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Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement

Karen Sugden, Eilis J. Hannon, Louise Arseneault, Daniel W. Belsky, David L. Corcoran, Helen L. Fisher, Renate M. Houts, Radhika Kandaswamy, Terrie E. Moffitt, Richie Poulton, Joseph A. Prinz, Line J.H. Rasmussen (+4 others)
2020 Patterns  
The most utilized method of assessing DNA methylation uses BeadChips, generating an epigenome-wide "snapshot" of >450,000 observations (probe measurements) per assay.  ...  However, the reliability of each of these measurements is not equal, and little consideration is paid to consequences for research.  ...  ACKNOWLEDGMENTS DECLARATION OF INTERESTS The authors declare no competing interests.  ... 
doi:10.1016/j.patter.2020.100014 pmid:33205092 pmcid:PMC7660408 fatcat:yh2bxdyp35gztmh7zbpxx7xtse

Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping

Tslil Gabrieli, Yael Michaeli, Sigal Avraham, Dmitry Torchinsky, Sapir Margalit, Leonie Schütz, Matyas Juhasz, Ceyda Coruh, Nissim Arbib, Zhaohui Sunny Zhou, Julie A Law, Elmar Weinhold (+1 others)
2022 Nucleic Acids Research  
A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs.  ...  DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification.  ...  ACKNOWLEDGEMENTS We thank Kerstin Glensk for the preparation of eM.SssI. We thank Joseph R. Ecker and Florian Jupe for providing A. thaliana DNA samples for initial experiments.  ... 
doi:10.1093/nar/gkac460 pmid:35657088 fatcat:f33n7z2nmzhpvoln4trevf4txm

DNA methylation pattern changes upon long-term culture and aging of human mesenchymal stromal cells

Simone Bork, Stefan Pfister, Hendrik Witt, Patrick Horn, Bernhard Korn, Anthony D. Ho, Wolfgang Wagner
2010 Aging Cell  
In this study, we have analyzed DNA methylation changes upon long-term culture of MSC by using the Human-Methylation27 BeadChip microarray assessing 27 578 unique CpG sites.  ...  Overall, methylation patterns were maintained throughout both long-term culture and aging but highly significant differences were observed at specific CpG sites.  ...  Acknowledgments We want to thank Anke Diehlmann (Department of Medicine V, Heidelberg, Germany) for assistance in MSC expansion, Juliane Rieber (DKFZ, Heidelberg, Germany) for help with DNA isolation,  ... 
doi:10.1111/j.1474-9726.2009.00535.x pmid:19895632 pmcid:PMC2814091 fatcat:ewyc3voiobhqxayc7dmdie7iai

A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data

Saurav Mallik, Soumita Seth, Tapas Bhadra, Zhongming Zhao
2020 Genes  
methylation through integrating DNA methylation data and corresponding TCGA gene expression data.  ...  In summary, our proposed framework that integrated linear regression, differential expression, deep learning provides a robust approach to better interpret DNA methylation analysis and gene expression  ...  The functions under the 'ENmix package are used to remove unwanted experimental noise and to improve accuracy and reproducibility of methylation measures.  ... 
doi:10.3390/genes11080931 pmid:32806782 fatcat:qehsy5q3tjbchjryvemozt7ffu

Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells

Alan Barnicle, Cathal Seoighe, Aaron Golden, John M. Greally, Laurence J. Egan
2016 Physiological Genomics  
Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells.  ...  Using purified epithelial cells and whole biopsies (n ϭ 19) from human subjects, we generated epigenome-wide DNA methylation data (using the HELP-tagging assay), comparing the methylation signatures of  ...  Sample processing for DNA methylation validation was performed by this group under the grant number P30CA-016056.  ... 
doi:10.1152/physiolgenomics.00046.2015 pmid:26812987 pmcid:PMC4824152 fatcat:rh64nfcp4fc53g5vxcm4r2tjqi

Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas

Carolyn E. Banister, Devin C. Koestler, Matthew A. Maccani, James F. Padbury, E. Andres Houseman, Carmen J. Marsit
2011 Epigenetics  
Acknowledgments The authors would like to thank Keila Vega, Joyce Lee and Gilda Ferro for collecting the placenta samples and patient information, and to Andrew Rainey and Alison Migliori for processing  ...  the samples in the laboratory.  ...  Our work demonstrates that patterns of DNA methylation in human placenta are reliably and significantly associated with infant growth and serve as a proof of principle that methylation status in the human  ... 
doi:10.4161/epi.6.7.16079 pmid:21758004 pmcid:PMC3154432 fatcat:22ijn6j3cjdq5av2ej5xfnprfu

Detection of CRISPR-mediated genome modifications through altered methylation patterns of CpG islands

M. Heath Farris, Pamela A. Texter, Agustin A. Mora, Michael V. Wiles, Ellen F. Mac Garrigle, Sybil A. Klaus, Kristine Rosfjord
2020 BMC Genomics  
With characterization of CpG methylation patterns using whole genome bisulfite sequencing, these CGI methylation disruptions trace the insertion of the donor DNA during the genomic edit.  ...  These insertions mediated by homology-directed recombination disrupt the generational methylation pattern stability of the edited CGI within the cells and their cellular lineage within the animal strain  ...  Results of the analysis provided a basis for determining targeted ranges for evaluating clustered CpG methylation variance across genomes.  ... 
doi:10.1186/s12864-020-07233-2 pmid:33267773 fatcat:74dpq3paivgwlhcw4jovmndwjy

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

Vanessa Lakis, APGI, Rita T. Lawlor, Felicity Newell, Ann-Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev (+26 others)
2021 Communications Biology  
AbstractHere we report the DNA methylation profile of 84 sporadic pancreatic neuroendocrine tumors (PanNETs) with associated clinical and genomic information.  ...  The T2 subgroup contained tumors with mutations in ATRX, DAXX and MEN1 and recurrent patterns of chromosomal losses in half of the genome with no association between regions with recurrent loss and methylation  ...  Acknowledgements We thank all patients and funding below that made this study possible.  ... 
doi:10.1038/s42003-020-01469-0 pmid:33536587 fatcat:kmxnwtbgfnaqnhbfrof44saw7y

DNA methylation patterns of replicative senescence are strand-specific and reflect changes in chromatin conformation [article]

Julia Franzen, Theodoros Georgomanolis, Anton Selich, Reinhard Stöger, Lilija Brant, Eduardo Fernandez-Rebollo, Clara Grezella, Alina Ostrowska, Matthias Begemann, Björn Rath, Anthony D. Ho, Michael Rothe (+3 others)
2018 bioRxiv   pre-print
AbstractReplicative senescence of cells in culture is associated with highly reproducible DNA methylation (DNAm) changes at specific sites in the genome.  ...  Notably, BBA-seq of hairpin-linked DNA molecules demonstrated that many CpG dyads are methylated only on the forward or the reverse strand.  ...  Acknowledgements We would like to thank all donors for their valuable support of our research.  ... 
doi:10.1101/445114 fatcat:nr2xpyha5zdgnksis7tf2r4hv4

Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

Suhua Feng, Zhenhui Zhong, Ming Wang, Steven E. Jacobsen
2020 Epigenetics & Chromatin  
Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation  ...  Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide  ...  High-throughput sequencing was performed at the UCLA Broad Stem Cell Research Center BioSequencing Core Facility.  ... 
doi:10.1186/s13072-020-00361-9 pmid:33028374 pmcid:PMC7542392 fatcat:tlajyrdtx5fgnnhxqzf3vf5bse

Prognostic Significance and Molecular Associations of Tumor Growth Pattern in Colorectal Cancer

Teppei Morikawa, Aya Kuchiba, Zhi Rong Qian, Mari Mino-Kenudson, Jason L. Hornick, Mai Yamauchi, Yu Imamura, Xiaoyun Liao, Reiko Nishihara, Jeffrey A. Meyerhardt, Charles S. Fuchs, Shuji Ogino
2011 Annals of Surgical Oncology  
However, little is known on prognostic significance of tumor growth pattern, independent of tumoral molecular alterations and other histological features.  ...  Background-Infiltrative growth pattern at the tumor margin has been associated with shorter patient survival.  ...  Acknowledgments We would like to thank the participants and staff of the Nurses' Health Study and the Health Professionals  ... 
doi:10.1245/s10434-011-2174-5 pmid:22189472 pmcid:PMC3321113 fatcat:vyaza3o475g2powwevm66rtodu

Prediction of the prognosis based on chromosomal instability-related DNA methylation patterns of ELOVL2 and UBAC2 in papillary thyroid carcinomas

Jun Han, Meijun Chen, Qingxiao Fang, Yanqing Zhang, Yihan Wang, Jamaspishvili Esma, Hong Qiao
2019 Molecular Therapy: Nucleic Acids  
DNA methylation plays an important role in the regulation of gene expression and CIN.  ...  With the use of the log-rank test, univariate Cox regression analyses, and the Kaplan-Meier method, DNA methylation patterns of UBAC2 and ELOVL2, highly correlated with CIN, provided potential prognostic  ...  be faithfully reproduced in the progeny of affected cells, and the methylation will then be propagated during clonal selection during the development of tumors. 29 DNA methylations are therefore more  ... 
doi:10.1016/j.omtn.2019.09.027 pmid:31698312 pmcid:PMC6906861 fatcat:65y2ws7wmfavlcztb4xvlkb7zy

DNA methylome analysis reveals distinct epigenetic patterns of ascending aortic dissection and bicuspid aortic valve

Sun Pan, Hao Lai, Yiru Shen, Charles Breeze, Stephan Beck, Tao Hong, Chunsheng Wang, Andrew E. Teschendorff
2017 Cardiovascular Research  
Thus, measuring the DNA methylome offers the opportunity to identify novel disease biomarkers and novel insights into disease mechanisms.  ...  In the case of AD, integrative DNA methylation gene expression analysis reveals that AD is characterized by a dedifferentiated smooth muscle cell phenotype.  ...  In our study, the integration of DNA methylation and mRNA expression in AD revealed downregulation of smooth muscle genes and targets of smooth muscle differentiation factors (e.g.  ... 
doi:10.1093/cvr/cvx050 pmid:28444195 fatcat:bwf5ri5m2ncchfkcsgijf6geje

Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis

Pengfei Liu, Weidong Tian
2020 PeerJ  
DNA methylation (DNAm) with the stability and reversibility often occurs in the early stage of tumorigenesis.  ...  The molecular biological function of genes with abnormal methylation were significantly associated with glycolysis/gluconeogenesis and signal transduction.  ...  ACKNOWLEDGEMENTS The authors appreciate the assistance of The Cancer Genome Atlas (TCGA), Gene Expression Omnibus database (GEO) and European Bioinformatics Institute (EMBL-EBI) for providing data.  ... 
doi:10.7717/peerj.9654 pmid:32832275 pmcid:PMC7409785 fatcat:oxy2dydvgre6zhy4zl7lkayigq

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

Katherine A. Hoadley, Christina Yau, Toshinori Hinoue, Denise M. Wolf, Alexander J. Lazar, Esther Drill, Ronglai Shen, Alison M. Taylor, Andrew D. Cherniack, Vésteinn Thorsson, Rehan Akbani, Reanne Bowlby (+736 others)
2018 Cell  
Highlights d An integrative data clustering method is applied to reclassify human tumors d Cell-of-origin influences, but does not fully determine, tumor classification d Immune features and copy-number  ...  aberrations define the most mixed tumor groups d Multi-cancer groups reveal new features with potential clinical utility  ...  DNA methylation patterns.  ... 
doi:10.1016/j.cell.2018.03.022 pmid:29625048 pmcid:PMC5957518 fatcat:mb7h6nnkordonoalcs754havi4
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