Epigenomics

In the past several years the impact of DNA methylation on gene expression, imprinting, and deregulation of epigenetic machinery has been implicated in more and more Mendelian diseases, human cancers, and drug resistance which is why at Sampled we have invested in some of the latest technology platforms to identify CpG methylated DNA islands.

Our fully automated library workflows include DNA methylation arrays as well as DNA methylation sequencing that provide industry leading turnaround times:

• Preparation for DNA methylation arrays requires 2 business days and 1 day for analysis.
• Preparation for DNA methylation sequencing takes 3-5 business days and 2 days for analysis- approximately one business week overall.

• We offer methylation array services on Illumina Epic arrays that contain ~75,000 defined probes. These arrays are subsequently run using Illumina iScan platforms.
• For data analysis, we provide methylation reports with hypomethylated and hypermethylated sites (beta value given).
• Sampled also provides custom arrays for investigating specific methylation sites of interest for clients who require specific sites to be investigated.
• Our methylation array services provide comprehensive genome-wide coverage including:
  • CpG islands
  • Non-CpG and differentially methylated sites
  • Enhancers
  • Open chromatin
  • Transcription factor binding sites
  • miRNA promoter regions
  • Assay reproducibility
  • > 98% reproducibility between technical replicates for all Infinium methylation arrays
  • 98% for the same samples on the legacy HumanMethylation450K array vs. the MethylationEPIC array
  • MethylationEPIC contains > 90% of the HumanMethylation450K content
  • User-friendly, streamlined workflow
  • MethylationEPIC has been validated with FFPE samples

DNA methylation sequencing

• We offer comprehensive DNA methylation sequencing arrays to investigate all the possible CpG sites in your sample’s genome using Illumina NovaSeq 6000 platforms.
• For data analysis we provide either methylation reports (that include number and location of hypomethylated and hypermethylated sites) and/or differentially methylated CpG islands if you provide control samples.
• We are also able to create custom panels for investigating methylation sites at a higher depth.
• Advantages of our methylation sequencing services also include:

• Discovery of methylation patterns of CpG, CHH, and CHG regions across the human genome
• Ability to view methylation at practically every cytosine in the genome across most species with whole-genome methyl-sequencing (WGMS), a genome-wide approach
• Being able to capture full sample diversity with small amounts of DNA
• Coverage of emerging regions of interest in the human genome identified by ENCODE, FANTOM5, and the Epigenomics RoadMap Consortium with targeted methylation sequencing

Coming soon

• Human Genome Methylation detection (concurrent with Genome Long Read Sequencing 20Kb)
• Microbial methylation detection using PacBio based long read sequencing (20kb read length) for analysis of epigenetic modifications in microbes such as bacteria and fungi.
• Eukaryotic methylation arrays using PacBio based long read sequencing (20kb read length) for analysis of epigenetic modifications in any eukaryotic cell.