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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. The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of ...

    Authors: Somkiat Sunpaweravong, Sacarin Bunbanjerdsuk, Tanjitti Pongrujikorn, Chaiwat Naktang, Patrapim Sunpaweravong, Anupong Nitiruangjaras, Tanadech Dechaphankul and Natini Jinawath

    Citation: BMC Cancer 2019 19:1174

    Content type: Research article

    Published on:

  2. Genetic testing for BRCA1/2 genes is widely used as a strategy to reduce incidence and morbidity of hereditary breast and ovarian cancer (HBOC). The purpose of this study is to analyse the demographic and molecul...

    Authors: Ainara Ruiz de Sabando, Edurne Urrutia Lafuente, Fermín García-Amigot, Angel Alonso Sánchez, Lourdes Morales Garofalo, Sira Moreno, Eva Ardanaz and Maria A. Ramos-Arroyo

    Citation: BMC Cancer 2019 19:1145

    Content type: Research article

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  3. The significance of very early chimerism assessment before day + 28, which is considered the moment of engraftment, is still unclear. In this retrospective study, we evaluated the clinical impact of very early...

    Authors: Monika Lejman, Agnieszka Zaucha-Prażmo, Joanna Zawitkowska, Aleksandra Mroczkowska, Dominik Grabowski, Jerzy R. Kowalczyk and Katarzyna Drabko

    Citation: BMC Cancer 2019 19:1141

    Content type: Research article

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  4. Hepatocellular carcinoma (HCC) is the sixth-most common malignancy worldwide. Multiple previous studies have assessed the relationship between TM6SF2 gene polymorphism and the risk of developing HCC, with disc...

    Authors: Shan Tang, Jing Zhang, Ting-Ting Mei, Hai-Qing Guo, Xin-Huan Wei, Wen-Yan Zhang, Ya-Li Liu, Shan Liang, Zuo-Peng Fan, Li-Xia Ma, Wei Lin, Yi-Rong Liu, Li-Xia Qiu and Hai-Bin Yu

    Citation: BMC Cancer 2019 19:1128

    Content type: Research article

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  5. The rs2057482 polymorphism in the hypoxia inducible factor 1 subunit alpha (HIF1A) gene has been reported to be associated with a risk of several types of cancer, but this association has not yet been definitivel...

    Authors: Li-Fang Wu, Gui-Ping Xu, Qing Zhao, Li-Jing Zhou, Ding Wang and Wei-Xian Chen

    Citation: BMC Cancer 2019 19:1123

    Content type: Research article

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  6. High grade serous ovarian carcinoma (HGSOC) is the most common subtype of epithelial ovarian cancers (EOC) with poor prognosis. In most cases EOC is widely disseminated at the time of diagnosis. Despite the op...

    Authors: H. Sallinen, S. Janhonen, P. Pölönen, H. Niskanen, O. H. Liu, A. Kivelä, J. M. Hartikainen, M. Anttila, M. Heinäniemi, S. Ylä-Herttuala and M. U. Kaikkonen

    Citation: BMC Cancer 2019 19:1121

    Content type: Research article

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  7. Standardized Nucleic Acid Quantification for SEQuencing (SNAQ-SEQ) is a novel method that utilizes synthetic DNA internal standards spiked into each sample prior to next generation sequencing (NGS) library pre...

    Authors: Daniel J. Craig, Thomas Morrison, Sadik A. Khuder, Erin L. Crawford, Leihong Wu, Joshua Xu, Thomas M. Blomquist and James C. Willey

    Citation: BMC Cancer 2019 19:1081

    Content type: Technical advance

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  8. Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-derived reactive oxygen species (ROS) not only can promote cancer progression, but also they have recently emerged as mediators of the mucosal immune...

    Authors: Sang Yeon Cho, Sungha Kim, Mi-Ju Son, Gwanghun Kim, Parul Singh, Ha Neul Kim, Hei-Gwon Choi, Heon Jong Yoo, Young Bok Ko, Byung Seok Lee and Hyuk Soo Eun

    Citation: BMC Cancer 2019 19:1078

    Content type: Research article

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  9. BRCA1 associated-protein 1 (BAP1) tumor predisposition syndrome is associated with an increased risk for malignant mesotheliomas, uveal and cutaneous melanomas, renal cell carcinomas, and singular cutaneous lesio...

    Authors: Bianca Costa Soares de Sá, Mariana Petaccia de Macedo, Giovana Tardin Torrezan, Juliana Casagrande Tavoloni Braga, Felipe Fidalgo, Luciana Facure Moredo, Rute Lellis, João Pereira Duprat and Dirce Maria Carraro

    Citation: BMC Cancer 2019 19:1077

    Content type: Case report

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  10. The single-nucleotide polymorphism SLC39A6 rs1050631 is strongly implicated in esophageal squamous cell carcinoma, leading us to question whether it may also play a role in gastric adenocarcima (GA).

    Authors: Jian Gao, Wenjun Ren, Chunhong Xiao, Lie Wang, Qiaojia Huang, Zaizhong Zhang, Yuan Dang, Pengcheng Weng, Hui Wang, Xuehong Fang, Minxian Zhuang, Liying Lin and Shaoquan Chen

    Citation: BMC Cancer 2019 19:1069

    Content type: Research article

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  11. Accumulating evidence indicates inherited risk in the aetiology of lung cancer, although smoking exposure is the major attributing factor. Family history is a simple substitute for inherited susceptibility. Pr...

    Authors: Yue I. Cheng, Yun Cui Gan, Dan Liu, Michael P. A. Davies, Wei Min Li and John K. Field

    Citation: BMC Cancer 2019 19:1068

    Content type: Research article

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  12. Long non-coding RNAs (lncRNAs) play a fundamental role in colorectal cancer (CRC) development, however, lncRNA expression profiles in CRC and its precancerous stages remain to be explored. We aimed to study wh...

    Authors: Alexandra Kalmár, Zsófia Brigitta Nagy, Orsolya Galamb, István Csabai, András Bodor, Barnabás Wichmann, Gábor Valcz, Barbara Kinga Barták, Zsolt Tulassay, Peter Igaz and Béla Molnár

    Citation: BMC Cancer 2019 19:1059

    Content type: Research article

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  13. Resistance to chemotherapy is one of the major hurdles in current cancer therapy. With the increasing occurrence of drug resistance, a paradigm shift in treatment strategy is required. Recently “medication vac...

    Authors: Divya Niveditha, Harshita Sharma, Syamantak Majumder, Sudeshna Mukherjee, Rajdeep Chowdhury and Shibasish Chowdhury

    Citation: BMC Cancer 2019 19:1045

    Content type: Research article

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  14. Understanding mechanisms underlying specific chemotherapeutic responses in subtypes of cancer may improve identification of treatment strategies most likely to benefit particular patients. For example, triple-...

    Authors: David P. Hill, Akeena Harper, Joan Malcolm, Monica S. McAndrews, Susan M. Mockus, Sara E. Patterson, Timothy Reynolds, Erich J. Baker, Carol J. Bult, Elissa J. Chesler and Judith A. Blake

    Citation: BMC Cancer 2019 19:1039

    Content type: Research article

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  15. The deregulated alternative splicing of key glycolytic enzyme, Pyruvate Kinase muscle isoenzyme (PKM) is implicated in metabolic adaptation of cancer cells. The splicing switch from normal PKM1 to cancer-speci...

    Authors: Sandhya Yadav, Somnath D. Bhagat, Amit Gupta, Atul Samaiya, Aasheesh Srivastava and Sanjeev Shukla

    Citation: BMC Cancer 2019 19:1031

    Content type: Research article

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  16. Somatic PTEN mutation occurs in a proportion of ovarian endometrioid carcinomas. However, these cancers have seldom been reported in diseases associated with germline PTEN variants, such as Cowden syndrome (CS).

    Authors: Hiroyuki Matsubayashi, Satomi Higashigawa, Yoshimi Kiyozumi, Yasue Horiuchi, Yasuyuki Hirashima, Nobuhiro Kado, Masato Abe, Takuma Ohishi, Sumiko Ohnami, Kenichi Urakami and Ken Yamaguchi

    Citation: BMC Cancer 2019 19:1014

    Content type: Case report

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  17. The expression of microRNAs (miRNAs) is a promising prognostic and diagnostic tool in hepatocellular carcinoma (HCC). Here we performed small RNA sequencing (sRNA-seq) of tissue, serum and serum exosomes to in...

    Authors: Robin Mjelle, Simona O. Dima, Nicolae Bacalbasa, Konika Chawla, Andrei Sorop, Dana Cucu, Vlad Herlea, Pål Sætrom and Irinel Popescu

    Citation: BMC Cancer 2019 19:1007

    Content type: Research article

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  18. Acute T-cell lymphoblastic leukaemia (T-ALL) is an aggressive disorder derived from immature thymocytes. The variability observed in clinical responses on this type of tumours to treatments, the high toxicity ...

    Authors: Pablo Fernández-Navarro, Pilar López-Nieva, Elena Piñeiro-Yañez, Gonzalo Carreño-Tarragona, Joaquín Martinez-López, Raúl Sánchez Pérez, Ángel Aroca, Fátima Al-Shahrour, María Ángeles Cobos-Fernández and José Fernández-Piqueras

    Citation: BMC Cancer 2019 19:1005

    Content type: Research article

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  19. To examine differences in the plasma levels of miRNA-21, − 214, −34a, and -200a in patients with persistent high-risk human papillomavirus (hr-HPV) infection or with cervical lesions of different grades.

    Authors: Hongyun Wang, Dandan Zhang, Qing Chen and Ying Hong

    Citation: BMC Cancer 2019 19:986

    Content type: Research article

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  20. Multiple myeloma (MM) cells gain protection against drugs through interaction with bone marrow stromal cells (BMSCs). This form of resistance largely accounts for resistance to therapy in MM patients which war...

    Authors: Jahangir Abdi, Nasrin Rastgoo, Yan Chen, Guo An Chen and Hong Chang

    Citation: BMC Cancer 2019 19:975

    Content type: Research article

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  21. CpG Island Methylator Phenotype (CIMP) is an epigenetic phenotype in CRC characterized by hypermethylation of CpG islands in promoter regions of tumor suppressor genes, leading to their transcriptional silenci...

    Authors: Shailesh Mahesh Advani, Pragati Shailesh Advani, Derek W. Brown, Stacia M. DeSantis, Krittiya Korphaisarn, Helena M. VonVille, Jan Bressler, David S. Lopez, Jennifer S. Davis, Carrie R. Daniel, Amir Mehrvarz Sarshekeh, Dejana Braithwaite, Michael D. Swartz and Scott Kopetz

    Citation: BMC Cancer 2019 19:964

    Content type: Research article

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  22. We aimed to investigate the correlation of Circ-SMARCA5 with disease severity and prognosis in multiple myeloma (MM), and its underlying mechanisms in regulating cell proliferation and apoptosis.

    Authors: Haiyan Liu, Yan Wu, Shunye Wang, Jie Jiang, Chenlu Zhang, Yijing Jiang, Xingfeng Wang, Lewen Hong and Hongming Huang

    Citation: BMC Cancer 2019 19:937

    Content type: Research article

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  23. Although extensive use of tyrosine kinase inhibitors has resulted in high and durable response rate and prolonged survival time in patients with BCR-ABL1 positive chronic myeloid leukemia (CML) and acute leuke...

    Authors: Zhanglin Zhang, Zhiwei Chen, Mei Jiang, Shuyuan Liu, Yang Guo, Lagen Wan and Fei Li

    Citation: BMC Cancer 2019 19:935

    Content type: Research article

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  24. Single nucleotide polymorphisms (SNPs) in genes encoding mitotic kinases could influence development and progression of gastric cancer (GC).

    Authors: Aner Mesic, Marija Rogar, Petra Hudler, Nurija Bilalovic, Izet Eminovic and Radovan Komel

    Citation: BMC Cancer 2019 19:919

    Content type: Research article

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  25. Cancer is a genetic and epigenetic disease that involves inactivation of tumor suppressor genes and activation of proto-oncogenes. All-trans retinoic acid (ATRA) is an isomer of retinoic acid involved in the o...

    Authors: Lara Lima, Thaísa Cristina Tavares de Melo, Diego Marques, Jéssica Nayara Góes de Araújo, Isabela Samária Fernandes Leite, Camila Xavier Alves, Julieta Genre and Vivian Nogueira Silbiger

    Citation: BMC Cancer 2019 19:866

    Content type: Research article

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  26. Atypical teratoid/rhabdoid tumors (AT/RTs) are highly malignant brain tumors with inactivation of the SMARCB1 gene, which play a critical role in genomic transcriptional control. In this study, we analyzed the ge...

    Authors: Ji Hoon Phi, Choong-Hyun Sun, Se-Hoon Lee, Seungmook Lee, Inho Park, Seung Ah Choi, Sung-Hye Park, Ji Yeoun Lee, Kyu-Chang Wang, Seung-Ki Kim, Hongseok Yun and Chul-Kee Park

    Citation: BMC Cancer 2019 19:848

    Content type: Research article

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  27. Blood-based methods using cell-free DNA (cfDNA) are under development as an alternative to existing screening tests. However, early-stage detection of cancer using tumor-derived cfDNA has proven challenging be...

    Authors: Nathan Wan, David Weinberg, Tzu-Yu Liu, Katherine Niehaus, Eric A. Ariazi, Daniel Delubac, Ajay Kannan, Brandon White, Mitch Bailey, Marvin Bertin, Nathan Boley, Derek Bowen, James Cregg, Adam M. Drake, Riley Ennis, Signe Fransen…

    Citation: BMC Cancer 2019 19:832

    Content type: Research article

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  28. SMARCB1-deficient sinonasal carcinoma (SDSC) is an aggressive subtype of head and neck cancers that has a poor prognosis despite multimodal therapy. We present a unique case with next generation sequencing dat...

    Authors: Horacio Gomez-Acevedo, John D. Patterson, Sehrish Sardar, Murat Gokden, Bhaskar C. Das, David W. Ussery and Analiz Rodriguez

    Citation: BMC Cancer 2019 19:827

    Content type: Case report

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  29. Progression of breast cancer involves both genetic and epigenetic factors. Parkin gene has been identified as a tumor suppressor gene in the pathogenesis of various cancers. Nevertheless, the putative role of Par...

    Authors: Khushnuma Wahabi, Ahmad Perwez, Shabeena Kamarudheen, Zafar Iqbal Bhat, Anurag Mehta and M. Moshahid A. Rizvi

    Citation: BMC Cancer 2019 19:820

    Content type: Research article

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  30. The aim of this study was to investigate the potential of cell-free DNA (cfDNA) as a disease biomarker in oesophageal squamous cell carcinoma (ESCC) that can be used for treatment response evaluation and early...

    Authors: Pei Meng, Jiacong Wei, Yiqun Geng, Shaobin Chen, Miente Martijn Terpstra, Qiongyi Huang, Qian Zhang, Zuoqing Su, Wanchun Yu, Min Su, Klaas Kok, Anke van den Berg and Jiang Gu

    Citation: BMC Cancer 2019 19:818

    Content type: Research article

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  31. 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

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  32. 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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  33. 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

  34. 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

    Published on:

  35. 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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  36. 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

    Published on:

  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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