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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. Epidemiological evidence suggests that synchronous or metachronous presentation of breast and thyroid cancers exceeds that predicted by chance alone. The following potential explanations have been hypothesized...

    Authors: Bence Bakos, András Kiss, Kristóf Árvai, Balázs Szili, Barbara Deák-Kocsis, Bálint Tobiás, Zsuzsanna Putz, Richárd Ármós, Bernadett Balla, János Kósa, Magdolna Dank, Zsuzsanna Valkusz, István Takács, Ádám Tabák and Péter Lakatos

    Citation: BMC Cancer 2021 21:706

    Content type: Research article

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  2. Gastric cancer (GC) is one of the most common solid malignant tumors worldwide with a high-recurrence-rate. Identifying the molecular signatures and specific biomarkers of GC might provide novel clues for GC p...

    Authors: Xiao-Qing Lu, Jia-Qian Zhang, Sheng-Xiao Zhang, Jun Qiao, Meng-Ting Qiu, Xiang-Rong Liu, Xiao-Xia Chen, Chong Gao and Huan-Hu Zhang

    Citation: BMC Cancer 2021 21:697

    Content type: Research article

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  3. Abnormal expression of suppressor of cytokine signaling (SOCS) proteins regulates tumor angiogenesis and development in cancers. In this study, we aimed to perform a comprehensive bioinformatic analysis of SOC...

    Authors: Mingyu Sun, Chuangang Tang, Jun Liu, Wenli Jiang, Haifeng Yu, Fang Dong, Caiguo Huang and Youlutuziayi Rixiati

    Citation: BMC Cancer 2021 21:696

    Content type: Research article

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  4. The baculoviral IAP repeat containing 5 (BIRC5) related to epithelial-mesenchymal transition (EMT) plays a crucial role in the pathogenesis of hepatocellular carcinoma (HCC). However, it remains unclear whethe...

    Authors: Rongzhong Xu, Liubing Lin, Bo Zhang, Jian Wang, Fanchen Zhao, Xiaolin Liu, Yiping Li and Yan Li

    Citation: BMC Cancer 2021 21:687

    Content type: Research article

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  6. The tumour microenvironment (TME) not only plays a role during tumour progression and metastasis but also profoundly influences treatment efficacy. Environment-mediated drug resistance is a result of crosstalk...

    Authors: Xintong Lyu, Ping Wang, Qiao Qiao and Yuanjun Jiang

    Citation: BMC Cancer 2021 21:646

    Content type: Research article

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  7. Lung cancer is one of the most lethal and most prevalent malignant tumors worldwide, and lung squamous cell carcinoma (LUSC) is one of the major histological subtypes. Although numerous biomarkers have been fo...

    Authors: Guichuan Huang, Jing Zhang, Ling Gong, Yi Huang and Daishun Liu

    Citation: BMC Cancer 2021 21:626

    Content type: Research article

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  8. Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remains a major public health problem and its pathogenesis remains unresolved. A recent proteomics study discovered a lipid enzyme Sterol O-acyltr...

    Authors: Yulong Chen, Xunjun Yang, Yao Chen, Guorong Chen, Cheryl A. Winkler, Ping An and Jianxin Lyu

    Citation: BMC Cancer 2021 21:615

    Content type: Research article

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  9. The potential reversibility of aberrant DNA methylation indicates an opportunity for oncotherapy. This study aimed to integrate methylation-driven genes and pretreatment prognostic factors and then construct a...

    Authors: Dongsheng He, Shengyin Liao, Lifang Cai, Weiming Huang, Xuehua Xie and Mengxing You

    Citation: BMC Cancer 2021 21:599

    Content type: Research article

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  12. Adjuvant endocrine therapies are known to induce undesirable adverse effects such as vasomotor, vaginal and musculoskeletal symptoms among breast cancer patients. Drugs used in these therapies are often metabo...

    Authors: Carmen W. H. Chan, Bernard M. H. Law, Marques S. N. Ng, Corinna C. Y. Wong, Carissa W. Y. Wong, Morgan Quinley, Jessica M. Orgusyan, Ka Ming Chow and Mary M. Y. Waye

    Citation: BMC Cancer 2021 21:570

    Content type: Research article

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  13. Genetic alterations for epithelial ovarian cancer are insufficiently characterized. Previous studies are limited regarding included histologies, gene numbers, copy number variant (CNV) detection, and interpret...

    Authors: Nina Lapke, Chien-Hung Chen, Ting-Chang Chang, Angel Chao, Yen-Jung Lu, Chyong-Huey Lai, Kien Thiam Tan, Hua-Chien Chen, Hsiao-Yun Lu and Shu-Jen Chen

    Citation: BMC Cancer 2021 21:499

    Content type: Research article

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  14. In oncology, Whole Genome Sequencing (WGS) is not yet widely implemented due to uncertainties such as the required infrastructure and expertise, costs and reimbursements, and unknown pan-cancer clinical utilit...

    Authors: Michiel van de Ven, Martijn J. H. G. Simons, Hendrik Koffijberg, Manuela A. Joore, Maarten J. IJzerman, Valesca P. Retèl and Wim H. van Harten

    Citation: BMC Cancer 2021 21:488

    Content type: Research article

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  15. In our current work, we aimed to investigate the expressions of glypican (GPC) family genes at the mRNA level and assess their prognostic significances in patients with hepatocellular carcinoma (HCC).

    Authors: Jian-Yao Wang, Xiang-Kun Wang, Guang-Zhi Zhu, Xin Zhou, Jun Yao, Xiao-Peng Ma, Bin Wang and Tao Peng

    Citation: BMC Cancer 2021 21:462

    Content type: Research article

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  16. Accumulating evidence has revealed that long non-coding RNAs (lncRNAs) play vital roles in the progression of non-small cell lung cancer (NSCLC). But the relationship between lncRNAs and survival outcome of NS...

    Authors: Yong Yu and Kaiming Ren

    Citation: BMC Cancer 2021 21:457

    Content type: Research article

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  17. Preoperative evaluation of lymph node (LN) state is of pivotal significance for informing therapeutic decisions in gastric cancer (GC) patients. However, there are no non-invasive methods that can be used to p...

    Authors: Xin Zhong, Feichao Xuan, Yun Qian, Junhai Pan, Suihan Wang, Wenchao Chen, Tianyu Lin, Hepan Zhu, Xianfa Wang and Guanyu Wang

    Citation: BMC Cancer 2021 21:455

    Content type: Research article

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  18. 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

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  19. 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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  20. 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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  21. 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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  22. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  41. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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