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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. Hepatitis B virus (HBV) is the major risk factor for hepatocellular carcinoma (HCC). The molecular mechanisms underlying HBV-associated HCC pathogenesis is still unclear. Genetic alterations in cancer-related ...

    Authors: Fung-Yu Huang, Danny Ka-Ho Wong, Vivien Wai-Man Tsui, Wai-Kay Seto, Lung-Yi Mak, Tan-To Cheung, Keane K.-Y. Lai and Man-Fung Yuen

    Citation: BMC Cancer 2019 19:789

    Content type: Research article

    Published on:

  2. Inherited pathogenic variants in BRCA1 and BRCA2 are the most common causes of hereditary breast and ovarian cancer (HBOC). The risk of developing breast cancer by age 80 in women carrying a BRCA1 pathogenic vari...

    Authors: Ilnaz Sepahi, Ulrike Faust, Marc Sturm, Kristin Bosse, Martin Kehrer, Tilman Heinrich, Kathrin Grundman-Hauser, Peter Bauer, Stephan Ossowski, Hana Susak, Raymonda Varon, Evelin Schröck, Dieter Niederacher, Bernd Auber, Christian Sutter, Norbert Arnold…

    Citation: BMC Cancer 2019 19:787

    Content type: Research article

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  3. Data indicate that primary cutaneous melanomas are characterized by clonal heterogeneity associated with oncogenic drivers. Less data are available on the clonal changes occurring during melanoma progression. ...

    Authors: V. Doma, S. Kárpáti, E. Rásó, T. Barbai and J. Tímár

    Citation: BMC Cancer 2019 19:786

    Content type: Research article

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    The Correction to this article has been published in BMC Cancer 2019 19:853

  4. Numerous studies have highlighted that long non-coding RNAs (lncRNAs) can bind to microRNA (miRNA) sites as competing endogenous RNAs (ceRNAs), thereby affecting and regulating the expression of mRNAs and targ...

    Authors: Rui-Sheng Zhou, En-Xin Zhang, Qin-Feng Sun, Zeng-Jie Ye, Jian-Wei Liu, Dai-Han Zhou and Ying Tang

    Citation: BMC Cancer 2019 19:779

    Content type: Research article

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  5. Multiple primary melanomas (MPM) occur up to 8% of patients with cutaneous malignant melanoma (CMM). They are often sporadic harbouring several somatic mutations, but also familial cases harbouring a CDKN2A germl...

    Authors: Milena Casula, Panagiotis Paliogiannis, Fabrizio Ayala, Vincenzo De Giorgi, Ignazio Stanganelli, Mario Mandalà, Maria Colombino, Antonella Manca, Maria Cristina Sini, Corrado Caracò, Paolo Antonio Ascierto, Rosanna Rita Satta, Amelia Lissia, Antonio Cossu and Giuseppe Palmieri

    Citation: BMC Cancer 2019 19:772

    Content type: Research article

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  6. Human papillomavirus is recognized as a major cause of cervical cancer. It is estimated that annually, 7,095 women are diagnosed with cervical cancer and 4,732 die from the disease in Ethiopia. Understanding that...

    Authors: Kirubel Eshetu Ali, Ibrahim Ali Mohammed, Mesfin Nigussie Difabachew, Dawit Solomon Demeke, Tasew Haile, Robert-Jan ten Hove, Tsegaye Hailu Kumssa, Zufan Lakew Woldu, Eshetu Lemma Haile and Kassu Desta Tullu

    Citation: BMC Cancer 2019 19:768

    Content type: Research article

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  7. This study explored the attitudes of patients with advanced cancer towards MTP and return of results, prior to undergoing genomic testing within a research program.

    Authors: Megan C. Best, Nicole Bartley, Chris Jacobs, Ilona Juraskova, David Goldstein, Ainsley J. Newson, Jacqueline Savard, Bettina Meiser, Mandy Ballinger, Christine Napier, David Thomas, Barbara Biesecker and Phyllis Butow

    Citation: BMC Cancer 2019 19:753

    Content type: Research article

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  8. Expression of human chorionic gonadotropin beta subunit by cancers is extensively documented, yet regulation of the multiple genes that can code for this protein is poorly understood. The aim of the study was ...

    Authors: Aleksandra Śliwa, Marta Kubiczak, Anna Szczerba, Grzegorz Walkowiak, Ewa Nowak-Markwitz, Beata Burczyńska, Stephen Butler, Ray Iles, Piotr Białas and Anna Jankowska

    Citation: BMC Cancer 2019 19:746

    Content type: Research article

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  9. Gestational choriocarcinoma is a rare malignancy believed to arise from the trophoblast cells of the placenta. Despite the frequently aggressive clinical nature, choriocarcinoma has been routinely curable with...

    Authors: Philip Savage, David Monk, Jose R. Hernandez Mora, Nick van der Westhuizen, Jennifer Rauw, Anna Tinker, Wendy Robinson, Qianqian Song, Michael J. Seckl and Rosemary A. Fisher

    Citation: BMC Cancer 2019 19:744

    Content type: Research article

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  10. Prognostic markers specific to a particular cancer type can assist in the evaluation of survival probability of patients and help clinicians to assess the available treatment modalities.

    Authors: Deepankar Chakroborty, Maheswara Reddy Emani, Riku Klén, Camilla Böckelman, Jaana Hagström, Caj Haglund, Ari Ristimäki, Riitta Lahesmaa and Laura L. Elo

    Citation: BMC Cancer 2019 19:727

    Content type: Research article

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  11. Pathogenic variants (PVs) of BRCA genes entail a lifetime risk of developing breast cancer in 50–85% of carriers. Their prevalence in different populations has been previously reported. However, there is scarc...

    Authors: Omar Alejandro Zayas-Villanueva, Luis Daniel Campos-Acevedo, José de Jesús Lugo-Trampe, David Hernández-Barajas, Juan Francisco González-Guerrero, María Fernanda Noriega-Iriondo, Ilse Alejandra Ramírez-Sánchez and Laura Elia Martínez-de-Villarreal

    Citation: BMC Cancer 2019 19:722

    Content type: Research article

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  12. Ependymal tumors are pathologically defined intrinsic neoplasms originating in the intracranial compartments or the spinal cord that affect both children and adults. The recently integrated classification of e...

    Authors: Shaoyan Xi, Ke Sai, Wanming Hu, Fang Wang, Yinsheng Chen, Jing Wang, Jing Zeng and Zhongping Chen

    Citation: BMC Cancer 2019 19:717

    Content type: Research article

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  13. The rapid development of single-cell RNA sequencing (scRNA-seq) provides unprecedented opportunities to study the tumor ecosystem that involves a heterogeneous mixture of cell types. However, the majority of p...

    Authors: Xiaoqing Yu, Y. Ann Chen, Jose R. Conejo-Garcia, Christine H. Chung and Xuefeng Wang

    Citation: BMC Cancer 2019 19:715

    Content type: Research article

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  14. Genetic profiling of cancers for variations in copy number, structure or expression of certain genes has improved diagnosis, risk-stratification and therapeutic decision-making. However the tumor-restricted na...

    Authors: Jordan Mandel, Huabo Wang, Daniel P. Normolle, Wei Chen, Qi Yan, Peter C. Lucas, Panayiotis V. Benos and Edward V. Prochownik

    Citation: BMC Cancer 2019 19:686

    Content type: Research article

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  15. Sterol-regulatory element binding protein 1 (SREBP1), an intracellular cholesterol sensor located in the endoplasmic reticulum, regulates the intracellular cholesterol by the Insig-Srebp-Scap pathway. Over-exp...

    Authors: Yuyan Gao, Xianxiu Nan, Xinjue Shi, Xiaoqin Mu, Binbin Liu, Huifen Zhu, Bingqing Yao, Xinyi Liu, Tianyue Yang, Yiting Hu and Shulin Liu

    Citation: BMC Cancer 2019 19:685

    Content type: Research article

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  16. Canonical WNT signalling plays a critical role in the regulation of ovarian development; mis-regulation of this key pathway in the adult ovary is associated with subfertility and tumourigenesis. The roles of A...

    Authors: Noha-Ehssan Mohamed, Trevor Hay, Karen R. Reed, Matthew J. Smalley and Alan R. Clarke

    Citation: BMC Cancer 2019 19:677

    Content type: Research article

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  17. Analysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the ...

    Authors: Parvez M. Lokhandwala, Li-Hui Tseng, Erika Rodriguez, Gang Zheng, Aparna Pallavajjalla, Christopher D. Gocke, James R. Eshleman and Ming-Tseh Lin

    Citation: BMC Cancer 2019 19:665

    Content type: Research article

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  18. Studies have consistently indicated that the majority of individuals meeting the US Prevention Services Task Force guidelines for genetic testing have not had genetic counseling or testing. Despite increased a...

    Authors: Nadine Rayes, Deborah J. Bowen, Tara Coffin, Denise Nebgen, Christine Peterson, Mark F. Munsell, Kathleen Gavin, Rebecca Lechner, Jamie Crase, Deborah Polinsky, Iris Romero, Stephanie V. Blank, Douglas A. Levine, Barbara M. Norquist, Elizabeth M. Swisher and Karen H. Lu

    Citation: BMC Cancer 2019 19:648

    Content type: Study protocol

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  19. Zinc-finger E-box binding homeobox 1 (ZEB-1) plays crucial roles in epithelial-to-mesenchymal transition during tumor carcinogenesis. Published studies have examined the potential value of ZEB-1 as a biomarker...

    Authors: Borong Chen, Baisheng Chen, Zhipeng Zhu, Weipeng Ye, Junjie Zeng, Gang Liu, Shengjie Wang, Jin Gao, Guoxing Xu and Zhengjie Huang

    Citation: BMC Cancer 2019 19:635

    Content type: Research article

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  20. Hereditary cancer syndromes have inherited germline mutations which predispose to benign and malignant tumors. Understanding of the molecular causes in hereditary cancer syndromes has advanced cancer treatment...

    Authors: Yanting Jiang, Yue Sun, Jiandong Hu, Nan Yu, Hui Liu, Jiankun Fan, Xuelian Ning, Yilan Li, Baogang Liu, Yihua Sun, Jinwei Zhang, Xiaohong Qiu, Songbin Fu, Chunshui Zhou and Hui Xu

    Citation: BMC Cancer 2019 19:613

    Content type: Research article

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  21. Chemo-resistance is one of the major challenges in the therapy of small cell lung cancer (SCLC). Multiple mechanisms are thought to be involved in chemo-resistance during SCLC treatment, but unfortunately, the...

    Authors: Jinzhi Lai, Hainan Yang, Yanyang Zhu, Mei Ruan, Yayu Huang and Qiuyu Zhang

    Citation: BMC Cancer 2019 19:602

    Content type: Research article

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  22. Pulmonary sarcomatoid carcinoma (SC) consists of both carcinomatous and sarcomatous tumors with high degree of malignancy, rapid progression, and poor prognosis. However, little is known regarding how pulmonar...

    Authors: Jianjun Ge, Bin Yao, Jia Huang, Xue Wu, Hua Bao, Qiuxiang Ou, Yang W. Shao and Jun Chen

    Citation: BMC Cancer 2019 19:592

    Content type: Case report

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  23. Research into Philadelphia-negative chronic myeloproliferative neoplasms is heterogeneous. In addition, no systematization of studies of polycythemia vera (PV), essential thrombocythemia (ET) or primary myelof...

    Authors: Mónica Mejía-Ochoa, Paola Andrea Acevedo Toro and Jaiberth Antonio Cardona-Arias

    Citation: BMC Cancer 2019 19:590

    Content type: Research article

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  24. Detection of circulating tumor DNA (ctDNA) is a promising method for postoperative surveillance of lung cancer. However, relatively low positive rate in early stage patients restricts its application. Aberrant...

    Authors: Guannan Kang, Kezhong Chen, Fan Yang, Shannon Chuai, Heng Zhao, Kai Zhang, Bingsi Li, Zhihong Zhang and Jun Wang

    Citation: BMC Cancer 2019 19:579

    Content type: Study protocol

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  25. Triple-negative breast cancer (TNBC) is a type of breast cancer with a high degree of malignancy. Because of the remarkable biological characteristics of high invasion, metastasis and recurrence, TNBC is often...

    Authors: Cheng Wang, Cheng Xu, Ruijie Niu, Guangfu Hu, Zhangyuan Gu and Zhigang Zhuang

    Citation: BMC Cancer 2019 19:577

    Content type: Research article

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  26. Using a pathway-focused approach, we aimed to provide a subgroup-specific basis for finding novel therapeutic strategies and further refinement of the risk stratification in pediatric medulloblastoma.

    Authors: Ae Kyung Park, Ji Yeoun Lee, Heesun Cheong, Vijay Ramaswamy, Sung-Hye Park, Marcel Kool, Ji Hoon Phi, Seung Ah Choi, Florence Cavalli, Michael D. Taylor and Seung-Ki Kim

    Citation: BMC Cancer 2019 19:571

    Content type: Research article

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  27. Published genetic risk scores for breast cancer (BC) so far have been based on a relatively small number of markers and are not necessarily using the full potential of large-scale Genome-Wide Association Studi...

    Authors: Kristi Läll, Maarja Lepamets, Marili Palover, Tõnu Esko, Andres Metspalu, Neeme Tõnisson, Peeter Padrik, Reedik Mägi and Krista Fischer

    Citation: BMC Cancer 2019 19:557

    Content type: Research article

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  28. Liver function is routinely assessed in clinical practice as liver function tests provide sensitive indicators of hepatocellular injury. However, the prognostic value of enzymes that indicate hepatic injury ha...

    Authors: Ting-Xun Lu, Shuang Wu, Dong-Yan Cai, Ting-Ting Hong, Ying Zhang, Hua-Qiang Gao, Hai-Ying Hua and Xiao-Hong Wu

    Citation: BMC Cancer 2019 19:553

    Content type: Research article

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  29. Mutated BRCA1/2 genes are associated with hereditary breast and ovarian cancer (HBOC). So far most of the identified BRCA1/2 pathogenic variants are single nucleotide variants (SNVs) or insertions/deletions (Inde...

    Authors: Wen-Ming Cao, Ya-Bing Zheng, Yun Gao, Xiao-Wen Ding, Yan Sun, Yuan Huang, Cai-Jin Lou, Zhi-Wen Pan, Guang Peng and Xiao-Jia Wang

    Citation: BMC Cancer 2019 19:551

    Content type: Research article

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  30. Breast cancer is a leading cause of cancer-related death in women worldwide. Despite extensive studies in all areas of basic, clinical and applied research, accurate prognosis remains elusive, thus leading to ...

    Authors: Mariana Bustamante Eduardo, Vlad Popovici, Sara Imboden, Stefan Aebi, Nadja Ballabio, Hans Jörg Altermatt, Andreas Günthert and Rolf Jaggi

    Citation: BMC Cancer 2019 19:549

    Content type: Research article

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  31. The understanding of the molecular biology of pediatric neuronal and mixed neuronal-glial brain tumors is still insufficient due to low frequency and heterogeneity of those lesions which comprise several subty...

    Authors: Magdalena Zakrzewska, Renata Gruszka, Konrad Stawiski, Wojciech Fendler, Joanna Kordacka, Wiesława Grajkowska, Paweł Daszkiewicz, Paweł P. Liberski and Krzysztof Zakrzewski

    Citation: BMC Cancer 2019 19:544

    Content type: Research article

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  32. Hereditary cancer predisposition syndromes are responsible for approximately 5–10% of all diagnosed cancer cases. In the past, single-gene analysis of specific high risk genes was used for the determination of...

    Authors: Georgios N. Tsaousis, Eirini Papadopoulou, Angela Apessos, Konstantinos Agiannitopoulos, Georgia Pepe, Stavroula Kampouri, Nikolaos Diamantopoulos, Theofanis Floros, Rodoniki Iosifidou, Ourania Katopodi, Anna Koumarianou, Christos Markopoulos, Konstantinos Papazisis, Vasileios Venizelos, Ioannis Xanthakis, Grigorios Xepapadakis…

    Citation: BMC Cancer 2019 19:535

    Content type: Research article

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  33. C-C chemokine receptor 5 (CCR5) has attracted wide concern for its critical role in the progression of human immunodeficiency virus type 1 (HIV-1) infection. Several studies have demonstrated that CCR5 affects...

    Authors: Shuyuan Liu, Jun Chen, Zhiling Yan, Shuying Dai, Chuanyin Li, Yufeng Yao and Li Shi

    Citation: BMC Cancer 2019 19:525

    Content type: Research article

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  34. Patients with lymph node metastasis-negative (pN0) invasive breast cancer have favorable outcomes following initial treatment. However, false negatives which occur during routine histologic examination of lymp...

    Authors: Ryoko Kikuchi-Koike, Kazunori Nagasaka, Hitoshi Tsuda, Yasuyuki Ishii, Masaru Sakamoto, Yoshihiro Kikuchi, Shiho Fukui, Yuko Miyagawa, Haruko Hiraike, Takayuki Kobayashi, Takayuki Kinoshita, Yae Kanai, Tatsuhiro Shibata, Issei Imoto, Johji Inazawa, Osamu Matsubara…

    Citation: BMC Cancer 2019 19:521

    Content type: Research article

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  35. Chronic Lymphocytic Leukemia (CLL) is the most frequent lymphoproliferative disorder in western countries and is characterized by a remarkable clinical heterogeneity. During the last decade, multiple genomic s...

    Authors: Adrián Mosquera Orgueira, Beatriz Antelo Rodríguez, Natalia Alonso Vence, José Ángel Díaz Arias, Nicolás Díaz Varela, Manuel Mateo Pérez Encinas, Catarina Allegue Toscano, Elena María Goiricelaya Seco, Ángel Carracedo Álvarez and José Luis Bello López

    Citation: BMC Cancer 2019 19:515

    Content type: Research article

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  36. Deletion of the CDKN2A locus is centrally involved in the development of several malignancies. In malignant pleural mesothelioma (MPM), it is one of the most frequently reported genomic alteration. MPM is strongl...

    Authors: Eeva Kettunen, Sauli Savukoski, Kaisa Salmenkivi, Tom Böhling, Esa Vanhala, Eeva Kuosma, Sisko Anttila and Henrik Wolff

    Citation: BMC Cancer 2019 19:507

    Content type: Research article

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  37. Breast cancer ranks first in women, and is the second cause of death in this gender. In addition to genetics, the environment contributes to the development of the disease, although the factors involved are no...

    Authors: Julio Plaza-Díaz, Ana I. Álvarez-Mercado, Carmen M Ruiz-Marín, Iris Reina-Pérez, Alejandro J. Pérez-Alonso, María Belén Sánchez-Andujar, Pablo Torné, Tania Gallart-Aragón, María Teresa Sánchez-Barrón, Saturnino Reyes Lartategui, Federico García, Natalia Chueca, Ana Moreno-Delgado, Katia Torres-Martínez, María José Sáez-Lara, Cándido Robles-Sánchez…

    Citation: BMC Cancer 2019 19:495

    Content type: Study protocol

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  38. Telomere genetics has recently been emerged as an important field in molecular oncology. Various genome-wide association studies in different population groups have revealed that polymorphisms in Telomere main...

    Authors: Gh. Rasool Bhat, Amrita Bhat, Sonali Verma, Itty Sethi, Ruchi Shah, Varun Sharma, Khursheed A. Dar, Deepak Abrol, Subiya Kaneez, Sandeep Kaul, Ramesh Ganju and Rakesh Kumar

    Citation: BMC Cancer 2019 19:493

    Content type: Research article

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  39. The relationship between polymorphisms in vascular endothelial growth factor (VEGF) and gastric cancer is still inconclusive. We investigated whether there is an association between VEGF genetic polymorphisms ...

    Authors: Yeon-Ji Kim, Woo Chul/ Chung, Kyong-Hwa Jun and Hyung-Min Chin

    Citation: BMC Cancer 2019 19:483

    Content type: Research article

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  40. Recent studies have extensively investigated the role of miRNAs in colorectal cancer (CRC), and several associations have been reported. In addition, single nucleotide polymorphisms (SNPs) in promoter regions ...

    Authors: Eun-Gyo Kim, Jung Oh Kim, Han Sung Park, Chang Soo Ryu, Jisu Oh, Hak Hoon Jun, Jong Woo Kim and Nam Keun Kim

    Citation: BMC Cancer 2019 19:480

    Content type: Research article

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  41. Gene variants are dependable and sensitive biomarkers for target-specific therapies in breast cancer (BC). However, detection of mutations within tissues has many limitations. Plasma circulating free DNA (cfDN...

    Authors: Xin Yang, Kuo Zhang, Caiji Zhang, Rongxue Peng and Chengming Sun

    Citation: BMC Cancer 2019 19:465

    Content type: Research article

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  42. Helicobacter pylori infection is recognized as the main risk factor for gastric cancer (GC), the fifth most common neoplasia worldwide. H. pylori interacts with the immune system, disrupting the cytokine network ...

    Authors: Cecilia Martínez-Campos, Kirvis Torres-Poveda, Margarita Camorlinga-Ponce, Lourdes Flores-Luna, Carmen Maldonado-Bernal, Vicente Madrid-Marina and Javier Torres

    Citation: BMC Cancer 2019 19:453

    Content type: Research article

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  43. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies and is not a clinically homogeneous disease, but subsets of patients with distinct prognosis and response to therapy can be identi...

    Authors: Maria Cristina Curia, Fabiana Fantini, Rossano Lattanzio, Francesca Tavano, Francesco Di Mola, Mauro Piantelli, Pasquale Battista, Pierluigi Di Sebastiano and Alessandro Cama

    Citation: BMC Cancer 2019 19:452

    Content type: Research article

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  44. TIMP-2 gene plays an important role in the development of breast cancer. The present study was conducted to evaluate whether TIMP-2 gene polymorphisms are associated with breast cancer risk in a Han Chinese cohor...

    Authors: Kai Wang, Guanying Wang, Shangke Huang, Anqi Luo, Xin Jing, Gang Li, Yi Zhou and Xinhan Zhao

    Citation: BMC Cancer 2019 19:446

    Content type: Research article

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  45. The progress of treatments of childhood acute lymphoblastic leukemia (ALL) has made it possible to reach a survival rate superior to 80%. However, the treatments lead to several long-term adverse effects, incl...

    Authors: Maxime Caru, Kateryna Petrykey, Simon Drouin, Patrick Beaulieu, Pascal St-Onge, Valérie Lemay, Laurence Bertout, Caroline Laverdiere, Gregor Andelfinger, Maja Krajinovic, Daniel Sinnett and Daniel Curnier

    Citation: BMC Cancer 2019 19:443

    Content type: Research article

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