Epigenomic Sequencing Services

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Flexible options enable your epigenomic studies

Identifying sites of epigenetic modification can shed light on developmental pathways, pathogenic processes, transcriptional regulation, and serve as biomarkers for disease.

HudsonAlpha Discovery provides a range of epigenetic sequencing services to advance all phases of research studies, including basic, discovery, translational, pre-clinical, and clinical research.


Advance insight into the regulation of gene expression with epigenetic sequencing
Flexible and customizable end-to-end services
Illumina’s Infinium MethylationEPIC BeadChip 850K Array technology

Single-cell ATAC-seq with 10x Genomics technology
Next generation sequencing (NGS) of bisulfite-treated libraries



Biomarker discovery

Disease research

All research phases and activities

Basic discovery, Translational and pre-clinical, Clinical

Highlights of our epigenetic sequencing services

Whether you need end-to-end support or a subset of what we can provide, we’ll help you customize a service project to best meet your study objectives.

Here are a few examples of what we offer:
Nucleic acid extraction and library preparation
  • Optimized extraction protocols for nearly any sample type
  • Optimized protocols for working with ultra-low amounts of nucleic acid
  • Dual concurrent RNA-DNA extraction from challenging sample types such as FFPE tissue— read the white paper »
Assay Technologies
  • Whole Genome Bisulfite Sequencing
  • Illumina’s Infinium MethylationEPIC BeadChip 850K Array technology
  • Single cell chromatin accessibility studies with ATAC-seq (10x Genomics)
  • Oxford Nanopore DNA methylation analysis
  • NGS sequencing of already-prepared libraries including bisulfite-treated DNA
Bioinformatics analysis and data storage
  • Tier 1: Raw BCL and FASTQ file output
  • Tier 2: Standard application-specific and quality report outputs (BCL, FASTQ, aligned BAM files and sequencing QC reports
  • Tier 3: Standard output plus variant calling (VCF, g-VCF) and genomic interpretation reports
  • Additional custom reporting options including Ingenuity Variant Analysis (Qiagen) consolidated variant reports as well as options for genomic variant annotation
  • Flexible data delivery and storage options
  • 90 days storage included with service pricing
  • Long term storage available

The HudsonAlpha Discovery Difference

Epigenetic Sequencing
Flexible and creative problem solving with expert scientific guidance
Optimized protocols and automated workflows that reduce technical bias
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Stringent quality control parameters—we consistently exceed manufacturer specifications—for reproducible, accurate results
Massive scale with 10 Illumina NovaSeq 6000 sequencers as well as NextSeqs, MiSeqs, and iSeqs
A decade of proven experience spanning thousands of projects and hundreds of publications
See Recent Publications
Leverage the power of the HudsonAlpha Discovery division:
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Featured Paper

Epigenetic analysis for biomarker discovery

Longitudinal study of leukocyte DNA methylation and biomarkers for cancer risk in older adults

Bartlett AH, et al. Biomark Res. 2019; 7: 10. PMCID: PMC6537435.

In this study, completed when the HudsonAlpha Discovery lab was still the HudsonAlpha Institute Genomic Services Lab, our epigenetic sequencing services enabled an exploration of methylation at CpG islands over the course of 5-years in a small cohort of adults between the ages of 70 and 78 at the study start time.

Their findings: “Our analysis detected global changes in the methylome that are partly due to cellular heterogeneity and also due to changes at specific CpGs that could indicate cancer development and progression. From the multiple lines of evidence, we posit methylation in RPTOR as a potential biomarker of cancer that justifies further investigation and validation.”1

The significance of this work: This is one of the few studies to examine how the methylome changes over time, and the implications for cancer biomarker discovery.1

Recent Publications
  1. Bartlett AH, et al. Longitudinal study of leukocyte DNA methylation and biomarkers for cancer risk in older adults. Biomark Res. 2019; 7: 10. PMCID: PMC6537435.
  2. McCoy CR, et al. Altered DNA Methylation in the Developing Brains of Rats Genetically Prone to High versus Low Anxiety. J Neurosci. 2019 Apr 17; 39(16): 3144–3158. PMCID: PMC6468100.
  3. Glover ME, et al. Perinatal exposure to the SSRI paroxetine alters the methylome landscape of the developing dentate gyrus. Eur J Neurosci. 2019 Jul;50(2):1843-1870. PMID: 30585666.

Get more information about our DNA and RNA sequencing services

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