Methylation mapping is inherently more complex than genome sequencing, because the methylome exhibits much more variability than the genome. While each of us has only one genome, methylomes vary with age and between tissues, are altered by environmental factors, and show aberrations in diseases. Thus, mapping a person’s methylome at different ages, in different tissue types, and in various disease states is expected to yield valuable information about the mechanisms that lead to aging and disease.
What are the methods for analyzing DNA methylation?
A variety of methods to tackle the complex question of DNA methylation have evolved over time, including bisulfite conversion, digestion with methylation-sensitive restriction enzymes, and antibody- or 5-methylcytosine binding protein–based purification of methylated DNA.
Targeted DNA methylation analysis by bisulfite conversion and amplicon sequencing enables quantitative methylation analysis at single nucleotide resolution for targets of interest. Ion AmpliSeq targeted sequencing technology on the Ion GeneStudio S5 System provides a targeted DNA methylation analysis solution with high accuracy, ease of use, and short time to answer with low DNA input.
Three genome-wide methylation profiling strategies are available for the Ion GeneStudio S5 Series. The size of the target genome and the level of resolution you require will determine which solution will best suit your needs.
| Affinity enrichment | Restriction enzyme | Bisulfite conversion |
| Summary | Antibodies and methylated-CpG binding proteins are used to pull capture and enrich methylated genomic regions for analysis | Methylation sensitive restriction enzymes used to cleave the recognition site leaving either intact methylated or unmethylated sequences for analysis | Bisulfite treatment converts unmodified cytosine to uracil, but methylated cytosine is protected and unchanged |
| Resolution | ~250 bp | Single-base | Single-base |
| CpGs covered | ~23 million CpGs | ~2 million CpGs | >28 million CpGs |
| Pros |
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| Cons |
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Table 1. Comparison of genome-wide approaches for DNA methylation profiling. Adapted from Barros-Silva D, et al. Genes 9:429 (2018).
Video: Dr. David Berman explains why he uses Ion AmpliSeq targeted NGS technology to study DNA methylation in cancer
DNA methylation in cancer research
Step-by-step guide to DNA methylation analysis
The three traditional methylation profiling strategies can be successfully adapted onto the Ion GeneStudio System for a much more complete epigenomic mapping. Depending upon your specific scientific question, you might consider the following approaches:
- Enzymatic genomic partition
Separate the genome into methylated and unmethylated compartments with methylation sensitive or dependent restriction enzymes - Bisulfite conversion
Chemical modification of the unmethylated cytosines in the genome - Enrichment of methylated DNA
Purification of methylated genomic fragments
For help choosing the best strategy for your research, please contact your field application specialist.
MethylCode Bisulfite Conversion Kit
Fast and easy way to convert unmethylated cytosines from a DNA sample into uracils while methylated cytosines remain unchanged. The modified DNA is ideal for PCR amplification for downstream analyses, including restriction endonuclease digestion, sequencing, and microarrays.
Ion AmpliSeq Methylation Panel for Cancer Research
Analyze clinically relevant targets using bisulfite method for identifying specific methylation patterns within a DNA or FFPE DNA sample. With low DNA input, the panel provides high accuracy, ease of use and short time to answer.
Ordering information
Ion AmpliSeq Methylation Panel for Cancer Research – to order the panel:
1. Visit Ion AmpliSeq Designer at ampliseq.com and sign in. If you do not have an account, follow the registration process to create a new account.
2. After signing in, go to Fixed Panels > Community Panels located in the top navigation to find the Ion AmpliSeq Methylation Panel for Cancer Research and place your order.
Complete the project cost request form if you’d like to inquire about ordering an Ion Torrent NGS system.
Run sequence using Ion GeneStudio Series system. Learn more ›
Analyze sequencing output from the Ion AmpliSeq Methylation Panel for Cancer Research using Torrent Suite and Torrent Suite plugin under the name “methylation_analysis”, available from the Themo Fisher Scientific Plugin store.
Additional third-party tools are available for the methylation data analysis workflow. Reach out to your sales representative for more information.
The three traditional methylation profiling strategies can be successfully adapted onto the Ion GeneStudio System for a much more complete epigenomic mapping. Depending upon your specific scientific question, you might consider the following approaches:
- Enzymatic genomic partition
Separate the genome into methylated and unmethylated compartments with methylation sensitive or dependent restriction enzymes - Bisulfite conversion
Chemical modification of the unmethylated cytosines in the genome - Enrichment of methylated DNA
Purification of methylated genomic fragments
For help choosing the best strategy for your research, please contact your field application specialist.
MethylCode Bisulfite Conversion Kit
Fast and easy way to convert unmethylated cytosines from a DNA sample into uracils while methylated cytosines remain unchanged. The modified DNA is ideal for PCR amplification for downstream analyses, including restriction endonuclease digestion, sequencing, and microarrays.
Ion AmpliSeq Methylation Panel for Cancer Research
Analyze clinically relevant targets using bisulfite method for identifying specific methylation patterns within a DNA or FFPE DNA sample. With low DNA input, the panel provides high accuracy, ease of use and short time to answer.
Ordering information
Ion AmpliSeq Methylation Panel for Cancer Research – to order the panel:
1. Visit Ion AmpliSeq Designer at ampliseq.com and sign in. If you do not have an account, follow the registration process to create a new account.
2. After signing in, go to Fixed Panels > Community Panels located in the top navigation to find the Ion AmpliSeq Methylation Panel for Cancer Research and place your order.
Complete the project cost request form if you’d like to inquire about ordering an Ion Torrent NGS system.
Run sequence using Ion GeneStudio Series system. Learn more ›
Analyze sequencing output from the Ion AmpliSeq Methylation Panel for Cancer Research using Torrent Suite and Torrent Suite plugin under the name “methylation_analysis”, available from the Themo Fisher Scientific Plugin store.
Additional third-party tools are available for the methylation data analysis workflow. Reach out to your sales representative for more information.
Application notes
Posters
Publications
- Increased methylation variation in epigenetic domains across cancer typesPublication: Nature Genetics (2011)
- High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq TechnologyPublication: PLoS One, 2011
Step-by-step guide to DNA methylation analysis
The three traditional methylation profiling strategies can be successfully adapted onto the Ion GeneStudio System for a much more complete epigenomic mapping. Depending upon your specific scientific question, you might consider the following approaches:
- Enzymatic genomic partition
Separate the genome into methylated and unmethylated compartments with methylation sensitive or dependent restriction enzymes - Bisulfite conversion
Chemical modification of the unmethylated cytosines in the genome - Enrichment of methylated DNA
Purification of methylated genomic fragments
For help choosing the best strategy for your research, please contact your field application specialist.
MethylCode Bisulfite Conversion Kit
Fast and easy way to convert unmethylated cytosines from a DNA sample into uracils while methylated cytosines remain unchanged. The modified DNA is ideal for PCR amplification for downstream analyses, including restriction endonuclease digestion, sequencing, and microarrays.
Ion AmpliSeq Methylation Panel for Cancer Research
Analyze clinically relevant targets using bisulfite method for identifying specific methylation patterns within a DNA or FFPE DNA sample. With low DNA input, the panel provides high accuracy, ease of use and short time to answer.
Ordering information
Ion AmpliSeq Methylation Panel for Cancer Research – to order the panel:
1. Visit Ion AmpliSeq Designer at ampliseq.com and sign in. If you do not have an account, follow the registration process to create a new account.
2. After signing in, go to Fixed Panels > Community Panels located in the top navigation to find the Ion AmpliSeq Methylation Panel for Cancer Research and place your order.
Complete the project cost request form if you’d like to inquire about ordering an Ion Torrent NGS system.
Run sequence using Ion GeneStudio Series system. Learn more ›
Analyze sequencing output from the Ion AmpliSeq Methylation Panel for Cancer Research using Torrent Suite and Torrent Suite plugin under the name “methylation_analysis”, available from the Themo Fisher Scientific Plugin store.
Additional third-party tools are available for the methylation data analysis workflow. Reach out to your sales representative for more information.
The three traditional methylation profiling strategies can be successfully adapted onto the Ion GeneStudio System for a much more complete epigenomic mapping. Depending upon your specific scientific question, you might consider the following approaches:
- Enzymatic genomic partition
Separate the genome into methylated and unmethylated compartments with methylation sensitive or dependent restriction enzymes - Bisulfite conversion
Chemical modification of the unmethylated cytosines in the genome - Enrichment of methylated DNA
Purification of methylated genomic fragments
For help choosing the best strategy for your research, please contact your field application specialist.
MethylCode Bisulfite Conversion Kit
Fast and easy way to convert unmethylated cytosines from a DNA sample into uracils while methylated cytosines remain unchanged. The modified DNA is ideal for PCR amplification for downstream analyses, including restriction endonuclease digestion, sequencing, and microarrays.
Ion AmpliSeq Methylation Panel for Cancer Research
Analyze clinically relevant targets using bisulfite method for identifying specific methylation patterns within a DNA or FFPE DNA sample. With low DNA input, the panel provides high accuracy, ease of use and short time to answer.
Ordering information
Ion AmpliSeq Methylation Panel for Cancer Research – to order the panel:
1. Visit Ion AmpliSeq Designer at ampliseq.com and sign in. If you do not have an account, follow the registration process to create a new account.
2. After signing in, go to Fixed Panels > Community Panels located in the top navigation to find the Ion AmpliSeq Methylation Panel for Cancer Research and place your order.
Complete the project cost request form if you’d like to inquire about ordering an Ion Torrent NGS system.
Run sequence using Ion GeneStudio Series system. Learn more ›
Analyze sequencing output from the Ion AmpliSeq Methylation Panel for Cancer Research using Torrent Suite and Torrent Suite plugin under the name “methylation_analysis”, available from the Themo Fisher Scientific Plugin store.
Additional third-party tools are available for the methylation data analysis workflow. Reach out to your sales representative for more information.
Application notes
Posters
Publications
- Increased methylation variation in epigenetic domains across cancer typesPublication: Nature Genetics (2011)
- High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq TechnologyPublication: PLoS One, 2011
Resources
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For Research Use Only. Not for use in diagnostic procedures.