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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed -wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
....05) (Fig. 1C,D). The number of genes with altered expression was similar between glioma subtypes despite their different DNA methylation profiles. Among the genes with aberrantly hyper- or hypomethylated CGI/promoters, 223 and 265 were down-regulated (82 in common), and 150 and 140 were up-regulated (44...
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Research: Enhancer methylation dynamics contribute to cancer plasticity and patient mortality
- Rachel E. Bell,
- Tamar Golan,
- Danna Sheinboim,
- Hagar Malcov,
- David Amar,
- Avi Salamon,
- Tamar Liron,
- Sahar Gelfman,
- Yankel Gabet,
- Ron Shamir,
- and Carmit Levy
Genome Res. May 2016 26: 601-611; Published in Advance February 23, 2016, doi:10.1101/gr.197194.115
...an integrative analysis of DNA methylation, RNA-seq, and small RNA-seq profiles from thousands of patients, including 25 diverse primary malignances and seven body sites of metastatic melanoma. We found that enhancers are consistently the most differentially methylated regions (DMR) as cancer progresses from...
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Resource: Dynamic DNA methylation across diverse human cell lines and tissues
- Katherine E. Varley,
- Jason Gertz,
- Kevin M. Bowling,
- Stephanie L. Parker,
- Timothy E. Reddy,
- Florencia Pauli-Behn,
- Marie K. Cross,
- Brian A. Williams,
- John A. Stamatoyannopoulos,
- Gregory E. Crawford,
- Devin M. Absher,
- Barbara J. Wold,
- and Richard M. Myers
Genome Res. March 2013 23: 555-567; Published in Advance January 16, 2013, doi:10.1101/gr.147942.112
...-base resolution DNA methylation profiling on a diverse collection of 82 human cell lines and tissues using reduced representation bisulfite sequencing (RRBS). Analysis integrating RNA-seq and ChIP-seq data illuminates the functional role of this dynamic mark. Loci that are hypermethylated across cancer types...
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Perspective: Translational genomics: The challenge of developing cancer biomarkers
- James D. Brooks
Genome Res. February 2012 22: 183-187; doi:10.1101/gr.124347.111
..., Young SR, McKenney JK, Peehl DM, Brooks JD, Myers RM, Sherlock G Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, Peehl DM, Brooks JD, Myers RM, Sherlock G. 2011. DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res 21...
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Research: Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
- Suhaida A. Selamat,
- Brian S. Chung,
- Luc Girard,
- Wei Zhang,
- Ying Zhang,
- Mihaela Campan,
- Kimberly D. Siegmund,
- Michael N. Koss,
- Jeffrey A. Hagen,
- Wan L. Lam,
- Stephen Lam,
- Adi F. Gazdar,
- and Ite A. Laird-Offringa
Genome Res. July 2012 22: 1197-1211; Published in Advance May 21, 2012, doi:10.1101/gr.132662.111
..., the comparison of lung adenocarcinoma DNAmethylation profiles with those of white blood cells and other types of cancers (e.g., through The Cancer Genome Atlas; http://cancer.nih.gov/), could lead to the development of improved DNA methylation-based blood biomarkers specific for lung adenocarcinoma (Esteller et...
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Method: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
- Mark D. Robinson,
- Clare Stirzaker,
- Aaron L. Statham,
- Marcel W. Coolen,
- Jenny Z. Song,
- Shalima S. Nair,
- Dario Strbenac,
- Terence P. Speed,
- and Susan J. Clark
Genome Res. December 2010 20: 1719-1729; Published in Advance November 2, 2010, doi:10.1101/gr.110601.110
...in Prostate Epithelial Growth Media (PrEGM; Cambrex Bio Science catalog no. CC-3166). Methylation profiling by MeDIP DNA was extracted from the cell lines using the Puragene extraction kit (Gentra Systems). For fully methylated positive control DNA, CpG universal methylated DNA was obtained from Millipore...
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Research: Unique DNA methylome profiles in CpG island methylator phenotype colon cancers
- Yaomin Xu,
- Bo Hu,
- Ae-Jin Choi,
- Banu Gopalan,
- Byron H. Lee,
- Matthew F. Kalady,
- James M. Church,
- and Angela H. Ting
Genome Res. February 2012 22: 283-291; Published in Advance October 11, 2011, doi:10.1101/gr.122788.111
...-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...These authors contributed equally to this review. Corresponding author: christopher.pearson@sickkids.caAbstractExpansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans...
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Research: Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
- Andrew Feber,
- Gareth A. Wilson,
- Lu Zhang,
- Nadege Presneau,
- Bernadine Idowu,
- Thomas A. Down,
- Vardhman K. Rakyan,
- Luke A. Noon,
- Alison C. Lloyd,
- Elia Stupka,
- Vassia Schiza,
- Andrew E. Teschendorff,
- Gary P. Schroth,
- Adrienne Flanagan,
- and Stephan Beck
Genome Res. April 2011 21: 515-524; Published in Advance February 1, 2011, doi:10.1101/gr.109678.110
...,239 46,587 b2mDMRs 41,886 45,230 cDMRs 48,391 53,075 DMRs were defined as a change of >33% in Batman methylation score between samples. Figure 1. Global DNA methylation profiles. (A–T) Global patterns of methylation in unique genomic features from the Ensembl database (Ensembl 52). Shown are the color...
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