+ Site Statistics
References:
54,258,434
Abstracts:
29,560,870
PMIDs:
28,072,757
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

The application of next generation sequencing in DNA methylation analysis



The application of next generation sequencing in DNA methylation analysis



Genes 1(1): 85-101



DNA methylation is a major form of epigenetic modification and plays essential roles in physiology and disease processes. In the human genome, about 80% of cytosines in the 56 million CpG sites are methylated to 5-methylcytosines. The methylation pattern of DNA is highly variable among cells types and developmental stages and influenced by disease processes and genetic factors, which brings considerable theoretical and technological challenges for its comprehensive mapping. Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods will greatly facilitate the profiling of the DNA methylation in the genomes of different species, individuals and cell types under healthy and disease states.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 056239987

Download citation: RISBibTeXText

PMID: 24710012

DOI: 10.3390/genes1010085


Related references

Enrichment-based DNA methylation analysis using next-generation sequencing: sample exclusion, estimating changes in global methylation, and the contribution of replicate lanes. Bmc Genomics 13 Suppl 8: S6-S6, 2013

Whole Genome DNA Methylation Analysis Using Next-Generation Sequencing (BS-seq). Methods in Molecular Biology 1667: 223-287, 2017

Targeted DNA methylation analysis by next-generation sequencing. Journal of Visualized Experiments 96): -, 2016

Next-Generation Sequencing-Based RiboMethSeq  Protocol for Analysis of tRNA 2'-O-Methylation. Biomolecules 7(1), 2017

Erratum to: Whole Genome DNA Methylation Analysis of Brachypodium distachyon Using Next-Generation Sequencing (BS-seq). Methods in Molecular Biology 1667: E1-E1, 2018

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biology 16(): 291-291, 2016

DNA Methylation Analysis by Bisulfite Conversion Coupled to Double Multiplexed Amplicon-Based Next-Generation Sequencing (NGS). Methods in Molecular Biology 1767: 367-382, 2018

Next-Generation Sequencing Approach in Methylation Analysis of HNF1B and GATA4 Genes: Searching for Biomarkers in Ovarian Cancer. International Journal of Molecular Sciences 18(2), 2017

Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing. Tumour Biology 37(10): 13111-13119, 2016

DNA methylation detection at single base resolution using targeted next generation bisulfite sequencing and cross validation using capillary sequencing. Gene 594(2): 259-267, 2016

Methylation analysis using bisulfite genomic sequencing: application to small numbers of intact cells. Biotechniques 22(2): 272-274, 1997

Next-generation Sequencing und hochparallele Genexpressionsanalyse in der klinischen Diagnostik / Next-generation sequencing and massively parallel analysis of gene expression: uses in clinical diagnostics. Laboratoriums Medizin 34(6): 349-356, 2010

Application of next generation sequencing in liquid biopsy analysis. European Journal of Surgical Oncology 42(11): S234-S235, 2016

Single-molecule polymerase chain reaction reduces bias: application to DNA methylation analysis by bisulfite sequencing. Analytical Biochemistry 377(1): 46-54, 2008

Correcting for binomial measurement error in predictors in regression with application to analysis of DNA methylation rates by bisulfite sequencing. Statistics in Medicine 35(22): 3987-4007, 2016