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Cancer epigenetics and diagnostics

Section information

Section Editors : Carmen Jeronimo and Maria Berdasco

Associate Editors : Nita Ahuja, James Chim (haematological-based cancers only); Jim Davie, James Flanagan, Mario Fraga, Michéle Hoffmann, Bozena Kaminska (gliomas), Gwen Lomberk, Graham K Packham, Arpad Patai (colorectal/GI cancers), Qian Tao, Raul Urrutia, Keishi Yamashita

The development of genome-wide techniques has rapidly improved the comprehensive knowledge of epigenetic alterations in cancer. Currently, a vast number of genes and their associated molecular pathways that show epigenetic differences between normal and tumoral cells have been identified, emphasizing the crucial role of epigenetic factors in cancer etiology and progression.  This section publishes original epigenetic research focused on the identification of epigenetic biomarkers associated with cancer diagnosis or tumor progression. Manuscripts on epigenetic biomarkers leading to a better definition of therapy response are also accepted (pharmacoepigenetics). Submissions on reports from human clinical trials providing insights on the clinical application of epigenetic biomarkers are welcomed.

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  1. Activation of transcription enhancers, especially super-enhancers, is one of the critical epigenetic features of tumorigenesis. However, very few studies have systematically identified the enhancers specific i...

    Authors: Qing-Lan Li, Dan-Ya Wang, Lin-Gao Ju, Jie Yao, Chuan Gao, Pin-Ji Lei, Lian-Yun Li, Xiao-Lu Zhao and Min Wu

    Citation: Clinical Epigenetics 2019 11:48

    Content type: Research

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  2. Epigenetic alternation is a common contributing factor to neoplastic transformation. Although previous studies have reported a cluster of aberrant promoter methylation changes associated with silencing of tumo...

    Authors: Simeng Gu, Shujuan Lin, Ding Ye, Sangni Qian, Danjie Jiang, Xiaocong Zhang, Qilong Li, Jinhua Yang, Xiaojiang Ying, Zhenjun Li, Mengling Tang, Jianbing Wang, Mingjuan Jin and Kun Chen

    Citation: Clinical Epigenetics 2019 11:41

    Content type: Research

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  3. Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct epithelial cell lining. The misdiagnosis of CCA and other biliary diseases may occur due to the similarity of clinical manifestations and blood tests...

    Authors: Wiphawan Wasenang, Ponlatham Chaiyarit, Siriporn Proungvitaya and Temduang Limpaiboon

    Citation: Clinical Epigenetics 2019 11:39

    Content type: Research

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  4. The current prognosis of thymic epithelial tumors (TETs) is according to the World Health Organization (WHO) histologic classification and the Masaoka staging system. These methods of prognosis have certain li...

    Authors: Songlin Li, Yuan Yuan, He Xiao, Jiajia Dai, Yunfei Ye, Qin Zhang, Zhimin Zhang, Yuhan Jiang, Jia Luo, Jing Hu, Chuan Chen and Ge Wang

    Citation: Clinical Epigenetics 2019 11:38

    Content type: Research

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  5. Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) varies between 30 and 40% approximately. To provide further insight into the prediction of pCR,...

    Authors: Begoña Pineda, Angel Diaz-Lagares, José Alejandro Pérez-Fidalgo, Octavio Burgués, Inés González-Barrallo, Ana B. Crujeiras, Juan Sandoval, Manel Esteller, Ana Lluch and Pilar Eroles

    Citation: Clinical Epigenetics 2019 11:33

    Content type: Research

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  6. Reactive oxygen species may be involved in epigenetic gene activation or silencing. We aimed to identify CpG sites, at which DNA methylation is related to urinary 8-isoprostane levels (biomarker of lipid perox...

    Authors: Xīn Gào, Yan Zhang, Barbara Burwinkel, Yang Xuan, Bernd Holleczek, Hermann Brenner and Ben Schöttker

    Citation: Clinical Epigenetics 2019 11:14

    Content type: Research

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  7. Efficient treatments against metastatic melanoma dissemination are still lacking. Here, we report that low-cytotoxic concentrations of 5-aza-2′-deoxycytidine, a DNA demethylating agent, prevent in vitro 3D inv...

    Authors: Cécile Desjobert, Arnaud Carrier, Audrey Delmas, Diego M. Marzese, Antoine Daunay, Florence Busato, Arnaud Pillon, Jörg Tost, Joëlle Riond, Gilles Favre, Chantal Etievant and Paola B. Arimondo

    Citation: Clinical Epigenetics 2019 11:9

    Content type: Research

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  8. Disruptor of telomeric silencing 1-like (DOT1L) is a non-SET domain containing methyltransferase known to catalyze mono-, di-, and tri-methylation of histone 3 on lysine 79 (H3K79me). DOT1L-mediated H3K79me ha...

    Authors: Vijayalakshmi Kari, Sanjay Kumar Raul, Jana Maria Henck, Julia Kitz, Frank Kramer, Robyn Laura Kosinsky, Nadine Übelmesser, Wael Yassin Mansour, Jessica Eggert, Melanie Spitzner, Zeynab Najafova, Holger Bastians, Marian Grade, Jochen Gaedcke, Florian Wegwitz and Steven A. Johnsen

    Citation: Clinical Epigenetics 2019 11:4

    Content type: Research

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  9. Succinate dehydrogenase (SDH)-deficient gastrointestinal stromal tumors (GISTs) constitute a small KIT/PDGFRA-WT GIST subgroup featuring DNA methylation which, although pervasive, appears nevertheless not randoml...

    Authors: Riccardo Ricci, Maurizio Martini, Gloria Ravegnini, Tonia Cenci, Massimo Milione, Paola Lanza, Francesco Pierconti, Donatella Santini, Sabrina Angelini, Alberto Biondi, Fausto Rosa, Sergio Alfieri, Gennaro Clemente, Roberto Persiani, Alessandra Cassano, Maria A. Pantaleo…

    Citation: Clinical Epigenetics 2019 11:2

    Content type: Research

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  10. Spatial and subclonal genetic heterogeneity in multiple myeloma (MM) have been demonstrated by sequencing of plasma cells from multi-focal regions, but studies of spatial epigenetic heterogeneity are scanty. H...

    Authors: Qiumei Yao, Gareth J. Morgan and Chor Sang Chim

    Citation: Clinical Epigenetics 2018 10:158

    Content type: Letter to the Editor

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  11. Different cell types possess different copies of mtDNA to support their specific requirements for cellular metabolism. Cell-specific mtDNA copy numbers are established through cell-specific mtDNA replication d...

    Authors: Xin Sun, Vijesh Vaghjiani, W. Samantha N. Jayasekara, Jason E. Cain and Justin C. St. John

    Citation: Clinical Epigenetics 2018 10:157

    Content type: Research

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  12. The transcription factor Snail2 is a repressor of E-cadherin expression during carcinogenesis; however, the specific mechanisms involved in this process in human colorectal cancer (CRC) remain largely unknown.

    Authors: Yue Hu, Mingrui Dai, Yayuan Zheng, Jiaxin Wu, Bin Yu, Haihong Zhang, Wei Kong, Hui Wu and Xianghui Yu

    Citation: Clinical Epigenetics 2018 10:154

    Content type: Research

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  13. B7 homolog 1 (B7-H1) overexpression on tumor cells is an important mechanism of immune evasion in gastric cancer (GC). Elucidation of the regulation of B7-H1 expression is urgently required to guide B7-H1-targ...

    Authors: Rui Deng, Peng Zhang, Weizhen Liu, Xiangyu Zeng, Xianxiong Ma, Liang Shi, Tao Wang, Yuping Yin, Weilong Chang, Pei Zhang, Guobin Wang and Kaixiong Tao

    Citation: Clinical Epigenetics 2018 10:153

    Content type: Research

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  14. Imprinted genes are regulated by DNA methylation at imprinting-associated differentially methylated regions (iDMRs). Abnormal expression of imprinted genes is implicated in imprinting disorders and tumors. In ...

    Authors: Hidenori Hidaka, Ken Higashimoto, Saori Aoki, Hiroyuki Mishima, Chisa Hayashida, Toshiyuki Maeda, Yasuo Koga, Hitomi Yatsuki, Keiichiro Joh, Hirokazu Noshiro, Ryuichi Iwakiri, Atsushi Kawaguchi, Koh-ichiro Yoshiura, Kazuma Fujimoto and Hidenobu Soejima

    Citation: Clinical Epigenetics 2018 10:150

    Content type: Research

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  15. Prevention of unnecessary biopsies and overtreatment of indolent disease remains a challenge in the management of prostate cancer. Novel non-invasive tests that can identify clinically significant (intermediat...

    Authors: Fang Zhao, Ekaterina Olkhov-Mitsel, Shivani Kamdar, Renu Jeyapala, Julia Garcia, Rachel Hurst, Marcelino Yazbek Hanna, Robert Mills, Alexandra V. Tuzova, Eve O’Reilly, Sarah Kelly, Colin Cooper, Daniel Brewer, Antoinette S. Perry, Jeremy Clark, Neil Fleshner…

    Citation: Clinical Epigenetics 2018 10:147

    Content type: Research

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  16. DNA methylation in miRNA genes has been reported as a mechanism that may cause dysregulation of mature miRNAs and consequently impact the gene expression. This mechanism is largely unstudied in papillary thyro...

    Authors: Isabella Maria Dias Payão Ortiz, Mateus Camargo Barros-Filho, Mariana Bisarro dos Reis, Caroline Moraes Beltrami, Fabio Albuquerque Marchi, Hellen Kuasne, Luísa Matos do Canto, Julia Bette Homem de Mello, Cecilie Abildgaard, Clóvis Antônio Lopes Pinto, Luiz Paulo Kowalski and Silvia Regina Rogatto

    Citation: Clinical Epigenetics 2018 10:144

    Content type: Research

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  17. The introduction of pathology tissue-chromatin immunoprecipitation (PAT-ChIP), a technique allowing chromatin immunoprecipitation (ChIP) from formalin-fixed paraffin-embedded (FFPE) tissues, has extended the a...

    Authors: Stefano Amatori, Giuseppe Persico, Claudio Paolicelli, Roman Hillje, Nora Sahnane, Francesco Corini, Daniela Furlan, Lucilla Luzi, Saverio Minucci, Marco Giorgio, Pier Giuseppe Pelicci and Mirco Fanelli

    Citation: Clinical Epigenetics 2018 10:143

    Content type: Methodology

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  18. Ovarian cancer is the most fatal tumor of the female reproductive system and the fifth leading cause of cancer death among women in the USA. The prognosis is poor due to the lack of biomarkers for treatment op...

    Authors: Wenna Guo, Liucun Zhu, Minghao Yu, Rui Zhu, Qihan Chen and Qiang Wang

    Citation: Clinical Epigenetics 2018 10:142

    Content type: Research

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  19. Altered methylation patterns are driving forces in colorectal carcinogenesis. The serrated adenocarcinoma (SAC) and sporadic colorectal carcinoma showing histological and molecular features of microsatellite i...

    Authors: José García-Solano, María C. Turpin, Daniel Torres-Moreno, Francisco Huertas-López, Anne Tuomisto, Markus J. Mäkinen, Ana Conesa and Pablo Conesa-Zamora

    Citation: Clinical Epigenetics 2018 10:141

    Content type: Research

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    The Data Descriptor to this article has been published in Scientific Data 2019 6:255

  20. Cancer treatments have substantially improved childhood cancer survival but are accompanied by long-term complications, notably chronic inflammatory diseases. We hypothesize that cancer treatments could lead t...

    Authors: Sara Daniel, Vibe Nylander, Lars R. Ingerslev, Ling Zhong, Odile Fabre, Briana Clifford, Karen Johnston, Richard J. Cohn, Romain Barres and David Simar

    Citation: Clinical Epigenetics 2018 10:138

    Content type: Research

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  21. Prostate cancer (PCa) is one of the most common cancers among men worldwide. Current screening methods for PCa display limited sensitivity and specificity, not stratifying for disease aggressiveness. Hence, de...

    Authors: Catarina Moreira-Barbosa, Daniela Barros-Silva, Pedro Costa-Pinheiro, Jorge Torres-Ferreira, Vera Constâncio, Rui Freitas, Jorge Oliveira, Luís Antunes, Rui Henrique and Carmen Jerónimo

    Citation: Clinical Epigenetics 2018 10:132

    Content type: Research

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  22. SUV39H2 (suppressor of variegation 3-9 homolog 2), which introduces H3K9me3 to induce transcriptional repression, has been reported to play critical roles in heterochromatin maintenance, DNA repair, and recent...

    Authors: Yu Zheng, Baihui Li, Jian Wang, Yanjuan Xiong, Kaiyuan Wang, Ying Qi, Houfang Sun, Lei Wu and Lili Yang

    Citation: Clinical Epigenetics 2018 10:129

    Content type: Research

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  23. In this letter, we respond to and discuss the recent publication by Al-Moghrabi et al.: Methylation of BRCA1 and MGMT genes in white blood cells are transmitted from mothers to daughters. We discuss their finding...

    Authors: Per Eystein Lønning and Stian Knappskog

    Citation: Clinical Epigenetics 2018 10:128

    Content type: Letter to the Editor

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  24. DNA methylation is a key epigenetic mark in mammalian organisms that plays key roles in chromatin organization and gene expression. Although DNA methylation in gene promoters is generally associated with gene ...

    Authors: Saigopal Somasundaram, Megan E Forrest, Helen Moinova, Allison Cohen, Vinay Varadan, Thomas LaFramboise, Sanford Markowitz and Ahmad M Khalil

    Citation: Clinical Epigenetics 2018 10:127

    Content type: Research

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  25. In colorectal cancer, CDX2 expression is lost in approximately 20% of cases and associated with poor outcome. Here, we aim to validate the clinical impact of CDX2 and investigate the role of promoter methylati...

    Authors: Janina Graule, Kristin Uth, Elia Fischer, Irene Centeno, José A. Galván, Micha Eichmann, Tilman T. Rau, Rupert Langer, Heather Dawson, Ulrich Nitsche, Peter Traeger, Martin D. Berger, Beat Schnüriger, Marion Hädrich, Peter Studer, Daniel Inderbitzin…

    Citation: Clinical Epigenetics 2018 10:120

    Content type: Research

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  26. The melanoma antigen gene (MAGE) proteins are a group of highly conserved family members that contain a common MAGE homology domain. Type I MAGEs are relevant cancer-testis antigens (CTAs), and originally cons...

    Authors: Yishui Lian, Lingjiao Meng, Pingan Ding and Meixiang Sang

    Citation: Clinical Epigenetics 2018 10:115

    Content type: Review

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  27. Age is one of the most important risk factors for developing breast cancer. However, age-related changes in normal breast tissue that potentially lead to breast cancer are incompletely understood. Quantifying ...

    Authors: Erin W. Hofstatter, Steve Horvath, Disha Dalela, Piyush Gupta, Anees B. Chagpar, Vikram B. Wali, Veerle Bossuyt, Anna Maria Storniolo, Christos Hatzis, Gauri Patwardhan, Marie-Kristin Von Wahlde, Meghan Butler, Lianne Epstein, Karen Stavris, Tracy Sturrock, Alexander Au…

    Citation: Clinical Epigenetics 2018 10:112

    Content type: Research

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  28. Inhibitor of differentiation protein 4 (ID4) is a dominant negative regulator of the basic helix-loop-helix (bHLH) family of transcription factors. During tumorigenesis, ID4 may act as a tumor suppressor or as...

    Authors: Daniela Nasif, Emanuel Campoy, Sergio Laurito, Richard Branham, Guillermo Urrutia, María Roqué and María T. Branham

    Citation: Clinical Epigenetics 2018 10:111

    Content type: Research

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  29. Lung cancer is the leading cause of cancer death worldwide. Recently, epigenetic dysregulation has been known to promote tumor progression and therefore may be a therapeutic target for anticancer therapy. JARI...

    Authors: Kuang-Tai Kuo, Wen-Chien Huang, Oluwaseun Adebayo Bamodu, Wei-Hwa Lee, Chun-Hua Wang, M. Hsiao, Liang-Shun Wang and Chi-Tai Yeh

    Citation: Clinical Epigenetics 2018 10:107

    Content type: Research

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  30. Colorectal cancer (CRC) is the third most commonly diagnosed human malignancy worldwide. Upregulation of inhibitory immune checkpoints by tumor-infiltrating immune cells (TIICs) or their ligands by tumor cells...

    Authors: Varun Sasidharan Nair, Salman M. Toor, Rowaida Z. Taha, Hibah Shaath and Eyad Elkord

    Citation: Clinical Epigenetics 2018 10:104

    Content type: Research

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  31. TET1 is a tumor suppressor gene (TSG) that codes for ten-eleven translocation methyl cytosine dioxygenase1 (TET1) catalyzing the conversion of 5-methylcytosine to 5-hydroxy methyl cytosine as a first step of T...

    Authors: Jiangxia Fan, Yan Zhang, Junhao Mu, Xiaoqian He, Bianfei Shao, Dishu Zhou, Weiyan Peng, Jun Tang, Yu Jiang, Guosheng Ren and Tingxiu Xiang

    Citation: Clinical Epigenetics 2018 10:103

    Content type: Research

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  32. 5-Hydroxymethylcytosine (5hmC) is converted from 5-methylcytosine (5mC) by a group of enzymes termed ten-eleven translocation (TET) family dioxygenases. The loss of 5hmC has been identified as a hallmark of mo...

    Authors: Ding Peng, Guangzhe Ge, Yanqing Gong, Yonghao Zhan, Shiming He, Bao Guan, Yifan Li, Ziying Xu, Han Hao, Zhisong He, Gengyan Xiong, Cuijian Zhang, Yue Shi, Yuanyuan Zhou, Weimin Ci, Xuesong Li…

    Citation: Clinical Epigenetics 2018 10:94

    Content type: Research

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  33. Methylation-associated SOX family genes have been proved to be involved in multiple essential processes during carcinogenesis and act as potential biomarkers for cancer diagnosis, staging, prediction of prognosis...

    Authors: Jing-dong Zhou, Yu-xin Wang, Ting-juan Zhang, Xi-xi Li, Yu Gu, Wei Zhang, Ji-chun Ma, Jiang Lin and Jun Qian

    Citation: Clinical Epigenetics 2018 10:92

    Content type: Research

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  34. Early screening for prostate cancer (PCA) remains controversial because of overdiagnosis and overtreatment of clinically insignificant cancers. Even though a number of diagnostic tests have been developed to i...

    Authors: Igor Brikun, Deborah Nusskern, Andrew Decatus, Eric Harvey, Lin Li and Diha Freije

    Citation: Clinical Epigenetics 2018 10:91

    Content type: Research

    Published on:

  35. Triple-negative breast cancer (TNBC) has been clinically difficult to manage because of tumor aggressiveness, cellular and histological heterogeneity, and molecular mechanisms’ complexity. All this in turn lea...

    Authors: Rubén Rodríguez Bautista, Alette Ortega Gómez, Alfredo Hidalgo Miranda, Alejandro Zentella Dehesa, Cynthia Villarreal-Garza, Federico Ávila-Moreno and Oscar Arrieta

    Citation: Clinical Epigenetics 2018 10:88

    Content type: Review

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    The Correction to this article has been published in Clinical Epigenetics 2018 10:106

  36. High expression of immune checkpoints in tumor microenvironment plays significant roles in inhibiting anti-tumor immunity, which is associated with poor prognosis and cancer progression. Major epigenetic modif...

    Authors: Varun Sasidharan Nair, Haytham El Salhat, Rowaida Z. Taha, Anne John, Bassam R. Ali and Eyad Elkord

    Citation: Clinical Epigenetics 2018 10:78

    Content type: Research

    Published on:

  37. Primary testing for high-risk HPV (hrHPV) is increasingly implemented in cervical cancer screening programs. Many hrHPV-positive women, however, harbor clinically irrelevant infections, demanding additional di...

    Authors: Iris Babion, Barbara C. Snoek, Putri W. Novianti, Annelieke Jaspers, Nienke van Trommel, Daniëlle A. M. Heideman, Chris J. L. M. Meijer, Peter J. F. Snijders, Renske D. M. Steenbergen and Saskia M. Wilting

    Citation: Clinical Epigenetics 2018 10:76

    Content type: Research

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  38. Active demethylation of 5-methyl-2′-deoxycytidine (5-mdC) in DNA occurs by oxidation to 5-(hydroxymethyl)-2′-deoxycytidine (5-hmdC) and further oxidation to 5-formyl-2′-deoxycytidine (5-fdC) and 5-carboxy-2′-d...

    Authors: Tomasz Dziaman, Daniel Gackowski, Jolanta Guz, Kinga Linowiecka, Magdalena Bodnar, Marta Starczak, Ewelina Zarakowska, Martyna Modrzejewska, Anna Szpila, Justyna Szpotan, Maciej Gawronski, Anna Labejszo, Ariel Liebert, Zbigniew Banaszkiewicz, Maria Klopocka, Marek Foksinski…

    Citation: Clinical Epigenetics 2018 10:72

    Content type: Research

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  39. Current standard methods used to detect and monitor bladder cancer (BC) are invasive or have low sensitivity. This study aimed to develop a urine methylation biomarker classifier for BC monitoring and validate...

    Authors: Antoine G. van der Heijden, Lourdes Mengual, Mercedes Ingelmo-Torres, Juan J. Lozano, Cindy C. M. van Rijt-van de Westerlo, Montserrat Baixauli, Bogdan Geavlete, Cristian Moldoveanud, Cosmin Ene, Colin P. Dinney, Bogdan Czerniak, Jack A. Schalken, Lambertus A. L. M. Kiemeney, Maria J. Ribal, J. Alfred Witjes and Antonio Alcaraz

    Citation: Clinical Epigenetics 2018 10:71

    Content type: Research

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  40. Reduced expression of retinoic acid-induced 2 (RAI2) was found in breast cancer. The regulation and function of RAI2 in human colorectal cancer (CRC) remain unclear.

    Authors: Wenji Yan, Kongming Wu, James G. Herman, Xiuduan Xu, Yunsheng Yang, Guanghai Dai and Mingzhou Guo

    Citation: Clinical Epigenetics 2018 10:69

    Content type: Research

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  41. Methylated genes detected in sputum are promise biomarkers for lung cancer. Yet the current PCR technologies for quantification of DNA methylation and diagnostic value of the sputum biomarkers are not sufficie...

    Authors: Yun Su, Hong Bin Fang and Feng Jiang

    Citation: Clinical Epigenetics 2018 10:68

    Content type: Research

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  42. The objective of this study was to discover DNA methylation biomarkers for detecting non-small lung cancer (NSCLC) in bronchial washings and understanding the association between DNA methylation and smoking ce...

    Authors: Sang-Won Um, Yujin Kim, Bo Bin Lee, Dongho Kim, Kyung-Jong Lee, Hong Kwan Kim, Joungho Han, Hojoong Kim, Young Mog Shim and Duk-Hwan Kim

    Citation: Clinical Epigenetics 2018 10:65

    Content type: Research

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  43. Cell-free circulating tumour-derived DNA (ctDNA) can be detected by testing for methylated BCAT1 and IKZF1 DNA, which has proven sensitivity for colorectal cancer (CRC). A prospective correlative biomarker study ...

    Authors: Erin L. Symonds, Susanne K. Pedersen, David H. Murray, Maher Jedi, Susan E. Byrne, Philippa Rabbitt, Rohan T. Baker, Dawn Bastin and Graeme P. Young

    Citation: Clinical Epigenetics 2018 10:63

    Content type: Research

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