Targeted methylation

Unbiased and genome-wide

Targeted sequencing of the methylome 

If you need to assess as many loci as possible without spending your budget on large data-files and complicated data-analysis, GenomeScan can provide the SeqCap Epi (Roche) application. This technique uses hybridization capture usually carefully designed probes, reducing the part of the genome that must be analysed to solely the relevant loci.

Select only epigenomic regions of interest

With SeqCap Epi you can choose your own content or select the CpGiant Enrichment Kit.  This off-the-shelf probe-set interrogates over 5.5 million methylation sites per sample at single-nucleotide resolution. This kit can serve as a screening tool to identify specific regions in the genome for methylation variation assessment. Capturing of known differentially methylated regions vastly reduces the sequencing output required to analyze the whole methylation landscape, compared to whole genome sequencing. Furthermore, it enables you to observe the methylation changes on both strands, while you can still study the SNPs in the targeted regions.

Only 10 ng of genomic DNA is required

Our ISO/IEC 17025 (L518) accredited workflow starts with only 10 ng of genomic DNA, due to a proprietary sample preparation method. This is a dramatic reduction of the 1000 ng that is recommended by the manufacturer. Cell-sorted DNA or serum- and plasma-derived cell free (cf)DNA can easily be analysed with this lowered input quantity.

SeqCap Epi benefits:

  • Input amount: starting from 10 ng genomic DNA
  • Hybridization capture that minimizes the chance of PCR-amplification artifacts
  • Flexibility: choose from a fixed content or custom target selection
  • High throughput: automated workflow ensures a high capacity, low handling costs, and consistent data-quality

The available kits:

  • SeqCap Epi CpGiant Enrichment Kit

    An off-the-shelf capture kit for targeted methylation sequencing. The fixed epigenome-wide design interrogates over 5.5 million methylation sites per sample at single-nucleotide resolution. This greatly surpasses the content of the MethylationEPIC BeadArray or ‘850K array’.

  • SeqCap Epi Choice Enrichment Kit

    Target capture kit to customize the probe-set -up to 90Mb- to assess only the relevant part of the epigenome.

  • SeqCap Epi Developer Enrichment Kit

    Customizable probe pools that can target any organisms’ bisulfite treated genomic DNA for targets up to 210 Mb or human targets between 90 and 210 Mb.

Benefits of the SeqCap Epi CpGiant Enrichment Kit:

  • Of the shelf panel with >5.5 million methylation sites connected with disease and development.
  • Minimization of sequencing costs due selection of targets within the genome
  • Observe methylation changes on both strands
  • Sample input of just 10 ng compared to 1000 ng recommended by the manufacturer
  • ISO 17025 (L518) accredited workflow with guaranteed results

Reduced Representation & Whole Genome Bisulfite Sequencing

Targeted methylation

MethylationEPIC ‘850K’ BeadChip

EpiRestore: restore all low integrity DNA