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DNA Methylation: Bisulphite Modification and Analysis
Published on: October 21, 2011
Analyzing the cancer methylome through targeted bisulfite sequencing.
Eun-Joon Lee1, Junfeng Luo, James M Wilson
1GHSU Cancer Center, Department of Biochemistry and Molecular Biology, Georgia Health Sciences University, Augusta, GA 30912, USA.
Cancer Letters
|December 4, 2012
Summary
Targeted bisulfite sequencing offers cost-effective DNA methylation analysis for large human cancer studies, overcoming limitations of whole-genome methods. This review covers its methods and bioinformatics tools.
Area of Science:
- Epigenetics and Genomics
- Cancer Research
Background:
- Whole-genome bisulfite sequencing (WGBS) effectively maps DNA methylation but is costly for large human cancer sample analysis.
- Analyzing DNA methylation landscapes is crucial for understanding cancer development and progression.
Purpose of the Study:
- To review targeted bisulfite sequencing methods as alternatives to WGBS for large-scale human cancer epigenomic studies.
- To discuss the characteristics, applications, and bioinformatics tools for targeted bisulfite sequencing.
Main Methods:
- Review of recent advances in targeted bisulfite sequencing technologies.
- Discussion of bioinformatic tools for probe design and sequence analysis in targeted bisulfite sequencing.
Main Results:
- Targeted bisulfite sequencing provides a more economical approach for comprehensive DNA methylation profiling in large cohorts.
- Various targeted bisulfite sequencing strategies offer flexibility for different research needs.
Conclusions:
- Targeted bisulfite sequencing is a viable and scalable alternative for epigenome-wide association studies in human cancers.
- Effective utilization of targeted bisulfite sequencing relies on appropriate bioinformatic tools for probe design and data analysis.
Keywords:
ACBS-seqAMLBSPPCGICOBRACpG islandDMHDNA methylationDREAMESHELPHpaII tiny fragment enrichment by ligation-mediated PCRICFMALDI-TOF MSMBDMCAMDSMIRAMIRA-seqMRE-seqMSPMeDIPMeDIP-seqNGSNext-generation sequencingPCRSHBS-seqSHSTBS-seqTargeted bisulfite sequencingWGBS-seqacute myeloid leukemiaarray capture bisulfite sequencingbisulfite padlock probescombined bisulfite and restriction analysisdifferential methylation hybridizationdigital restriction enzyme analysis of methylationembryonic stemimmunodeficiency, centromere instability and facial anomaliesmatrix-assisted laser desorption/ionization-time of flight mass spectrometrymethyl-binding domainmethylated CpG island amplificationmethylated CpG island recovery assaymethylated CpG island recovery assay sequencingmethylated DNA immunoprecipitationmethylated DNA immunoprecipitation sequencingmethylation sensitive restriction enzyme sequencingmethylation specific PCRmyelodysplastic syndromesnext-generation sequencingpolymerase chain reactionsolution hybrid selectionsolution hybrid selection bisulfite sequencingtargeted bisulfite sequencingwhole genome shotgun bisulfite sequencing
