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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. Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied env...

    Authors: Baidehi Basu, Joyeeta Chakraborty, Aditi Chandra, Atul Katarkar, Jadav Ritesh Kumar Baldevbhai, Debjit Dhar Chowdhury, Jay Gopal Ray, Keya Chaudhuri and Raghunath Chatterjee

    Citation: Clinical Epigenetics 2017 9:13

    Content type: Research

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  2. Molecular biomarkers assisting risk-group assignment and subsequent treatment stratification are urgently needed for patients with squamous cell cancer of the head and neck region (HNSCC). Aberrant methylation...

    Authors: Verena Sailer, Emily Eva Holmes, Heidrun Gevensleben, Diane Goltz, Freya Dröge, Alina Franzen, Jörn Dietrich, Glen Kristiansen, Friedrich Bootz, Andreas Schröck and Dimo Dietrich

    Citation: Clinical Epigenetics 2017 9:12

    Content type: Research

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  3. Differentially methylated regions (DMRs) within DNA isolated from whole blood can be used to estimate the proportions of circulating leukocyte subtypes. We use the term “immunomethylomics” to describe the appl...

    Authors: John K. Wiencke, Devin C. Koestler, Lucas A. Salas, Joseph L. Wiemels, Ritu P. Roy, Helen M. Hansen, Terri Rice, Lucie S. McCoy, Paige M. Bracci, Annette M. Molinaro, Karl T. Kelsey, Margaret R. Wrensch and Brock C. Christensen

    Citation: Clinical Epigenetics 2017 9:10

    Content type: Research

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  4. Bladder cancer (BC) is one of the most common cancers in the western world and ranks as the most expensive to manage, due to the need for cystoscopic examination. BC shows frequent changes in DNA methylation, ...

    Authors: Andrew Feber, Pawan Dhami, Liqin Dong, Patricia de Winter, Wei Shen Tan, Mónica Martínez-Fernández, Dirk S. Paul, Antony Hynes-Allen, Sheida Rezaee, Pratik Gurung, Simon Rodney, Ahmed Mehmood, Felipe Villacampa, Federico de la Rosa, Charles Jameson, Kar Keung Cheng…

    Citation: Clinical Epigenetics 2017 9:8

    Content type: Research

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  5. Cadherin-like protein 22 (CDH22) is a transmembrane glycoprotein involved in cell-cell adhesion and metastasis. Its role in cancer is controversial because it has been described as being upregulated in colorec...

    Authors: Esperanza Martín-Sánchez, Saioa Mendaza, Ane Ulazia-Garmendia, Iñaki Monreal-Santesteban, Alicia Córdoba, Francisco Vicente-García, Idoia Blanco-Luquin, Susana De La Cruz, Ana Aramendia and David Guerrero-Setas

    Citation: Clinical Epigenetics 2017 9:7

    Content type: Research

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  6. Biliary tract carcinoma (BTC) is a fatal malignancy which aggressiveness contrasts sharply with its relatively mild and late clinical presentation. Novel molecular markers for early diagnosis and precise treat...

    Authors: V. Branchi, P. Schaefer, A. Semaan, A. Kania, P. Lingohr, J. C. Kalff, N. Schäfer, G. Kristiansen, D. Dietrich and H. Matthaei

    Citation: Clinical Epigenetics 2016 8:133

    Content type: Research

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  7. Chronic lymphocytic leukemia (CLL) is the most common hematological malignancy in western countries, characterized by a heterogeneous clinical course. Although genetic studies have identified chromosomal aberr...

    Authors: Michaël Van Damme, Emerence Crompot, Nathalie Meuleman, Marie Maerevoet, Philippe Mineur, Dominique Bron, Laurence Lagneaux and Basile Stamatopoulos

    Citation: Clinical Epigenetics 2016 8:132

    Content type: Research

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  8. Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of thi...

    Authors: Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger and Kuo-Wang Tsai

    Citation: Clinical Epigenetics 2016 8:129

    Content type: Research

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  9. Newly established blood DNA methylation markers that are strongly associated with smoking might open new avenues for lung cancer (LC) screening. We aimed to assess the performance of the top hits from previous...

    Authors: Yan Zhang, Magdeldin Elgizouli, Ben Schöttker, Bernd Holleczek, Alexandra Nieters and Hermann Brenner

    Citation: Clinical Epigenetics 2016 8:127

    Content type: Research

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  10. A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of th...

    Authors: René A. M. Dirks, Hendrik G. Stunnenberg and Hendrik Marks

    Citation: Clinical Epigenetics 2016 8:122

    Content type: Review

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  11. Metastasis is a leading cause of death among cancer patients. In the tumor microenvironment, altered levels of extracellular matrix proteins, such as collagens, can facilitate the first steps of cancer cell me...

    Authors: Pulari U. Thangavelu, Tibor Krenács, Eloise Dray and Pascal H. G. Duijf

    Citation: Clinical Epigenetics 2016 8:120

    Content type: Research

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  12. Pancreatic cancer has a 5-year survival rate of only 5–7%. Difficulties in detecting pancreatic cancer at early stages results in the high mortality and substantiates the need for additional diagnostic tools. ...

    Authors: Stine Dam Henriksen, Poul Henning Madsen, Anders Christian Larsen, Martin Berg Johansen, Asbjørn Mohr Drewes, Inge Søkilde Pedersen, Henrik Krarup and Ole Thorlacius-Ussing

    Citation: Clinical Epigenetics 2016 8:117

    Content type: Research

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  13. The risk of developing Barrett’s esophagus (BE) and/or esophageal adenocarcinoma (EAC) is associated with specific demographic and behavioral factors, including gender, obesity/elevated body mass index (BMI), ...

    Authors: Andrew M. Kaz, Chao-Jen Wong, Vinay Varadan, Joseph E. Willis, Amitabh Chak and William M. Grady

    Citation: Clinical Epigenetics 2016 8:111

    Content type: Research

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    The Erratum to this article has been published in Clinical Epigenetics 2017 9:23

  14. Methyl-CpG-binding domain protein enriched genome-wide sequencing (MBD-Seq) is a robust and powerful method for analyzing methylated CpG-rich regions with complete genome-wide coverage. In chronic lymphocytic ...

    Authors: Santhilal Subhash, Per-Ola Andersson, Subazini Thankaswamy Kosalai, Chandrasekhar Kanduri and Meena Kanduri

    Citation: Clinical Epigenetics 2016 8:106

    Content type: Research

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  15. Identifying the subset of patients with clinically localized prostate cancer (PCa) at the highest risk of recurrence remains challenging, and better prognostic markers are needed. Gleason score is the best pre...

    Authors: Milan S. Geybels, Jonathan L. Wright, Marina Bibikova, Brandy Klotzle, Jian-Bing Fan, Shanshan Zhao, Ziding Feng, Elaine A. Ostrander, Daniel W. Lin, Peter S. Nelson and Janet L. Stanford

    Citation: Clinical Epigenetics 2016 8:97

    Content type: Research

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  16. The Pap smear has remained the foundation for cervical cancer screening for over 70 years. With advancements in molecular diagnostics, primary high-risk human papillomavirus (hrHPV) screening has recently beco...

    Authors: Jane Shen-Gunther, Chiou-Miin Wang, Graham M. Poage, Chun-Lin Lin, Luis Perez, Nancy A. Banks and Tim Hui-Ming Huang

    Citation: Clinical Epigenetics 2016 8:96

    Content type: Research

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  17. The prognostic value of aberrant DNA methylation of cell-free circulating DNA in plasma has not previously been evaluated in diffuse large B cell lymphoma (DLBCL). The aim of this study was to investigate if a...

    Authors: Lasse Sommer Kristensen, Jakob Werner Hansen, Søren Sommer Kristensen, Dorte Tholstrup, Laurine Bente Schram Harsløf, Ole Birger Pedersen, Peter De Nully Brown and Kirsten Grønbæk

    Citation: Clinical Epigenetics 2016 8:95

    Content type: Research

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  18. Alterations in histone modifications are now well known to result in epigenetic heterogeneity in tumor tissues; however, their prognostic value and association with resection margins still remain poorly unders...

    Authors: Shafqat Ali Khan, Ramchandra Amnekar, Bharat Khade, Savio George Barreto, Mukta Ramadwar, Shailesh V. Shrikhande and Sanjay Gupta

    Citation: Clinical Epigenetics 2016 8:88

    Content type: Research

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  19. Epigenetic events mediated by methylation and histone modifications have been associated with the development of metastasis in patients with uveal melanoma. The role of epigenetic events mediated by microRNA (...

    Authors: Pierre L. Triozzi, Susan Achberger, Wayne Aldrich, John W. Crabb, Yogen Saunthararajah and Arun D. Singh

    Citation: Clinical Epigenetics 2016 8:80

    Content type: Research

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  20. DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be f...

    Authors: Annette M. Lim, Nicholas C. Wong, Ruth Pidsley, Elena Zotenko, June Corry, Alexander Dobrovic, Susan J. Clark, Danny Rischin and Benjamin Solomon

    Citation: Clinical Epigenetics 2016 8:74

    Content type: Research

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  21. Human methylome mapping in health and disease states has largely relied on Illumina Human Methylation 450k array (450k array) technology. Accompanying this has been the necessary evolution of analysis pipeline...

    Authors: Emma Cazaly, Russell Thomson, James R. Marthick, Adele F. Holloway, Jac Charlesworth and Joanne L. Dickinson

    Citation: Clinical Epigenetics 2016 8:75

    Content type: Methodology

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  22. Aberrant patterns of DNA methylation are abundant in cancer, and epigenetic pathways are increasingly being targeted in cancer drug treatment. Genetic components of the folate-mediated one-carbon metabolism pa...

    Authors: Julia Krushkal, Yingdong Zhao, Curtis Hose, Anne Monks, James H. Doroshow and Richard Simon

    Citation: Clinical Epigenetics 2016 8:73

    Content type: Research

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  23. Opportunistic screening in hospitals is widely used to effectively reduce the incidence rate of cervical cancer in China and other developing countries. This study aimed to identify clinical risk factor algori...

    Authors: Yu-Ligh Liou, Tao-Lan Zhang, Tian Yan, Ching-Tung Yeh, Ya-Nan Kang, Lanqin Cao, Nayiyuan Wu, Chi-Feng Chang, Huei-Jen Wang, Carolyn Yen, Tang-Yuan Chu, Yi Zhang, Yu Zhang and Honghao Zhou

    Citation: Clinical Epigenetics 2016 8:66

    Content type: Case study

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  24. The quantification of global DNA methylation has been established in epigenetic screening. As more practicable alternatives to the HPLC-based gold standard, the methylation analysis of CpG islands in repeatabl...

    Authors: Claudia Knothe, Hiromi Shiratori, Eduard Resch, Alfred Ultsch, Gerd Geisslinger, Alexandra Doehring and Jörn Lötsch

    Citation: Clinical Epigenetics 2016 8:60

    Content type: Methodology

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  25. The tumor-specific microregional effects of the anticancer agent RRx-001, a novel epigenetic-based radio/chemosensitizer with nitrogen oxide-donating properties in phase II clinical trials, were investigated w...

    Authors: Bryan Oronsky, Jan Scicinski, Pedro Cabrales and Andrew Minchinton

    Citation: Clinical Epigenetics 2016 8:53

    Content type: Research

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  26. Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative neoplasm of childhood whose clinical heterogeneity is only poorly represented by gene sequence alterations. It was previously shown that aberrant...

    Authors: Silvia Fluhr, Melanie Boerries, Hauke Busch, Aikaterini Symeonidi, Tania Witte, Daniel B Lipka, Oliver Mücke, Peter Nöllke, Christopher Felix Krombholz, Charlotte M Niemeyer, Christoph Plass and Christian Flotho

    Citation: Clinical Epigenetics 2016 8:50

    Content type: Short report

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  27. The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) causes resistance of cancer cells to alkylating agents and, therefore, is a well-established predictive marker for high-grade gliomas that are ...

    Authors: Olivier J. Switzeny, Markus Christmann, Mirjam Renovanz, Alf Giese, Clemens Sommer and Bernd Kaina

    Citation: Clinical Epigenetics 2016 8:49

    Content type: Research

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  28. 5-Azacytidine (5-AZA), a DNA methyl transferase inhibitor, is a clinically used epigenetic drug for cancer therapy. Recently, we have shown that 5-AZA upregulates ten-eleven translocation (TET) protein express...

    Authors: Sahar Olsadat Sajadian, Chaturvedula Tripura, Fazel Sahraneshin Samani, Marc Ruoss, Steven Dooley, Hossein Baharvand and Andreas K. Nussler

    Citation: Clinical Epigenetics 2016 8:46

    Content type: Research

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  29. Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylati...

    Authors: Muriel X. G. Draht, Kim M. Smits, Valérie Jooste, Benjamin Tournier, Martijn Vervoort, Chantal Ramaekers, Caroline Chapusot, Matty P. Weijenberg, Manon van Engeland and Veerle Melotte

    Citation: Clinical Epigenetics 2016 8:44

    Content type: Research

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  30. Related to genetic alteration, frequent promoter hypermethylation is also a contributing factor in the development of human cancers. Recently, we discovered numerous novel genes that were aberrantly methylated...

    Authors: Yu-Lueng Shih, Chih-Chi Kuo, Ming-De Yan, Ya-Wen Lin, Chung-Bao Hsieh and Tsai-Yuan Hsieh

    Citation: Clinical Epigenetics 2016 8:41

    Content type: Research

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  31. In the January 2016 issue of Clinical Epigenetics, Quiñonez-Silva et al. (Clin Epigenetics 8:1, 2016) described a possible constitutional epimutation of the RB1 gene as a cause of hereditary predisposition to ret...

    Authors: Mathew A. Sloane, Robyn L. Ward and Luke B. Hesson

    Citation: Clinical Epigenetics 2016 8:39

    Content type: Letter to the Editor

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  32. Oncogene overexpression in primary cells often triggers the induction of a cellular safeguard response promoting senescence or apoptosis. Secondary cooperating genetic events are generally required for oncogen...

    Authors: Olga Aprelikova, Kenny Chen, Lara H. El Touny, Constance Brignatz-Guittard, Justin Han, Tinghu Qiu, Howard H. Yang, Maxwell P. Lee, Min Zhu and Jeffrey E. Green

    Citation: Clinical Epigenetics 2016 8:38

    Content type: Research

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  33. Low methylation status of LINE-1 in tumors is associated with poor survival in patients with colon cancer. Eastern Cooperative Oncology Group performance status (ECOG-PS) is a method to assess the functional stat...

    Authors: Duo Chen, Xianyu Wen, Young Seok Song, Ye-Young Rhee, Tae Hun Lee, Nam Yun Cho, Sae-Won Han, Tae-You Kim and Gyeong Hoon Kang

    Citation: Clinical Epigenetics 2016 8:36

    Content type: Research

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  34. Circulating hypermethylated RASSF1A could be a novel and potential useful marker for monitoring patients with metastatic breast cancer. Technical obstacles include fragmentation of the circulating DNA, fluctuatio...

    Authors: Søren Kristiansen, Dorte Nielsen and György Sölétormos

    Citation: Clinical Epigenetics 2016 8:35

    Content type: Methodology

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  35. Epigenetic regulation has emerged to be the critical steps for tumorigenesis and metastasis. Multiple histone methyltransferase and demethylase have been implicated as tumor suppressors or oncogenes recently. ...

    Authors: Quan-Yi Zhao, Pin-Ji Lei, Xiaoran Zhang, Jun-Yi Zheng, Hui-Yi Wang, Jiao Zhao, Yi-Ming Li, Mei Ye, Lianyun Li, Gang Wei and Min Wu

    Citation: Clinical Epigenetics 2016 8:34

    Content type: Research

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  36. An abundant class of intronic microRNAs (miRNAs) undergoes atypical Drosha-independent biogenesis in which the spliceosome governs the excision of hairpin miRNA precursors, called mirtrons. Although nearly 500...

    Authors: Stasė Butkytė, Laurynas Čiupas, Eglė Jakubauskienė, Laurynas Vilys, Paulius Mocevicius, Arvydas Kanopka and Giedrius Vilkaitis

    Citation: Clinical Epigenetics 2016 8:33

    Content type: Research

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  37. Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethy...

    Authors: Shivani N. Kamdar, Linh T. Ho, Ken J. Kron, Ruth Isserlin, Theodorus van der Kwast, Alexandre R. Zlotta, Neil E. Fleshner, Gary Bader and Bharati Bapat

    Citation: Clinical Epigenetics 2016 8:32

    Content type: Research

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  38. Primary hyperparathyroidism is characterized by enlarged parathyroid glands due to an adenoma (80–85 %) or multiglandular disease (~15 %) causing hypersecretion of parathyroid hormone (PTH) and generally hyper...

    Authors: Elham Barazeghi, Anthony J. Gill, Stan Sidhu, Olov Norlén, Roberto Dina, F. Fausto Palazzo, Per Hellman, Peter Stålberg and Gunnar Westin

    Citation: Clinical Epigenetics 2016 8:31

    Content type: Research

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  39. Assessment of DNA promoter methylation markers in cervical scrapings for the detection of cervical intraepithelial neoplasia (CIN) and cervical cancer is feasible, but finding methylation markers with both hig...

    Authors: A. Boers, R. Wang, R. W. van Leeuwen, H. G. Klip, G. H. de Bock, H. Hollema, W. van Criekinge, T. de Meyer, S. Denil, A. G J. van der Zee, E. Schuuring and G. B. A. Wisman

    Citation: Clinical Epigenetics 2016 8:29

    Content type: Research

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  40. A long-term analysis by the Early Breast Cancer Trialist Group (EBCTG) revealed a strong correlation between local control and cancer-specific mortality. MicroRNAs (miRs), short (20–25 nucleotides) non-coding ...

    Authors: Franz Zehentmayr, Cornelia Hauser-Kronberger, Barbara Zellinger, Falk Hlubek, Claudia Schuster, Ulrich Bodenhofer, Gerd Fastner, Heinz Deutschmann, Philipp Steininger, Roland Reitsamer, Thorsten Fischer and Felix Sedlmayer

    Citation: Clinical Epigenetics 2016 8:28

    Content type: Research

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  41. Methylation-sensitive restriction enzymes—polymerase chain reaction (MSRE-PCR) has been used in epigenetic research to identify genome-wide and gene-specific DNA methylation. Currently, epigenome-wide discover...

    Authors: Ram Vinay Pandey, Walter Pulverer, Rainer Kallmeyer, Gabriel Beikircher, Stephan Pabinger, Albert Kriegner and Andreas Weinhäusel

    Citation: Clinical Epigenetics 2016 8:26

    Content type: Methodology

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    The Erratum to this article has been published in Clinical Epigenetics 2016 8:84

  42. Contradictory results were reported for the prognostic role of CpG island methylator phenotype (CIMP) among colorectal cancer (CRC) patients. Differences in the definitions of CIMP were the most common explana...

    Authors: Min Jia, Xu Gao, Yan Zhang, Michael Hoffmeister and Hermann Brenner

    Citation: Clinical Epigenetics 2016 8:25

    Content type: Review

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  43. Cytology remains the gold standard for the detection of malignant cells in ascites. However, its sensitivity is limited. The aim of this study was to evaluate DNA methylation biomarkers for the differential di...

    Authors: Maria Jung, Svenja Pützer, Heidrun Gevensleben, Sebastian Meller, Glen Kristiansen and Dimo Dietrich

    Citation: Clinical Epigenetics 2016 8:24

    Content type: Research

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  44. We examined whether differences in tumor DNA methylation were associated with more aggressive hormone receptor-negative breast cancer in an ethnically diverse group of patients in the Breast Cancer Care in Chi...

    Authors: Elizaveta V. Benevolenskaya, Abul B. M. M. K. Islam, Habibul Ahsan, Muhammad G. Kibriya, Farzana Jasmine, Ben Wolff, Umaima Al-Alem, Elizabeth Wiley, Andre Kajdacsy-Balla, Virgilia Macias and Garth H. Rauscher

    Citation: Clinical Epigenetics 2016 8:17

    Content type: Research

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  45. While localized prostate cancer (PCa) can be effectively cured, metastatic disease inevitably progresses to a lethal state called castration-resistant prostate cancer (CRPC). Emerging evidence suggests that ab...

    Authors: Pier-Luc Clermont, Francesco Crea, Yan Ting Chiang, Dong Lin, Amy Zhang, James Z. L. Wang, Abhijit Parolia, Rebecca Wu, Hui Xue, Yuwei Wang, Jiarui Ding, Kelsie L. Thu, Wan L. Lam, Sohrab P. Shah, Colin C. Collins, Yuzhuo Wang…

    Citation: Clinical Epigenetics 2016 8:16

    Content type: Research

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  46. 5-Hydroxymethylcytosine (5hmC) is lost in multiple human cancers, including colorectal cancer (CRC). Decreased ten-eleven translocation 1 (TET1) messenger RNA (mRNA), but not other two TET family members, has ...

    Authors: Yuji Huang, Guanghui Wang, Zhonglin Liang, Yili Yang, Long Cui and Chen-Ying Liu

    Citation: Clinical Epigenetics 2016 8:9

    Content type: Letter to the Editor

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  47. A key focus in cancer research is the discovery of biomarkers that accurately diagnose early lesions in non-invasive tissues. Several studies have identified malignancy-associated DNA methylation changes in bl...

    Authors: Leonie Roos, Jenny van Dongen, Christopher G. Bell, Andrea Burri, Panos Deloukas, Dorret I. Boomsma, Tim D. Spector and Jordana T. Bell

    Citation: Clinical Epigenetics 2016 8:7

    Content type: Research

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