during B/T lymphocyte development has been used as a marker to track the clonality of B/T cell populations.

    Authors: Kar-Tong Tan, Ling-Wen Ding, Qiao-Yang Sun, Zhen-Tang Lao, Wenwen Chien, Xi Ren, Jin-Fen Xiao, Xin Yi Loh, Liang Xu, Michael Lill, Anand Mayakonda, De-Chen Lin, Henry Yang and H. Phillip Koeffler

    Citation: BMC Cancer 2018 18:940

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  35. Content type: Study protocol

    Improved risk stratification, more effective therapy and better supportive care have resulted in survival rates after childhood cancer of around 80% in developed countries. Treatment however can be harsh, and ...

    Authors: Anne-Lotte L. F. van der Kooi, Eva Clemens, Linda Broer, Oliver Zolk, Julianne Byrne, Helen Campbell, Marleen van den Berg, Claire Berger, Gabriele Calaminus, Uta Dirksen, Jeanette Falck Winther, Sophie D Fosså, Desiree Grabow, Riccardo Haupt, Melanie Kaiser, Tomas Kepak…

    Citation: BMC Cancer 2018 18:930

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  36. Content type: Research article

    Breast cancer is the most common cancer in women. 12–15% of all tumors are triple-negative breast cancers (TNBC). So far, TNBC has been mainly associated with mutations in BRCA1. The presence of other predispo...

    Authors: Juliane Hoyer, Georgia Vasileiou, Steffen Uebe, Marius Wunderle, Cornelia Kraus, Peter A. Fasching, Christian T. Thiel, Arndt Hartmann, Matthias W. Beckmann, Michael P. Lux and André Reis

    Citation: BMC Cancer 2018 18:926

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  37. Content type: Research article

    Total P16 methylation (P16M), including P16 hydroxymethylation (P16H) and true-P16M, correlates with malignant transformation of oral epithelial dysplasia (OED). Both true-P16M and P16H are early events in carcin...

    Authors: Hongwei Liu, Zhaojun Liu, Xue-wei Liu, Si Xu, Lei Wang, Yang Liu, Jing Zhou, Liankun Gu, Yan Gao, Xiao-yong Liu, Huidong Shi, Zheng Sun and Dajun Deng

    Citation: BMC Cancer 2018 18:918

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  38. Content type: Research article

    Triple Negative Breast Cancer (TNBC) is an aggressive form of breast cancer, that represents 10–20% of all breast carcinomas and characterized by the lack of a specific cell surface marker compared to other br...

    Authors: Farah Jouali, Nabila Marchoudi, Salwa Talbi, Basma Bilal, Mohamed El Khasmi, Houria Rhaissi and Jamal Fekkak

    Citation: BMC Cancer 2018 18:900

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  39. Content type: Research article

    Our goal was to investigate the prevalence of the epidermal growth factor receptor (EGFR) mutation in Middle East and African countries and to compare its prevalence with that shown in other populations.

    Authors: Zineb Benbrahim, Teresita Antonia and Nawfel Mellas

    Citation: BMC Cancer 2018 18:891

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  40. Content type: Case report

    We report on a female patient who underwent primary radical resection for a stage 2B Her-2-positive Barrett’s-type esophageal adenocarcinoma (EAC). Despite Her-2 targeted therapy, her disease recurred and requ...

    Authors: Federica Isidori, Deborah Malvi, Silvia Fittipaldi, Claudio Forcato, Isotta Bozzarelli, Claudia Sala, Giovanni Raulli, Antonia D’Errico, Michelangelo Fiorentino, Marco Seri, Kausilia K. Krishnadath, Elena Bonora and Sandro Mattioli

    Citation: BMC Cancer 2018 18:889

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  41. Content type: Research article

    Numerous studies have investigated the relationship between COX-2 8473 T > C polymorphism and cancer susceptibility, however, the results remain controversial. Therefore, we carried out the present meta-analysis ...

    Authors: Qiuping Li, Chao Ma, Zhihui Zhang, Suhua Chen, Weiguo Zhi, Lei Zhang, Guoyao Zhang, Lei Shi, Fei Cao and Tianjiang Ma

    Citation: BMC Cancer 2018 18:847

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  42. Content type: Research article

    Chronic inflammation and repeated infection with Opisthorchis viverrini (O. viverrini) induces intrahepatic cholangiocarcinoma (ICC). Inflammatory cytokines such as interleukin (IL) and tumor necrosis factor (TNF...

    Authors: Supannee Promthet, Nopparat Songserm, Somkiattiyos Woradet, Chamsai Pientong, Tipaya Ekalaksananan, Surapon Wiangnon and Akhtar Ali

    Citation: BMC Cancer 2018 18:846

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  43. Content type: Research article

    Breast (mammary) cancers in human (BC) and canine (CMT) patients share clinical, pathological, and molecular similarities that suggest dogs may be a useful translational model. Many cancers, including BC, shed...

    Authors: Eric J. Fish, Kristopher J. Irizarry, Patricia DeInnocentes, Connor J. Ellis, Nripesh Prasad, Anthony G. Moss and R. Curt Bird

    Citation: BMC Cancer 2018 18:832

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  44. Content type: Technical advance

    Gene fusion events resulting from chromosomal rearrangements play an important role in initiation of lung adenocarcinoma. The recent association of four oncogenic driver genes, ALK, ROS1, RET, and NTRK1, as lung ...

    Authors: Cecily P. Vaughn, José Luis Costa, Harriet E. Feilotter, Rosella Petraroli, Varun Bagai, Anna Maria Rachiglio, Federica Zito Marino, Bastiaan Tops, Henriette M. Kurth, Kazuko Sakai, Andrea Mafficini, Roy R. L. Bastien, Anne Reiman, Delphine Le Corre, Alexander Boag, Susan Crocker…

    Citation: BMC Cancer 2018 18:828

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  45. Content type: Research article

    Based on the possible shared mechanisms of chemotherapy-induced peripheral neuropathy (CIPN) for different drugs, we aimed to aggregate results of all previously published genome-wide association studies (GWAS...

    Authors: Seyed Hamidreza Mahmoudpour, Obul Reddy Bandapalli, Miguel Inácio da Silva Filho, Chiara Campo, Kari Hemminki, Hartmut Goldschmidt, Maximilian Merz and Asta Försti

    Citation: BMC Cancer 2018 18:820

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  46. Content type: Research article

    ADAMs (a disintegrin and metalloproteinase) have long been associated with tumor progression. Recent findings indicate that members of the closely related ADAMTS (ADAMs with thrombospondin motifs) family are a...

    Authors: Felix Kordowski, Julia Kolarova, Clemens Schafmayer, Stephan Buch, Torsten Goldmann, Sebastian Marwitz, Christian Kugler, Swetlana Scheufele, Volker Gassling, Christopher G. Németh, Mario Brosch, Jochen Hampe, Ralph Lucius, Christian Röder, Holger Kalthoff, Reiner Siebert…

    Citation: BMC Cancer 2018 18:796

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  47. Content type: Research article

    The incidence of oral squamous cell carcinoma (OSCC) continues to increase each year. Clinical examination and biopsy usually detect OSCC at an advanced stage that is difficult to treat, leading to poor progno...

    Authors: C. Puttipanyalears, A. Arayataweegool, K. Chalertpet, P. Rattanachayoto, P. Mahattanasakul, N. Tangjaturonsasme, V. Kerekhanjanarong, A. Mutirangura and N. Kitkumthorn

    Citation: BMC Cancer 2018 18:786

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  48. Content type: Research article

    High-grade gliomas (HGGs) exhibit marked heterogeneity in clinical behavior. The purpose of this study was to identify a novel biomarker that predicts patient outcome, which is helpful in HGG patient management.

    Authors: Di Du, Jian Yuan, Wencai Ma, Jing Ning, John N. Weinstein, Xianrui Yuan, Greg N. Fuller and Yuexin Liu

    Citation: BMC Cancer 2018 18:773

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