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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. Muscle invasive urothelial bladder carcinoma (MIBC) present RB1 and TP53 somatic alterations in a variable percentage of tumors throughout all molecular subtypes. MIBCs with neuroendocrine features have a high...

    Authors: Ramon Gonzalez Manzano, Ana Catalan-Latorre and Antonio Brugarolas

    Citation: BMC Cancer 2021 21:432

    Content type: Research article

    Published on:

  2. Bronchoscopy is a common procedure used for evaluation of suspicious lung nodules, but the low diagnostic sensitivity of bronchoscopy often results in inconclusive results and delays in treatment. Percepta Gen...

    Authors: Marla K. Johnson, Shuyang Wu, Daniel G. Pankratz, Grazyna Fedorowicz, Jessica Anderson, Jie Ding, Mei Wong, Manqiu Cao, Joshua Babiarz, Lori Lofaro, P. Sean Walsh, Giulia C. Kennedy and Jing Huang

    Citation: BMC Cancer 2021 21:400

    Content type: Research article

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  3. Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, associated with a high rate of morbidity and mortality. However, the target genes of miR-221-3p and the underlying mecha...

    Authors: Ziyan Zhou, Wenling Wu, Jixi Li, Chang Liu, Zixi Xiao, Qinqiao Lai, Rongxing Qin, Mingjun Shen, Shuo Shi and Min Kang

    Citation: BMC Cancer 2021 21:395

    Content type: Research article

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  4. Synonymous mutations do not change the protein sequences. Automatically, they have been regarded as neutral events and are ignored in the mutation-based cancer studies. However, synonymous mutations will chang...

    Authors: Qun Li, Jian Li, Chun-peng Yu, Shuai Chang, Ling-ling Xie and Song Wang

    Citation: BMC Cancer 2021 21:388

    Content type: Research article

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  5. The role of glycolysis in tumorigenesis has received increasing attention and multiple glycolysis-related genes (GRGs) have been proven to be associated with tumor metastasis. Hence, we aimed to construct a pr...

    Authors: Qianwei Xing, Tengyue Zeng, Shouyong Liu, Hong Cheng, Limin Ma and Yi Wang

    Citation: BMC Cancer 2021 21:381

    Content type: Research article

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  6. Germline RET mutations and variants are involved in development of multiple endocrine neoplasia type 2 (MEN2). The present study investigated a spectrum of RET variants, analyzed genotype-phenotype relationships,...

    Authors: Xiao-Ping Qi, Jian-Qiang Zhao, Xu-Dong Fang, Bi-Jun Lian, Feng Li, Hui-Hong Wang, Zhi-Lie Cao, Wei-Hui Zheng, Juan Cao and Yu Chen

    Citation: BMC Cancer 2021 21:369

    Content type: Research article

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  8. Next generation sequencing (NGS) has been a handy tool in clinical practice, mainly due to its efficiency and cost-effectiveness. It has been widely used in genetic diagnosis of several inherited diseases, and...

    Authors: Amanda Ferreira Vidal, Rafaella Sousa Ferraz, Antonette El-Husny, Caio Santos Silva, Tatiana Vinasco-Sandoval, Leandro Magalhães, Milene Raiol-Moraes, Williams Fernandes Barra, Cynthia Lara Brito Lins Pereira, Paulo Pimentel de Assumpção, Leonardo Miranda de Brito, Ricardo Assunção Vialle, Sidney Santos, Ândrea Ribeiro-dos-Santos and André M. Ribeiro-dos-Santos

    Citation: BMC Cancer 2021 21:363

    Content type: Research article

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  9. Numerous studies have reported the correlation between AXIN2 polymorphism and cancer risk, but the results seem not consistent. In order to get an overall, accurate and updated results about AXIN2 polymorphism an...

    Authors: Xi Li, Yiming Li, Guodong Liu and Wei Wu

    Citation: BMC Cancer 2021 21:353

    Content type: Research article

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  10. The essence of energy metabolism has spread to the field of esophageal cancer (ESC) cells. Herein, we tried to develop a prognostic prediction model for patients with ESC based on the expression profiles of en...

    Authors: Weifeng Zheng, Chaoying Chen, Jianghao Yu, Chengfeng Jin and Tiemei Han

    Citation: BMC Cancer 2021 21:345

    Content type: Research article

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  11. ABL-class and JAK-STAT signaling pathway activating alterations have been associated with both a poor post-induction minimal residual disease (MRD) response and an inferior outcome in B-cell acute lymphoblasti...

    Authors: Rimvydas Norvilas, Vaidas Dirse, Ruta Semaskeviciene, Orinta Mickeviciute, Egle Gineikiene, Mindaugas Stoskus, Goda Vaitkeviciene, Jelena Rascon and Laimonas Griskevicius

    Citation: BMC Cancer 2021 21:326

    Content type: Research article

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  12. Cervical cancer is a gynecologic cancer type that develops in the cervix, accounting for 8% mortality of all female cancer patients. Infection with specific human papillomavirus (HPV) types is considered the m...

    Authors: Shahana Sharmin, Fatima Tuj Zohura, Md. Sajedul Islam, Anika Shimonty, Md. Abdullah-Al-Kamran Khan, Rehana Parveen, Foujia Sharmin, Chowdhury Rafiqul Ahsan, Abul Bashar Mir Md. Khademul Islam and Mahmuda Yasmin

    Citation: BMC Cancer 2021 21:289

    Content type: Research article

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  14. Lung adenocarcinoma (LUAD) is the most frequently diagnosed histological subtype of lung cancer. Our purpose was to explore molecular subtypes and core genes for LUAD using multi-omics analysis.

    Authors: Yue Zhao, Yakun Gao, Xiaodong Xu, Jiwu Zhou and He Wang

    Citation: BMC Cancer 2021 21:257

    Content type: Research article

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  15. Neuroendocrine tumours (NETs) arise from hormone-producing or nervous system cells and can develop from anywhere in the body. They have heterogeneous origins from skin to gastrointestinal track and a complicat...

    Authors: Guney Isa Burak, Sonmezler Ozge, Mujde Cem, Buyukdereli Gulgun, Dogruca Yapar Zeynep and Bisgin Atil

    Citation: BMC Cancer 2021 21:234

    Content type: Research article

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  16. High grade serous ovarian cancer (HGSOC) accounts for nearly 60% of total cases of epithelial ovarian cancer. It is the most aggressive subtype, which shows poor prognosis and low patient survival. For better ...

    Authors: Rachel Topno, Ibha Singh, Manoj Kumar and Pallavi Agarwal

    Citation: BMC Cancer 2021 21:220

    Content type: Research article

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  17. Colorectal cancer (CRC) is one of the most common cancers worldwide; it is the fourth leading cause of death in the world and the third in Brazil. Mutations in the APC, DCC, KRAS and TP53 genes have been associat...

    Authors: Aline Simoneti Fonseca, Anelisa Ramão, Matheus Carvalho Bürger, Jorge Estefano Santana de Souza, Dalila Lucíola Zanette, Greice Andreotti de Molfetta, Luiza Ferreira de Araújo, Rafaela de Barros e Lima Bueno, Graziela Moura Aguiar, Jessica Rodrigues Plaça, Cleidson de Pádua Alves, Anemari Ramos Dinarte dos Santos, Daniel Onofre Vidal, Gyl Eanes Barros Silva, Rodrigo Alexandre Panepucci, Fernanda Maris Peria…

    Citation: BMC Cancer 2021 21:207

    Content type: Research article

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  18. Breast cancer is one of the leading causes of cancer-related deaths in women, and there is a demand in developing an Asian-based genetic profiling database for breast cancer in improving the treatment response...

    Authors: Chi-Cheng Huang, Yi-Fang Tsai, Chun-Yu Liu, Ta-Chung Chao, Pei-Ju Lien, Yen-Shu Lin, Chin-Jung Feng, Jen-Hwey Chiu, Chih-Yi Hsu and Ling-Ming Tseng

    Citation: BMC Cancer 2021 21:199

    Content type: Research article

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  19. Genome-wide association studies (GWAS) have identified multiple common CRC-related (colorectal cancer) SNPs (single nucleotide polymorphisms) including the Cadherin 1(CDH1) rs9929218 may act by increasing the ...

    Authors: Huiyan Wang, Dongying Gu, Miao Yu, Yanjun Hu, Zhe Chen, Xinying Huo, Tao Yu, Jinfei Chen and Yang Zheng

    Citation: BMC Cancer 2021 21:190

    Content type: Research article

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  20. Super-enhancer-associated long noncoding RNAs (SE-lncRNAs) have been reported to play essential roles in tumorigenesis, but the fundamental mechanism of SE-lncRNAs in colorectal cancer (CRC) remains largely un...

    Authors: Linping Yan, Huanhuan Chen, Li Tang, Pan Jiang and Feng Yan

    Citation: BMC Cancer 2021 21:187

    Content type: Research article

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  21. Targeting Protein for Xenopus Kinesin Like Protein 2 (TPX2) is a microtubule associated protein that functions in mitotic spindle assembly. TPX2 also localizes to the nucleus where it functions in DNA damage r...

    Authors: Daniel R. Matson, Ryan A. Denu, Lauren M. Zasadil, Mark E. Burkard, Beth A. Weaver, Christopher Flynn and P. Todd Stukenberg

    Citation: BMC Cancer 2021 21:186

    Content type: Research article

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  22. Activating Gαq signalling mutations are considered an early event in the development of uveal melanoma. Whereas most tumours harbour a mutation in GNAQ or GNA11, CYSLTR2 (encoding G-protein coupled receptor CysLT

    Authors: Rogier J. Nell, Nino V. Menger, Mieke Versluis, Gregorius P. M. Luyten, Robert M. Verdijk, Michele C. Madigan, Martine J. Jager and Pieter A. van der Velden

    Citation: BMC Cancer 2021 21:164

    Content type: Research article

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  23. Urothelial carcinoma (UC) is the most common genitourinary malignancy in China. In this study, we surveyed the genomic features in Chinese UC patients and investigated the concordance of genetic alterations be...

    Authors: Bo Yang, Xiao Zhao, Chong Wan, Xin Ma, Shaoxi Niu, Aitao Guo, Jieli Wang, Jinliang Wang, Decong Sun and Shunchang Jiao

    Citation: BMC Cancer 2021 21:162

    Content type: Research article

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  25. The RAS family protooncogenes, including KRAS, NRAS and HRAS, encode proteins responsible for the regulation of growth, differentiation and survival of many cell types. The HRAS and KRAS oncogene mutations are we...

    Authors: Milena Pązik, Katarzyna Michalska, Marta Żebrowska-Nawrocka, Izabela Zawadzka, Mariusz Łochowski and Ewa Balcerczak

    Citation: BMC Cancer 2021 21:130

    Content type: Research article

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  27. Intrahepatic cholangiocarcinoma (iCCA) is a highly lethal malignancy of the biliary tract. Analysis of somatic mutational profiling can reveal new prognostic markers and actionable treatment targets. In this s...

    Authors: Rui Zhang, Qi Li, Jialu Fu, Zhechuan Jin, Jingbo Su, Jian Zhang, Chen Chen, Zhimin Geng and Dong Zhang

    Citation: BMC Cancer 2021 21:112

    Content type: Research article

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  28. Patients with small intestinal neuroendocrine tumors (SINETs) frequently present with lymph node and liver metastases at the time of diagnosis, but the molecular changes that lead to the progression of these t...

    Authors: Tobias Hofving, Erik Elias, Anna Rehammar, Linda Inge, Gülay Altiparmak, Marta Persson, Erik Kristiansson, Martin E. Johansson, Ola Nilsson and Yvonne Arvidsson

    Citation: BMC Cancer 2021 21:101

    Content type: Research article

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  29. Due to tumor heterogeneity, the diagnosis, treatment, and prognosis of patients with lung squamous cell carcinoma (LUSC) are difficult. DNA methylation is an important regulator of gene expression, which may h...

    Authors: Xiu-Shen Li, Ke-Chao Nie, Zhi-Hua Zheng, Rui-Sheng Zhou, Yu-Sheng Huang, Zeng-Jie Ye, Fan He and Ying Tang

    Citation: BMC Cancer 2021 21:96

    Content type: Research article

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  30. Breast cancer is the most frequently diagnosed malignancy among women. However, the role of microRNA (miRNA) expression in breast cancer progression is not fully understood. In this study we examined predictiv...

    Authors: Adriane F. Evangelista, Renato J. Oliveira, Viviane A. O. Silva, Rene A. D. C. Vieira, Rui M. Reis and Marcia M. C. Marques

    Citation: BMC Cancer 2021 21:76

    Content type: Research article

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  31. Although arsenic trioxide (ATO) and all-trans retinoic acid (ATRA) are well-tolerated and effective treatments for Acute Promyelocytic Leukemia (APL), Differentiation Syndrome (DS) is a lethal side effect in s...

    Authors: Zahra Mohammadzadeh, Azadeh Omidkhoda, Bahram Chahardouli, Ghazaleh Hoseinzadeh, Kamran Ali Moghaddam, Seyed Asadollah Mousavi and Shahrbano Rostami

    Citation: BMC Cancer 2021 21:46

    Content type: Research article

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  32. Lynch syndrome (LS) is the most common hereditary colorectal cancer (CRC) syndrome. Comparison of prognosis between LS and sporadic CRC (SCRC) were rare, with conflicting results. This study aimed to compare t...

    Authors: Yun Xu, Cong Li, Charlie Zhi-Lin Zheng, Yu-Qin Zhang, Tian-An Guo, Fang-Qi Liu and Ye Xu

    Citation: BMC Cancer 2021 21:45

    Content type: Research article

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  33. In recent years, the relationship between tumor-associated macrophages (TAMs) and solid tumors has become a research hotspot. This study aims to explore the close relationship of TAMs with metabolic reprogramm...

    Authors: Junyu Huo, Liqun Wu, Yunjin Zang, Hongjing Dong, Xiaoqiang Liu, Fu He and Xiao Zhang

    Citation: BMC Cancer 2021 21:31

    Content type: Research article

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  34. Ataxia telangiectasia-mutated (ATM) gene contributes to repair damaged DNA and to regulate cell cycle; therefore, ATM variants seem to increase breast cancer risk; however, the results are controversial. So we...

    Authors: Masoumeh Moslemi, Yousef Moradi, Hojat Dehghanbanadaki, Hamed Afkhami, Mansoor Khaledi, Najmeh Sedighimehr, Javad Fathi and Ehsan Sohrabi

    Citation: BMC Cancer 2021 21:27

    Content type: Research article

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  35. Hepatocellular carcinoma (HCC) remains the most frequent liver cancer, accounting for approximately 90% of primary liver cancers worldwide. The recurrence-free survival (RFS) of HCC patients is a critical fact...

    Authors: Wenhua Wang, Lingchen Wang, Xinsheng Xie, Yehong Yan, Yue Li and Quqin Lu

    Citation: BMC Cancer 2021 21:6

    Content type: Research article

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  36. Studies of epigenomic alterations associated with diseases primarily focus on methylation profiles of promoter regions of genes, but not of other genomic regions. In our past work (Das et al. 2019) on patients...

    Authors: Srija Mukhopadhyay, Sahana Ghosh, Debodipta Das, P. Arun, Bidyut Roy, Nidhan K. Biswas, Arindam Maitra and Partha P. Majumder

    Citation: BMC Cancer 2020 20:1219

    Content type: Research article

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  37. Tetraspanin CD82 is a tumor metastasis suppressor that is known to down regulate in various metastatic cancers. However, the exact mechanism by which CD82 prevents cancer metastasis is unclear. This study aims...

    Authors: Pushpaja Dodla, Vanitha Bhoopalan, Sok Kean Khoo, Cindy Miranti and Suganthi Sridhar

    Citation: BMC Cancer 2020 20:1211

    Content type: Research article

    Published on:

  38. There were scarcely germline variants of familial lung cancer (LC) identified. We conducted an study with whole-exome sequencing of pedigrees with familial lung cancer to analyze the potential genetic suscepti...

    Authors: Huan Lin, Gong Zhang, Xu-chao Zhang, Xin-lei Lian, Wen-zhao Zhong, Jian Su, Shi-liang Chen and Yi-long Wu

    Citation: BMC Cancer 2020 20:1209

    Content type: Research article

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  39. Glycolysis is a central metabolic pathway for tumor cells. However, the potential roles of glycolysis-related genes in renal cell carcinoma (RCC) have not been investigated.

    Authors: Fangshi Xu, Yibing Guan, Li Xue, Shanlong Huang, Ke Gao, Zhen Yang and Tie Chong

    Citation: BMC Cancer 2020 20:1207

    Content type: Research article

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  40. Gastric and colorectal cancers are the most common malignant tumours, leading to a significant number of cancer-related deaths worldwide. Recently, increasing evidence has demonstrated that cancer cells exhibi...

    Authors: Azer Farah, Maria Kabbage, Salsabil Atafi, Amira Jaballah Gabteni, Mouadh Barbirou, Mouna Madhioub, Lamine Hamzaoui, Mousadak Azzouz Mohamed, Hassen Touinsi, Asma Ouakaa Kchaou, Emna Chelbi, Samir Boubaker, Rahma Ben Abderrazek and Balkiss Bouhaouala-Zahar

    Citation: BMC Cancer 2020 20:1179

    Content type: Research article

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  41. Aggressive systemic mastocytosis (ASM) is a rare malignant disease characterized by disordered mast cell accumulation in various organs. We here describe a female ASM patient with a previous history of ovarian...

    Authors: Makiko Tsutsumi, Hiroki Miura, Hidehito Inagaki, Yasuko Shinkai, Asuka Kato, Takema Kato, Susumu Hamada-Tsutsumi, Makito Tanaka, Kazuko Kudo, Tetsushi Yoshikawa and Hiroki Kurahashi

    Citation: BMC Cancer 2020 20:1162

    Content type: Research article

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  42. Research focusing on the relationship between five types of tumor necrosis factor-alpha (TNF-α) SNPs and the risk of hepatocellular carcinoma (HCC) were still controversial. Hereby, we performed a meta-analysi...

    Authors: Citrawati Dyah Kencono Wungu, Fis Citra Ariyanto, Gwenny Ichsan Prabowo, Soetjipto and Retno Handajani

    Citation: BMC Cancer 2020 20:1134

    Content type: Research article

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  43. Hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC) are malignancies with a leading lethality. With reference to interferons (IFNs) known to mediate antitumor activities, this study inve...

    Authors: Henriette Huschka and Sabine Mihm

    Citation: BMC Cancer 2020 20:1131

    Content type: Research article

    Published on:

  44. Resistance to chemotherapy is the most common cause of treatment failure in acute myeloid leukemia (AML) and the drug efflux pump ABCB1 is a critical mediator. Recent studies have identified promoter transloca...

    Authors: Mark S. Williams, Naseer J. Basma, Fabio M. R. Amaral, Gillian Williams, John P. Weightman, Wolfgang Breitwieser, Louisa Nelson, Stephen S. Taylor, Daniel H. Wiseman and Tim C. P. Somervaille

    Citation: BMC Cancer 2020 20:1075

    Content type: Research article

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  45. The nuclear transport system has been proposed to be indispensable for cell proliferation and invasion in cancers. Prognostic biomarkers and molecular targets in nuclear transport systems have been developed. ...

    Authors: Zheng Zhu, Yang Lan, Lihong Wang, Jia Ge, Jiao Wang, Feng Liu, Zhicheng He, Hua Zhang, Min Luo, Dandan Lin, Yaoyao Tan, Yuanyuan Xu and Tao Luo

    Citation: BMC Cancer 2020 20:1072

    Content type: Research article

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  46. Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SN...

    Authors: Larissa B. Reis, Renato M. Bakos, Fernanda S. L. Vianna, Gabriel S. Macedo, Vanessa C. Jacovas, André M. Ribeiro-dos-Santos, Sidney Santos, Lúcio Bakos and Patricia Ashton-Prolla

    Citation: BMC Cancer 2020 20:1069

    Content type: Research article

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  47. Germline TP53 mutations are associated with Li-Fraumeni syndrome, a severe and rare hereditary cancer syndrome. Despite the rarity of germline TP53 mutations, the clinical implication for mutation carriers and th...

    Authors: Ava Kwong, Vivian Yvonne Shin, Cecilia Y. S. Ho, Chun Hang Au, Thomas P. Slavin, Jeffrey N. Weitzel, Tsun-Leung Chan and Edmond S. K. Ma

    Citation: BMC Cancer 2020 20:1053

    Content type: Research article

    Published on:

  49. β-catenin activation plays a crucial role for tumourigenesis in the large intestine but except for Lynch syndrome (LS) associated cancers stabilizing mutations of β-catenin gene (CTNNB1) are rare in colorectal ca...

    Authors: Alexander Arnold, Moritz Tronser, Christine Sers, Aysel Ahadova, Volker Endris, Soulafa Mamlouk, David Horst, Markus Möbs, Philip Bischoff, Matthias Kloor and Hendrik Bläker

    Citation: BMC Cancer 2020 20:1038

    Content type: Research article

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    The Correction to this article has been published in BMC Cancer 2020 20:1151

  50. Treating patients with advanced sarcomas is challenging due to great histologic diversity among its subtypes. Leiomyosarcoma (LMS) and de-differentiated liposarcoma (DDLPS) are two common and aggressive subtyp...

    Authors: Wenshuai Liu, Hanxing Tong, Chenlu Zhang, Rongyuan Zhuang, He Guo, Chentao Lv, Hua Yang, Qiaowei Lin, Xi Guo, Zhiming Wang, Yan Wang, Feng Shen, Shengzhou Wang, Chun Dai, Guan Wang, Jun Liu…

    Citation: BMC Cancer 2020 20:1035

    Content type: Research article

    Published on:

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