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Brief Report

Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

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Pages 829-833 | Received 12 Mar 2014, Accepted 04 Apr 2014, Published online: 14 Apr 2014

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Aleix Noguera-Castells, Carlos A. García-Prieto, Damiana Álvarez-Errico & Manel Esteller. (2023) Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome. Epigenetics 18:1.
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Basharat Bhat & Gregory T. Jones. 2022. Chromatin. Chromatin 23 45 .
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Teresia Kling & Helena Carén. 2019. Tumor Profiling. Tumor Profiling 205 217 .
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Byeong Yun, Jingshu Guo & Robert Turesky. (2018) Formalin-Fixed Paraffin-Embedded Tissues—An Untapped Biospecimen for Biomonitoring DNA Adducts by Mass Spectrometry. Toxics 6:2, pages 30.
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Chuan Jiao, Chunling Zhang, Rujia Dai, Yan Xia, Kangli Wang, Gina Giase, Chao Chen & Chunyu Liu. (2018) Positional effects revealed in Illumina methylation array and the impact on analysis. Epigenomics 10:5, pages 643-659.
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Crossref
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Teresia Kling, Anna Wenger, Stephan Beck & Helena Carén. (2017) Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours. Clinical Epigenetics 9:1.
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Sebastián Moran, Anna Martinez-Cardús, Stergios Boussios & Manel Esteller. (2017) Precision medicine based on epigenomics: the paradigm of carcinoma of unknown primary. Nature Reviews Clinical Oncology 14:11, pages 682-694.
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Crossref
Sebastian Moran, Anna Martínez-Cardús & Manel Esteller. (2017) Journal club: epigenetic profiling to classify cancer of unknown primary – Authors' reply. The Lancet Oncology 18:3, pages e131.
Crossref
Allyson C. Espinal, Dan Wang, Li Yan, Song Liu, Li Tang, Qiang Hu, Carl D. Morrison, Christine B. Ambrosone, Michael J. Higgins & Lara E. Sucheston-Campbell. (2017) A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors. Oncotarget 8:9, pages 14821-14829.
Crossref
Pan Zhang, Brian D. Lehmann, Yu Shyr & Yan Guo. (2017) The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. International Journal of Genomics 2017, pages 1-9.
Crossref
Sebastian Moran. 2017. Neuroepigenomics in Aging and Disease. Neuroepigenomics in Aging and Disease 477 488 .
Sebastian Moran, Anna Martínez-Cardús, Sergi Sayols, Eva Musulén, Carme Balañá, Anna Estival-Gonzalez, Cátia Moutinho, Holger Heyn, Angel Diaz-Lagares, Manuel Castro de Moura, Giulia M Stella, Paolo M Comoglio, Maria Ruiz-Miró, Xavier Matias-Guiu, Roberto Pazo-Cid, Antonio Antón, Rafael Lopez-Lopez, Gemma Soler, Federico Longo, Isabel Guerra, Sara Fernandez, Yassen Assenov, Christoph Plass, Rafael Morales, Joan Carles, David Bowtell, Linda Mileshkin, Daniela Sia, Richard Tothill, Josep Tabernero, Josep M Llovet & Manel Esteller. (2016) Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis. The Lancet Oncology 17:10, pages 1386-1395.
Crossref
Giorgio Stanta, Stephan Wenzel Jahn, Serena Bonin & Gerald Hoefler. (2016) Tumour heterogeneity: principles and practical consequences. Virchows Archiv 469:4, pages 371-384.
Crossref
Sebastian Moran, Carles Arribas & Manel Esteller. (2016) Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics 8:3, pages 389-399.
Crossref
R.A. Hlady & K.D. Robertson. 2016. Chromatin Signaling and Diseases. Chromatin Signaling and Diseases 403 421 .
Eneda Toska & F. Javier Carmona Sanz. 2016. Epigenetic Biomarkers and Diagnostics. Epigenetic Biomarkers and Diagnostics 119 135 .
Marina Bibikova. 2016. Epigenomics in Health and Disease. Epigenomics in Health and Disease 19 46 .
Jörg Tost. 2016. DNA Methyltransferases - Role and Function. DNA Methyltransferases - Role and Function 343 430 .
Kevin C. Johnson, Devin C. Koestler, Thomas Fleischer, Panpan Chen, Erik G. Jenson, Jonathan D. Marotti, Tracy Onega, Vessela N. Kristensen & Brock C. Christensen. (2015) DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer. Clinical Epigenetics 7:1.
Crossref
Ee Ming Wong, JiHoon E. Joo, Catriona A. McLean, Laura Baglietto, Dallas R. English, Gianluca Severi, John L. Hopper, Roger L. Milne, Liesel M. FitzGerald, Graham G. Giles & Melissa C. Southey. (2015) Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies. BMC Research Notes 8:1.
Crossref
Yuanyuan Zhang, Junying Zhang, Zhaowen Liu, Yajun Liu & Shouheng Tuo. (2015) A network-based approach to identify disease-associated gene modules through integrating DNA methylation and gene expression. Biochemical and Biophysical Research Communications 465:3, pages 437-442.
Crossref
Zhifu Sun, Julie Cunningham, Susan Slager & Jean-Pierre Kocher. (2015) Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis. Epigenomics 7:5, pages 813-828.
Crossref
Tim C de Ruijter, Joep PJ de Hoon, Jeroen Slaats, Bart de Vries, Marjolein JFW Janssen, Tom van Wezel, Maureen JB Aarts, Manon van Engeland, Vivianne CG Tjan-Heijnen, Leander Van Neste & Jürgen Veeck. (2015) Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays. Laboratory Investigation 95:7, pages 833-842.
Crossref
Sarah R. Greytak, Kelly B. Engel, B. Paige Bass & Helen M. Moore. (2015) Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Research 75:8, pages 1541-1547.
Crossref
Gitte Brinch Andersen, Henrik Hager, Lise Lotte Hansen & Jörg Tost. (2015) Improved reproducibility in genome-wide DNA methylation analysis for PAXgene-fixed samples compared with restored formalin-fixed and paraffin-embedded DNA. Analytical Biochemistry 468, pages 50-58.
Crossref
Alicia K. Smith, Varun Kilaru, Torsten Klengel, Kristina B. Mercer, Bekh Bradley, Karen N. Conneely, Kerry J. Ressler & Elisabeth B. Binder. (2015) DNA extracted from saliva for methylation studies of psychiatric traits: Evidence tissue specificity and relatedness to brain. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 168:1, pages 36-44.
Crossref