ArticleNucleic acids research2011
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 66 citations in OpenAlex.
- TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing.Nature communications · 2023Article
- Target-enriched enzymatic methyl sequencing: Flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation.PloS one · 2023Article
- Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.Frontiers in plant science · 2023Review
- Epigenetics of wheat-rust interaction: an update.Planta · 2022Review
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Molecular bases of responses to abiotic stress in trees.Journal of experimental botany · 2020Review
- Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability.Cancers · 2020Article
- Latest techniques to study DNA methylation.Essays in biochemistry · 2019Review
- Detection of somatic epigenetic variation in Norway spruce via targeted bisulfite sequencing.Ecology and evolution · 2018Article
- Topological Characterization of Human and Mouse mInternational journal of genomics · 2018Article
- SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing.Nucleic acids research · 2017Article
- DNA Methylome Analyses Implicate Fallopian Tube Epithelia as the Origin for High-Grade Serous Ovarian Cancer.Molecular cancer research : MCR · 2016Article
- Targeted bisulfite sequencing of the dynamic DNA methylome.Epigenetics & chromatin · 2016Article
- Review
- Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison.Scientific reports · 2015Article
- Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.Nucleic acids research · 2015Article
- Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Article
- Genome-wide assays that identify and quantify modified cytosines in human disease studies.Epigenetics & chromatin · 2015Review
- Advances in the profiling of DNA modifications: cytosine methylation and beyond.Nature reviews. Genetics · 2014Review
Corrections and comments
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Authors and funding
14 authors at 5 institutions in 1 country.
Funding
Abstract
We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21,408 CGIs and more than 15,946 transcriptional regulatory regions. Of the CpGs analyzed, 77-84% fell on or near capture probe sequences; 69-75% fell within CGIs. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5'-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.