Comprehensive exploration of the methylome

NGS enhances epigenetic studies with high coverage density and flexibility

Methylation Sequencing

Cytosine methylation can significantly modify temporal and spatial gene expression and chromatin remodeling. Leveraging the power of next-generation sequencing (NGS), both genome-wide analysis and targeted approaches can provide insight into methylation patterns at a single nucleotide level.

Advantages of Methylation Sequencing:

  • With whole genome bisulfite sequencing, view methylation at practically every cytosine in the genome across most species
  • Capture full sample diversity with small amounts of DNA
  • With targeted methylation sequencing, cover emerging regions of interest in the human genome identified by ENCODE, FANTOM5, and the Epigenomics RoadMap Consortium.
  • Discover methylation patterns of CpG, CHH, and CHG regions across the human genome
Advancing DNA Methylation Studies with NGS

This ebook discusses genomics applications in gene expression and regulation research. See how workflows can impact study results.

Download Now

Many approaches leverage the high quality and sensitivity of NGS for methylation analysis. Most methods rely on bisulfite conversion of DNA to detect unmethylated cytosines. Bisulfite conversion changes unmethylated cytosines to uracil during library preparation. Converted bases are identified (after PCR) as thymine in the sequencing data, and read counts are used to determine the % methylated cytosines.

Bisulfite conversion sequencing can be done with targeted methods such as amplicon methyl-seq, target enrichment, or with whole-genome bisulfite sequencing (WGBS). Additionally, alternative chemistries like OxBS and TAB-Seq can be used with NGS for identification of hydroxymethylation (5-hMc) in conjunction with methylation (5-mc) analysis.

For a deep dive into methylation analysis methods, please see the Field Guide to DNA Methylation Analysis. View Guide.

Perturbation of Methylation

More than 90% of the world’s sequencing data is generated using Illumina NGS technology.*

In addition to industry-leading technology, Illumina offers a fully supported workflow, from library preparation to data analysis, for methylation sequencing.

Click on the below to view products for each workflow step.

TruSeq DNA Methylation Kit

Whole-genome bisulfite sequencing libraries from as little as 50 ng DNA.

TruSeq Methyl Capture EPIC Library Prep Kit

Target enrichment bisulfite sequencing libraries from as little as 500ng DNA.

NextSeq 500/550 System

Flexible desktop sequencer supporting multiple applications, sequencing 1 DNA sample per 2 flow cells.

HiSeq 2500 System

Power and efficiency to sequence 2 DNA samples per flow cell.

HiSeq 3000/HiSeq 4000 Systems

Maximum throughput and lowest cost to sequence 2-3 samples per flow cell.

NovaSeq Series

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

MethylSeq App

For WGBS or targeted methylation sequencing. Maps bisulfite-treated sequencing reads to the genome of interest and performs methylation calls using the Bismark algorithm. Bowtie 2, an ultrafast, memory-efficient tool, aligns the reads to long reference sequences.

MethylKit App

MethylKit analyzes sequencing data from reduced-representation bisulfite sequencing (RRBS) as well as whole-genome bisulfite sequencing. It calculates methylation statistics and also differential methylation regions.

BaseSpace Data Repository

View example WGBS data generated using the TruSeq DNA Methylation Kit and Illumina sequencing instruments (use the “Methyl-Seq” category filter).

Methods Guide

Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.

Access Guide
Methods Guide
Epigenetic Changes in Cancer
Epigenetic Changes in Cancer

Studies of epigenetic alterations in cancer, such as aberrant methylation and altered transcription factor binding, can provide insight into important tumorigenic pathways. As altered methylation often activates or silences genes, changes in the epigenome can affect gene expression and the rate of cancer progression. Learn more about cancer epigenetics.

Complex Disease Genomics
Methylation Profiling for Complex Disease

Genome-wide methylation profiling can help researchers understand the functional mechanisms at work in complex disease cases. Aberrant cytosine methylation can impact gene expression, and has been implicated in many disease processes, such as Alzheimer’s disease and asthma. Learn more about complex disease research.

The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells.

J Biotechnol 199 38-46 2015

View Summary

Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics.

Cell Rep 10 1386-97 2015

View Summary

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors.

Nat Biotechnol 33 769-74 2015

View Summary
Interested in receiving newsletters, case studies, and information on genomic analysis techniques? Enter your email address.
Peter Laird: Epigenetics, DNA Methylation, and Arrays
Peter Laird: Epigenetics, DNA Methylation, and Arrays

Peter Laird, PhD, discusses his studies of epigenetics and the role DNA methylation may play in contributing to cancer.

View Video
Whole-Genome Bisulfite Sequencing Library Prep
Whole-Genome Bisulfite Sequencing Library Prep

Efficient nanogram-scale library preparation, sequencing, and analysis of DNA methylation.

Access PDF
Epigenetic Contributions to Addiction
Epigenetic Contributions to Addiction

Marilee Morgan discusses the use of NGS to correlate epigenetic signatures with brain image scans of substance abusers.

Read Interview
Field Guide to Methylation Methods
Field Guide to Methylation Methods

An overview of the impact of cytosine methylation and the primary methods used to detect cytosine modifications.

Read Guide
Epigenetic Contributions to Addiction
Epigenetics and Gene Expression

Visit our content hub to learn how combining gene expression with epigenetic studies can provide a more comprehensive view of biology.

Learn More
Library Prep for WGBS with Fraz Syed
Library Prep for WGBS with Fraz Syed

Illumina scientist Fraz Syed explains library preparation for whole-genome bisulfite sequencing.

View Video
Library Prep for WGBS with Fraz Syed
MethylSeq App for DNA Methylation Calling

Learn more about this bioinformatics solution for analyzing NGS methylation data.

Read Blog Post
Methylation and Metastasis
Methylation and Metastasis

Researchers investigate the epigenetics behind cancer metastasis using DNA methylation microarrays and NGS.

Read Interview

*Data calculations on file. Illumina, Inc., 2015