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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. Wilms’ tumor is also called nephroblastoma and is the most common pediatric renal cancer. Several genetic and epigenetic factors have been found to account for the development of Wilms’ tumor. MiRNAs play impo...

    Authors: Zhuo Liu, Feng He, Shengrong OuYang, Yuanyuan Li, Feifei Ma, Huibo Chang, Dingding Cao and Jianxin Wu

    Citation: BMC Cancer 2019 19:405

    Content type: Research article

    Published on:

  2. With the introduction of Olaparib treatment for BRCA-deficient recurrent ovarian cancer, testing for somatic and/or germline mutations in BRCA1/2 genes in tumor tissues became essential for treatment decisions. I...

    Authors: Falk Zakrzewski, Laura Gieldon, Andreas Rump, Michael Seifert, Konrad Grützmann, Alexander Krüger, Sina Loos, Silke Zeugner, Karl Hackmann, Joseph Porrmann, Johannes Wagner, Karin Kast, Pauline Wimberger, Gustavo Baretton, Evelin Schröck, Daniela Aust…

    Citation: BMC Cancer 2019 19:396

    Content type: Technical advance

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  3. The impact of Tet oncogene family member 2 (TET2) mutations on the prognosis of acute myeloid leukemia (AML) is still controversial. A meta analysis is needed in order to assess the prognostic significance of TET...

    Authors: Ruiqi Wang, Xiaoning Gao and Li Yu

    Citation: BMC Cancer 2019 19:389

    Content type: Research article

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  4. Gene expression profiling provides key information for prognosis of breast cancer to establish treatment strategy. However, the genetic assessment should be available before induction of treatment to be useful...

    Authors: Jeeyeon Lee, Eun Hye Lee, Ho Yong Park, Wan Wook Kim, Ryu Kyung Lee, Yee Soo Chae, Soo Jung Lee, Jee-Eun Kim, Byeong-il Kang, Jee Young Park, Ji-Young Park and Jin Hyang Jung

    Citation: BMC Cancer 2019 19:388

    Content type: Research article

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  5. Intratumoral epidermal growth factor receptor (EGFR) mutational heterogeneity is yet controversial in non-small cell lung cancer (NSCLC) patients. Single-cell analysis provides the genetic profile of single cance...

    Authors: Longhua Guo, Zhihong Chen, Chongrui Xu, Xuchao Zhang, Honghong Yan, Jian Su, Jinji Yang, Zhi Xie, Weibang Guo, Feng Li, Yilong Wu and Qing Zhou

    Citation: BMC Cancer 2019 19:369

    Content type: Research article

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  7. Osteosarcoma is the most common malignant bone tumor in children. Survival remains poor among histologically poor responders, and there is a need to identify them at diagnosis to avoid delivering ineffective t...

    Authors: Krithika Bhuvaneshwar, Michael Harris, Yuriy Gusev, Subha Madhavan, Ramaswamy Iyer, Thierry Vilboux, John Deeken, Elizabeth Yang and Sadhna Shankar

    Citation: BMC Cancer 2019 19:357

    Content type: Research article

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  8. High risk human papillomaviruses (HPV) plays important roles in the development of cervical cancer, a number of other anogenital cancer and they are increasingly found in oropharyngeal squamous cell carcinoma ...

    Authors: Ge Gao, Jintu Wang, Jan L. Kasperbauer, Nicole M. Tombers, Fei Teng, Honglan Gou, Yonggang Zhao, Zhenhong Bao and David I. Smith

    Citation: BMC Cancer 2019 19:352

    Content type: Research article

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  9. Visceral organ metastasis is associated with poor survival outcomes in terms of metastasis free- and overall survival in breast carcinomas. Identification of a gene expression profile in tumours that selects a...

    Authors: C. D. Savci-Heijink, H. Halfwerk, J. Koster, H. M. Horlings and M. J. van de Vijver

    Citation: BMC Cancer 2019 19:333

    Content type: Research article

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  10. Non-muscular invasive bladder cancer (NMIBC) has a high risk of recurrence. As androgen receptor (AR) reportedly affects bladder cancer, we assessed the correlation between NMIBC recurrence and tumor AR expressio...

    Authors: Masato Yasui, Takashi Kawahara, Koji Izumi, Masahiro Yao, Yukari Ishiguro, Hitoshi Ishiguro, Hiroji Uemura and Yasuhide Miyoshi

    Citation: BMC Cancer 2019 19:331

    Content type: Research article

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  12. In the majority of familial breast cancer (BC) families, the etiology of the disease remains unresolved. To identify missing BC heritability resulting from relatively rare variants (minor allele frequency ≤ 1%...

    Authors: Rajendra Bahadur Shahi, Sylvia De Brakeleer, Ben Caljon, Ingrid Pauwels, Maryse Bonduelle, Sofie Joris, Christel Fontaine, Marian Vanhoeij, Sonia Van Dooren, Erik Teugels and Jacques De Grève

    Citation: BMC Cancer 2019 19:313

    Content type: Research article

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  13. Feline injection-site sarcoma (FISS), an aggressive iatrogenic subcutaneous malignancy, is challenging to manage clinically and little is known about the molecular basis of its pathogenesis. Tumor transcriptom...

    Authors: Qi Wei, Stephen A. Ramsey, Maureen K. Larson, Noah E. Berlow, Donasian Ochola, Christopher Shiprack, Amita Kashyap, Bernard Séguin, Charles Keller and Christiane V. Löhr

    Citation: BMC Cancer 2019 19:311

    Content type: Research article

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  14. High-grade serous ovarian cancer is a detrimental disease. Treatment options in patients with a recurrent disease are dependent on BRCA1/2 mutation status since only patients with known BRCA mutation are eligible...

    Authors: Andreja Gornjec, Srdjan Novakovic, Vida Stegel, Marko Hocevar, Ziva Pohar Marinsek, Barbara Gazic, Mateja Krajc and Erik Skof

    Citation: BMC Cancer 2019 19:296

    Content type: Research article

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  15. Lung adenocarcinoma is the most common type of lung cancers. Whole-genome sequencing studies disclosed the genomic landscape of lung adenocarcinomas. however, it remains unclear if the genetic alternations cou...

    Authors: Jiaxian Yu, Yueming Hu, Yafei Xu, Jue Wang, Jiajie Kuang, Wei Zhang, Jianlin Shao, Dianjing Guo and Yejun Wang

    Citation: BMC Cancer 2019 19:263

    Content type: Research article

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  16. To systematically assess the prevalence of BRCA1 and BRCA2 gene mutations in women with Hereditary Breast and/or Ovarian Cancer (HBOC) in Arab countries and to describe the variability in the BRCA gene mutatio...

    Authors: Khadiga Abdulrashid, Nour AlHussaini, Wifag Ahmed and Lukman Thalib

    Citation: BMC Cancer 2019 19:256

    Content type: Research article

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  17. Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the United States. High-throughput genotyping has enabled discovery of germline ...

    Authors: Tarun Karthik Kumar Mamidi, Jiande Wu and Chindo Hicks

    Citation: BMC Cancer 2019 19:229

    Content type: Research article

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  18. Gastric cancer (GC) is one of the most commonly occuring gastrointestinal tumor types, and early diagnosis and operation have a notable effect on the prognosis of patients. Although certain markers, including ...

    Authors: Jiaxin Liu, Zhao Liu, Xiaozhi Zhang, Tuotuo Gong and Demao Yao

    Citation: BMC Cancer 2019 19:227

    Content type: Research article

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    The Correction to this article has been published in BMC Cancer 2019 19:759

  19. Non-small cell lung cancer (NSCLC) as the most frequent type of lung cancer is associated with extensive mortality. Researchers have studied the suitability of several molecules as biomarkers for early detecti...

    Authors: Farbod Esfandi, Mohammad Taheri, Mir Davood Omrani, Mohammad Behgam Shadmehr, Shahram Arsang-Jang, Roshanak Shams and Soudeh Ghafouri-Fard

    Citation: BMC Cancer 2019 19:222

    Content type: Research article

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  20. Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The a...

    Authors: Bernardo P. de Almeida, Joana Dias Apolónio, Alexandra Binnie and Pedro Castelo-Branco

    Citation: BMC Cancer 2019 19:219

    Content type: Research article

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  21. Although surgical resection provides a cure for patients with intrahepatic cholangiocarcinoma (ICC), the risk of mortality and recurrence remains high. Several biomarkers are reported to be associated with the...

    Authors: Chao Bi, Mei Liu, Weiqi Rong, Fan Wu, Yang Zhang, Shengtao Lin, Yunhe Liu, Jianxiong Wu and Liming Wang

    Citation: BMC Cancer 2019 19:213

    Content type: Research article

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  22. Cancer immunotherapy with immune checkpoint blockade (CKB) is now standard of care for multiple cancers. The clinical response to CKB is associated with T cell immunity targeting cancer-induced mutations that ...

    Authors: Pooja Narang, Meixuan Chen, Amit A. Sharma, Karen S. Anderson and Melissa A. Wilson

    Citation: BMC Cancer 2019 19:200

    Content type: Research article

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  23. IDH1/2 mutated glioma has been associated with a germline risk variant, the rs55705857 G allele. The Utah Population Database (UPDB), a computerized genealogy of people in Utah, is a unique resource to evaluate c...

    Authors: Sarah Hummel, Wendy Kohlmann, Thomas M. Kollmeyer, Robert Jenkins, Joshua Sonnen, Cheryl A. Palmer, Howard Colman, Diana Abbott, Lisa Cannon-Albright and Adam L. Cohen

    Citation: BMC Cancer 2019 19:190

    Content type: Research article

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  24. Primary paediatric epidural sarcomas are extremely rare. Overall, there remains a paucity of knowledge in paediatric epidural sarcomas owing to the infrequent number of cases. The Archer FusionPlex Sarcoma Kit...

    Authors: Sharon Y. Y. Low, Chik Hong Kuick, Wan Yi Seow, Nurfahanah Bte Syed Sulaiman, Huiyi Chen, Derrick W. Q. Lian, Kenneth T. E. Chang, Enrica E. K. Tan, Shui Yen Soh, Grace I. L. Tan, Lee Ping Ng, Wan Tew Seow and David C. Y. Low

    Citation: BMC Cancer 2019 19:182

    Content type: Case report

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  25. Colorectal cancer (CRC) is one of the most common cancers worldwide, and genetic variations exert distinct roles in its pathogenesis. Single nucleotide polymorphisms (SNPs) in interleukin 1 alpha (IL1A) were repo...

    Authors: Hong Ji, Le Lu, Jingjing Huang, Yang Liu, Binchao Zhang, Hui Tang, Dangze Sun, Yafei Zhang, Hao Shang, Yiming Li and Hongwei Lu

    Citation: BMC Cancer 2019 19:181

    Content type: Research article

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  26. In lung cancer, epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor sensitizing mutations co-existing with rare minor EGFR mutations are known as compound mutations. These minor EGFR mutations can l...

    Authors: Kei Namba, Shuta Tomida, Takehiro Matsubara, Yuta Takahashi, Eisuke Kurihara, Yusuke Ogoshi, Takahiro Yoshioka, Tatsuaki Takeda, Hidejiro Torigoe, Hiroki Sato, Kazuhiko Shien, Hiromasa Yamamoto, Junichi Soh, Kazunori Tsukuda and Shinichi Toyooka

    Citation: BMC Cancer 2019 19:175

    Content type: Research article

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  27. Langerhans cell histiocytosis (LCH) is a rare clonal disease, characterized by hyperproliferation of Langerhans cells. It may rarely involve the thyroid gland. Its association with papillary thyroid carcinoma ...

    Authors: Mohammad A. Al Hamad, Hassan M. Albisher, Weam R. Al Saeed, Ahmed T. Almumtin, Fatimah M. Allabbad and Mohammed A. Shawarby

    Citation: BMC Cancer 2019 19:170

    Content type: Case report

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  28. Liver metastases of breast cancer are frequent and can recur even after “complete/R0” resection in combination with systemic and hormonal treatments. The aim of this study was to analyze throughout repeat hepa...

    Authors: Aldrick Ruiz, Mylène Sebagh, Raphaël Saffroy, Marc-Antoine Allard, Nelly Bosselut, Giulia Hardoin, Julie Vasseur, Jocelyne Hamelin, René Adam, Jean-François Morère and Antoinette Lemoine

    Citation: BMC Cancer 2019 19:169

    Content type: Research article

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  29. 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

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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    The Correction to this article has been published in BMC Cancer 2019 19:437

  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

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  45. 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

    Content type: Research article

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  46. 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

    Content type: Research article

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  47. 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

    Content type: Research article

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  48. 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

    Content type: Research article

    Published on:

  49. 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

    Content type: Research article

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  50. 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

    Content type: Research article

    Published on:

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