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Ruth Pidsley, Elena Zotenko, Timothy J Peters, Mitchell G Lawrence, Gail P Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J Clark
BACKGROUND: In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform. RESULTS: EPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs...
October 7, 2016: Genome Biology
Jingting Xu, Hong Hu, Yang Dai
BACKGROUND: The identification of enhancers is a challenging task. Various types of epigenetic information including histone modification have been utilized in the construction of enhancer prediction models based on a diverse panel of machine learning schemes. However, DNA methylation profiles generated from the whole genome bisulfite sequencing (WGBS) have not been fully explored for their potential in enhancer prediction despite the fact that low methylated regions (LMRs) have been implied to be distal active regulatory regions...
2016: PloS One
Per Wahlberg, Anders Lundmark, Jessica Nordlund, Stephan Busche, Amanda Raine, Karolina Tandre, Lars Rönnblom, Daniel Sinnett, Erik Forestier, Tomi Pastinen, Gudmar Lönnerholm, Ann-Christine Syvänen
AIM: To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. MATERIALS & METHODS: Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set. RESULTS: Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient...
October 2016: Epigenomics
Haifeng Chen, Andrew D Smith, Ting Chen
: Whole-genome bisulfite sequencing (WGBS) has emerged as the gold-standard technique in genome-scale studies of DNA methylation. Mapping reads from WGBS requires unique considerations that make the process more time-consuming than in other sequencing applications. Typical WGBS data sets contain several hundred million reads, adding to this analysis challenge. We present theWALT tool for mapping WGBS reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup compared with the most efficient methods currently available...
July 27, 2016: Bioinformatics
Saskia Trump, Matthias Bieg, Zuguang Gu, Loreen Thürmann, Tobias Bauer, Mario Bauer, Naveed Ishaque, Stefan Röder, Lei Gu, Gunda Herberth, Christian Lawerenz, Michael Borte, Matthias Schlesner, Christoph Plass, Nicolle Diessl, Markus Eszlinger, Oliver Mücke, Horst-Dietrich Elvers, Dirk K Wissenbach, Martin von Bergen, Carl Herrmann, Dieter Weichenhan, Rosalind J Wright, Irina Lehmann, Roland Eils
Psychological stress during pregnancy increases the risk of childhood wheeze and asthma. However, the transmitting mechanisms remain largely unknown. Since epigenetic alterations have emerged as a link between perturbations in the prenatal environment and an increased disease risk we used whole genome bisulfite sequencing (WGBS) to analyze changes in DNA methylation in mothers and their children related to prenatal psychosocial stress and assessed its role in the development of wheeze in the child. We evaluated genomic regions altered in their methylation level due to maternal stress based of WGBS data of 10 mother-child-pairs...
2016: Scientific Reports
Emanuele Libertini, Simon C Heath, Rifat A Hamoudi, Marta Gut, Michael J Ziller, Agata Czyz, Victor Ruotti, Hendrik G Stunnenberg, Mattia Frontini, Willem H Ouwehand, Alexander Meissner, Ivo G Gut, Stephan Beck
The cost of whole-genome bisulfite sequencing (WGBS) remains a bottleneck for many studies and it is therefore imperative to extract as much information as possible from a given dataset. This is particularly important because even at the recommend 30X coverage for reference methylomes, up to 50% of high-resolution features such as differentially methylated positions (DMPs) cannot be called with current methods as determined by saturation analysis. To address this limitation, we have developed a tool that dynamically segments WGBS methylomes into blocks of comethylation (COMETs) from which lost information can be recovered in the form of differentially methylated COMETs (DMCs)...
2016: Nature Communications
Nicola Prezza, Francesco Vezzi, Max Käller, Alberto Policriti
BACKGROUND: Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of low-methylated genomic regions, and C-to-T mismatches may reflect cytosine unmethylation rather than SNPs or sequencing errors. Further challenges arise both during and after the alignment phase: data structures used by the aligner should be fast and should fit into main memory, and the methylation-caller output should be somehow compressed, due to its significant size...
2016: BMC Bioinformatics
Lindsay L Waite, Benjamin Weaver, Kenneth Day, Xinrui Li, Kevin Roberts, Andrew W Gibson, Jeffrey C Edberg, Robert P Kimberly, Devin M Absher, Hemant K Tiwari
DNA methylation levels vary markedly by cell-type makeup of a sample. Understanding these differences and estimating the cell-type makeup of a sample is an important aspect of studying DNA methylation. DNA from leukocytes in whole blood is simple to obtain and pervasive in research. However, leukocytes contain many distinct cell types and subtypes. We propose a two-stage model that estimates the proportions of six main cell types in whole blood (CD4+ T cells, CD8+ T cells, monocytes, B cells, granulocytes, and natural killer cells) as well as subtypes of T and B cells...
2016: Frontiers in Genetics
Jong-Hun Lee, Sung-Joon Park, Nakai Kenta
BACKGROUND: Whole genome bisulfite sequencing (WGBS) is a high-throughput technique for profiling genome-wide DNA methylation at single nucleotide resolution. However, the applications of WGBS are limited by low accuracy resulting from bisulfite-induced damage on DNA fragments. Although many computer programs have been developed for accurate detecting, most of the programs have barely succeeded in improving either quantity or quality of the methylation results. To improve both, we attempted to develop a novel integration of most widely used bisulfite-read mappers: Bismark, BSMAP, and BS-seeker2...
2015: BMC Genomics
Wen-Wei Liao, Ming-Ren Yen, Evaline Ju, Fei-Man Hsu, Larry Lam, Pao-Yang Chen
BACKGROUND: DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach to measure DNA methylation is bisulfite sequencing (BS-Seq). BS-Seq couples bisulfite conversion of DNA with next-generation sequencing to profile genome-wide DNA methylation at single base resolution. The analysis of BS-Seq data involves the use of customized aligners for mapping bisulfite converted reads and the bioinformatic pipelines for downstream data analysis...
2015: BMC Genomics
Junko Tsuji, Zhiping Weng
Cytosine methylation regulates many biological processes such as gene expression, chromatin structure and chromosome stability. The whole genome bisulfite sequencing (WGBS) technique measures the methylation level at each cytosine throughout the genome. There are an increasing number of publicly available pipelines for analyzing WGBS data, reflecting many choices of read mapping algorithms as well as preprocessing and postprocessing methods. We simulated single-end and paired-end reads based on three experimental data sets, and comprehensively evaluated 192 combinations of three preprocessing, five postprocessing and five widely used read mapping algorithms...
December 1, 2015: Briefings in Bioinformatics
Amanda J Lea, Jenny Tung, Xiang Zhou
Identifying sources of variation in DNA methylation levels is important for understanding gene regulation. Recently, bisulfite sequencing has become a popular tool for investigating DNA methylation levels. However, modeling bisulfite sequencing data is complicated by dramatic variation in coverage across sites and individual samples, and because of the computational challenges of controlling for genetic covariance in count data. To address these challenges, we present a binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation...
November 2015: PLoS Genetics
Takao Yokoyama, Fumihito Miura, Hiromitsu Araki, Kohji Okamura, Takashi Ito
BACKGROUND: Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods include many parameters to be carefully tuned and/or fail to exploit the unsurpassed resolution of the data. Furthermore, there is no simple method that displays the composition of the domains to grasp global trends in each methylome. RESULTS: We propose to use changepoint detection for domain demarcation based on base-resolution methylome data...
2015: BMC Genomics
Karin van Veldhoven, Silvia Polidoro, Laura Baglietto, Gianluca Severi, Carlotta Sacerdote, Salvatore Panico, Amalia Mattiello, Domenico Palli, Giovanna Masala, Vittorio Krogh, Claudia Agnoli, Rosario Tumino, Graziella Frasca, Kirsty Flower, Ed Curry, Nicholas Orr, Katarzyna Tomczyk, Michael E Jones, Alan Ashworth, Anthony Swerdlow, Marc Chadeau-Hyam, Eiliv Lund, Montserrat Garcia-Closas, Torkjel M Sandanger, James M Flanagan, Paolo Vineis
BACKGROUND: Interest in the potential of DNA methylation in peripheral blood as a biomarker of cancer risk is increasing. We aimed to assess whether epigenome-wide DNA methylation measured in peripheral blood samples obtained before onset of the disease is associated with increased risk of breast cancer. We report on three independent prospective nested case-control studies from the European Prospective Investigation into Cancer and Nutrition (EPIC-Italy; n = 162 matched case-control pairs), the Norwegian Women and Cancer study (NOWAC; n = 168 matched pairs), and the Breakthrough Generations Study (BGS; n = 548 matched pairs)...
2015: Clinical Epigenetics
Hao Wu, Tianlei Xu, Hao Feng, Li Chen, Ben Li, Bing Yao, Zhaohui Qin, Peng Jin, Karen N Conneely
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Recent developments in whole genome bisulfite sequencing (WGBS) technology have enabled genome-wide measurements of DNA methylation at single base pair resolution. Many experiments have been conducted to compare DNA methylation profiles under different biological contexts, with the goal of identifying differentially methylated regions (DMRs). Due to the high cost of WGBS experiments, many studies are still conducted without biological replicates...
December 2, 2015: Nucleic Acids Research
Zhen Wang, Xianfeng Li, Yi Jiang, Qianzhi Shao, Qi Liu, BingYu Chen, Dongsheng Huang
DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents an important milestone in the detection of DNA methylation. Characterization of differential methylated regions (DMRs) is fundamental as well for further functional analysis. In this study, we present swDMR ( for the comprehensive analysis of DMRs from whole genome methylation profiles by a sliding window approach...
2015: PloS One
Alexandre How-Kit, Antoine Daunay, Nicolas Mazaleyrat, Florence Busato, Christian Daviaud, Emeline Teyssier, Jean-François Deleuze, Philippe Gallusci, Jörg Tost
Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations...
July 2015: Plant Molecular Biology
Ting Wang, Weihua Guan, Jerome Lin, Nadia Boutaoui, Glorisa Canino, Jianhua Luo, Juan Carlos Celedón, Wei Chen
DNA methylation plays an important role in disease etiology. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a widely used platform in large-scale epidemiologic studies. This platform can efficiently and simultaneously measure methylation levels at ∼480,000 CpG sites in the human genome in multiple study samples. Due to the intrinsic chip design of 2 types of chemistry probes, data normalization or preprocessing is a critical step to consider before data analysis. To date, numerous methods and pipelines have been developed for this purpose, and some studies have been conducted to evaluate different methods...
2015: Epigenetics: Official Journal of the DNA Methylation Society
Sofia Gkountela, Kelvin X Zhang, Tiasha A Shafiq, Wen-Wei Liao, Joseph Hargan-Calvopiña, Pao-Yang Chen, Amander T Clark
Global DNA demethylation in humans is a fundamental process that occurs in pre-implantation embryos and reversion to naive ground state pluripotent stem cells (PSCs). However, the extent of DNA methylation reprogramming in human germline cells is unknown. Here, we performed whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) of human prenatal germline cells from 53 to 137 days of development. We discovered that the transcriptome and methylome of human germline is distinct from both human PSCs and the inner cell mass (ICM) of human blastocysts...
June 4, 2015: Cell
Hong Hu, Jingting Xu, Yang Dai
Recent studies on methylomes obtained from the whole genome bisulfite sequencing (WGBS) indicate that low-methylated regions (LMRs) are related to potential active distal regulatory regions such as enhancers in mammalian genomes. To investigate the potential effect of regulatory elements in LMRs on gene expression, we proposed penalized logistic regression models to predict the directional change of differentially expressed genes using predicted transcription factor binding sites (TFBSs) in LMRs that are distinctive between two cell types...
July 2015: IEEE Journal of Biomedical and Health Informatics
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