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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 13

  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. Content type: Research article

    With the development of sequencing technologies, there may be some disputes on sequencing analysis. The aim of this study was to investigate different allele frequency thresholds of mutations in targeted genes...

    Authors: Jie Ma, Yong Fu, Yao-yao Tu, Ying Liu, Yi-ran Tan, Wu-tong Ju, Curtis R. Pickering, Jeffrey N. Myers, Zhi-yuan Zhang and Lai-ping Zhong

    Citation: BMC Cancer 2018 18:758

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  17. Content type: Research article

    HER2 positive (HER2+) breast cancers involve chromosomal structural alterations that act as oncogenic driver events.

    Authors: George Vasmatzis, Xue Wang, James B. Smadbeck, Stephen J. Murphy, Katherine B. Geiersbach, Sarah H. Johnson, Athanasios G. Gaitatzes, Yan W. Asmann, Farhad Kosari, Mitesh J. Borad, Daniel J. Serie, Sarah A. McLaughlin, Jennifer M. Kachergus, Brian M. Necela and E. Aubrey Thompson

    Citation: BMC Cancer 2018 18:738

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  18. Content type: Research article

    The theory of field effect suggests that the tumor-adjacent area, besides histopathologically normal, undergoes genetic and epigenetic changes that can eventually affect epithelial homeostasis, predisposing th...

    Authors: Camile B. Lopes, Leandro L. Magalhães, Carolina R. Teófilo, Ana Paula N. N. Alves, Raquel C. Montenegro, Massimo Negrini and Ândrea Ribeiro-dos-Santos

    Citation: BMC Cancer 2018 18:721

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  19. Content type: Research article

    YAP, a potent oncogene and major downstream effector of the mammalian Hippo tumor suppressor pathway can act as either oncogene or tumor suppressor gene based on the type of tissue involved. Despite various st...

    Authors: Sumayya Abdul Sattar Real, Farah Parveen, Asad Ur Rehman, Mohammad Aasif Khan, Sankaravamasam Venkata Suryanarayan Deo, Nootan Kumar Shukla and Syed Akhtar Husain

    Citation: BMC Cancer 2018 18:711

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  20. Content type: Research article

    The treatment of acute lymphoblastic leukemia (ALL) and osteosarcoma (OSC) is very effective: the vast majority of patients recover and survive for decades. However, they still need to face serious adverse eff...

    Authors: Judit C. Sági, Bálint Egyed, Andrea Kelemen, Nóra Kutszegi, Márta Hegyi, András Gézsi, Martina Ayaka Herlitschke, Andrea Rzepiel, Lili E. Fodor, Gábor Ottóffy, Gábor T. Kovács, Dániel J. Erdélyi, Csaba Szalai and Ágnes F. Semsei

    Citation: BMC Cancer 2018 18:704

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  21. Content type: Research article

    Heat Shock Proteins (HSPs), a family of genes with key roles in proteostasis, have been extensively associated with cancer behaviour. However, the HSP family is quite large and many of its members have not bee...

    Authors: Felipe C. M. Zoppino, Martin E. Guerrero-Gimenez, Gisela N. Castro and Daniel R. Ciocca

    Citation: BMC Cancer 2018 18:700

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  22. Content type: Research article

    DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome me...

    Authors: Béla Molnár, Orsolya Galamb, Bálint Péterfia, Barnabás Wichmann, István Csabai, András Bodor, Alexandra Kalmár, Krisztina Andrea Szigeti, Barbara Kinga Barták, Zsófia Brigitta Nagy, Gábor Valcz, Árpád V. Patai, Péter Igaz and Zsolt Tulassay

    Citation: BMC Cancer 2018 18:695

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  23. Content type: Research article

    Genes associated with hereditary breast and ovarian cancer (HBOC) and colorectal cancer (CRC) predisposition have been shown to play a role in pancreatic cancer susceptibility. Growing evidence suggests that p...

    Authors: Erin L. Young, Bryony A. Thompson, Deborah W. Neklason, Matthew A. Firpo, Theresa Werner, Russell Bell, Justin Berger, Alison Fraser, Amanda Gammon, Cathryn Koptiuch, Wendy K. Kohlmann, Leigh Neumayer, David E. Goldgar, Sean J. Mulvihill, Lisa A. Cannon-Albright and Sean V. Tavtigian

    Citation: BMC Cancer 2018 18:697

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  24. Content type: Research article

    Deletions of 6q15–16.1 are recurrently found in pediatric T-cell acute lymphoblastic leukemia (T-ALL). This chromosomal region includes the mitogen-activated protein kinase kinase kinase 7 (MAP3K7) gene which has...

    Authors: David M. Cordas dos Santos, Juliane Eilers, Alfonso Sosa Vizcaino, Elena Orlova, Martin Zimmermann, Martin Stanulla, Martin Schrappe, Kathleen Börner, Dirk Grimm, Martina U. Muckenthaler, Andreas E. Kulozik and Joachim B. Kunz

    Citation: BMC Cancer 2018 18:663

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  25. Content type: Research article

    The gold standard for bladder cancer detection is cystoscopy, which is an invasive procedure that causes discomfort in patients. The currently available non-invasive approaches either show limited sensitivity ...

    Authors: Hao Liu, Wang He, Bo Wang, Kewei Xu, Jinli Han, Junjiong Zheng, Jun Ren, Lin Shao, Shiping Bo, Sijia Lu, Tianxin Lin and Jian Huang

    Citation: BMC Cancer 2018 18:659

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  26. Content type: Research article

    CHD5 is a conventional tumour-suppressing gene in many tumours. The aim of this study was to determine whether CHD5 variants contribute to the risk of hepatocellular carcinoma (HCC).

    Authors: Qin Xiao, Lianzhou Chen, Haiqing Luo, Hongmei Li, Qingming Kong, Fei Jiao, Shifeng Pang, Ming Zhang, Feifei Lan, Wenguo Fan, Hui Luo, Tao Tao and Xiao Zhu

    Citation: BMC Cancer 2018 18:658

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  27. Content type: Research article

    The BRCA1/2 mutation profile varies in Spain according to the geographical area studied. The mutational profile of BRCA1/2 in families at risk for hereditary breast and ovarian cancer has not so far been repor...

    Authors: Bella Pajares, Javier Porta, Jose María Porta, Cristina Fernández-de Sousa, Ignacio Moreno, Daniel Porta, Gema Durán, Tamara Vega, Inmaculada Ortiz, Carolina Muriel, Emilio Alba and Antonia Márquez

    Citation: BMC Cancer 2018 18:647

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  28. Content type: Research article

    The genetic profile for human papilloma virus positive (HPV+) oropharyngeal squamous cell carcinomas (OPSCC) remains largely unknown. The purpose of this study was to sequence tissue material from a large coho...

    Authors: Christian Grønhøj, David H. Jensen, Tina Agander, Katalin Kiss, Estrid Høgdall, Lena Specht, Frederik Otzen Bagger, Finn Cilius Nielsen and Christian von Buchwald

    Citation: BMC Cancer 2018 18:640

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  29. Content type: Research article

    The right drug to the right patient at the right time is one of the ideals of Individualized Medicine (IM) and remains one of the most compelling promises of the post-genomic age. The addition of genomic infor...

    Authors: Michael T. Zimmermann, Terry M. Therneau and Jean-Pierre A. Kocher

    Citation: BMC Cancer 2018 18:577

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    The Correction to this article has been published in BMC Cancer 2018 18:743

  30. Content type: Case report

    Lynch syndrome is an autosomal dominant inherited disease caused by germline mutations in mismatch repair genes. Analysis for microsatellite instability (MSI) and immunohistochemistry (IHC) of protein expressi...

    Authors: Takanori Yokoyama, Kazuhiro Takehara, Nao Sugimoto, Keika Kaneko, Etsuko Fujimoto, Mika Okazawa-Sakai, Shinichi Okame, Yuko Shiroyama, Takashi Yokoyama, Norihiro Teramoto, Shozo Ohsumi, Shinya Saito, Kazuho Imai and Kokichi Sugano

    Citation: BMC Cancer 2018 18:576

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  31. Content type: Research article

    Immune surveillance acts as a defense mechanism in cancer, and its disruption is involved in cancer progression. DNA methylation reflects the phenotypic identity of cells and recent data suggested that DNA met...

    Authors: Surabhi Parashar, David Cheishvili, Niaz Mahmood, Ani Arakelian, Imrana Tanvir, Haseeb Ahmed Khan, Richard Kremer, Catalin Mihalcioiu, Moshe Szyf and Shafaat A. Rabbani

    Citation: BMC Cancer 2018 18:574

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  32. Content type: Research article

    Multiple myeloma (MM), like other cancers, is caused by the accumulation of genetic abnormalities. Heterogeneity exists in the patients’ response to treatments, for example, bortezomib. This urges efforts to i...

    Authors: Xinyan Zhang, Bingzong Li, Huiying Han, Sha Song, Hongxia Xu, Yating Hong, Nengjun Yi and Wenzhuo Zhuang

    Citation: BMC Cancer 2018 18:551

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  33. Content type: Research article

    Several studies have reported the role of CYP2A6 genetic polymorphisms in smoking and lung cancer risk with some contradictory results in different populations. The purpose of the current study is to assess th...

    Authors: Nada Ezzeldin, Dalia El-Lebedy, Amira Darwish, Ahmed El Bastawisy, Shereen Hamdy Abd Elaziz, Mirhane Mohamed Hassan and Amal Saad-Hussein

    Citation: BMC Cancer 2018 18:525

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  34. Content type: Research article

    Colorectal cancer (CRC) is a leading cause of cancer-related death. The biologic response of CRC to standard of care adjuvant therapies such as chemotherapy and radiation are poorly understood. MicroRNAs (miRs...

    Authors: Rebecca Ruhl, Shushan Rana, Katherine Kelley, Cristina Espinosa-Diez, Clayton Hudson, Christian Lanciault, Charles R. Thomas Jr, V. Liana Tsikitis and Sudarshan Anand

    Citation: BMC Cancer 2018 18:517

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  35. Content type: Research article

    Somatic amplifications of the LYL1 gene are relatively common occurrences in patients who develop uterine corpus endometrial carcinoma (UCEC) as opposed to other cancers. This study was undertaken to determine wh...

    Authors: Se Ik Kim, Ji Won Lee, Nara Lee, Maria Lee, Hee Seung Kim, Hyun Hoon Chung, Jae-Weon Kim, Noh Hyun Park, Yong-Sang Song and Jeong-Sun Seo

    Citation: BMC Cancer 2018 18:494

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  36. Content type: Research article

    The relationship between cholesterol and prostate cancer has been extensively studied for decades, where high levels of cellular cholesterol are generally associated with cancer progression and less favorable ...

    Authors: Morten Beck Rye, Helena Bertilsson, Maria K. Andersen, Kjersti Rise, Tone F. Bathen, Finn Drabløs and May-Britt Tessem

    Citation: BMC Cancer 2018 18:478

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  37. Content type: Research article

    Cetuximab, an anti-EGFR monoclonal antibody, is used in combination with chemotherapy in clinic to enhance the outcome in metastatic colorectal cancer (mCRC) patients with only ~ 20% response rate. To date onl...

    Authors: Zhu Mei, Yang W. Shao, Peinan Lin, Xiaomin Cai, Biao Wang, Yan Ding, Xiangyuan Ma, Xue Wu, Yewei Xia, Dongqin Zhu, Yongqian Shu, Zan Fu and Yanhong Gu

    Citation: BMC Cancer 2018 18:479

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  38. Content type: Study protocol

    Advances in genomics offer promise for earlier detection or prevention of cancer, by personalisation of medical care tailored to an individual’s genomic risk status. However genome sequencing can generate an u...

    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 18:454

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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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