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Explore our advanced sequencing products for turning complex molecular signals into high-confidence readouts across clinical testing, RNA quality control, and translational methylation programs.
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Neuron Cell-Death Test
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MethylMap™
Native-Read Methylation Sequencing
Older woman discussing a clinical diagnosis with a female doctor who is reviewing a tablet in a medical office.
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End-to-end sequencing services supporting genomic, epigenomic, and transcriptomic analysis, from experimental design and assay development to bioinformatics, interpretation, and data delivery.
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Explore how our products and services help solve difficult biological and genomic problems, from liquid biopsy signals to complex regions and emerging biomarker development.
Hard-to-Sequence Genes & Complex Regions
Liquid Biopsy cfDNA Analysis
Custom Multiomic Panel Development
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Company
Building the future of precision diagnostics through sequencing innovation, scientific rigor, and collaborative partnerships.
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  • Applications
  • Applications
    Telomeres, the protective caps at the end of our chromosomes, sit at the intersection of aging, cancer, and neurodegeneration research.
    Telomeres, the protective caps at the end of our chromosomes, sit at the intersection of aging.
    Research & Translation
    Biopharma Research
    Clinical Development
  • Company
  • Company
    Building the future of precision diagnostics through sequencing innovation, scientific rigor, and collaborative partnerships.
    About Us
    Team
Renew Service

Direct Methylation Sequencing (cfDNA)

  • A cell-free DNA (cfDNA) methylome sequencing service optimized for native methylation analysis.
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Overview

Direct Methylation Sequencing (dMS) combines proprietary library preparation protocols with native Oxford Nanopore cfDNA sequencing to support cfDNA methylome profiling and liquid biopsy biomarker development without bisulfite conversion or PCR amplification.
  • Native cfDNA sequencing optimized for methylation analysis
  • Native 5mC, 5hmC, and 6mA profiling without bisulfite conversion
  • Integrated sequence and methylation analysis in a single workflow
Multiomic Liquid Biopsy
Integrated genomic and epigenetic analysis from one dataset
Expanded CpG coverage beyond traditional methylation arrays
Broad Sample Compatibility
Compatible with plasma, serum, CSF, and seminal fluid
Flexible support for research and biomarker development
Tissue-of-Origin Analysis
Native methylation profiling of circulating cfDNA fragments
Cell- and tissue-of-origin inference and characterization
Technology
Workflow
Performance
Data Outputs

Technology and Compatibility

dMS applies native ONT sequencing to cell-free DNA, enabling cfDNA methylome analysis and liquid biopsy biomarker discovery across diverse biofluids and research applications.
  • Compatible with
  • Human and animal cfDNA samples
  • Plasma, serum, CSF, and seminal fluid biofluids
  • Research, translational, and biomarker development workflows
  • Component
    Technology
  • Sequencing Chemistry
    Native Oxford Nanopore cfDNA Sequencing
  • Preparation
    Renew dMS library preparation
  • Sequencing Platform
    Oxford Nanopore PromethION

Workflow

Direct Methylation Sequencing uses Renew’s optimized native cfDNA sequencing workflow for methylome profiling and liquid biopsy analysis. Renew provides full-service support from cfDNA extraction through library preparation, sequencing, analysis, and data delivery.
  • 1. cfDNA Extraction
    High-quality cfDNA is isolated from samples.
  • 2. Library Preparation
    Proprietary dMS library preparation and adapter ligation.
  • 3. cfDNA Sequencing
    Native cfDNA is sequenced via PromethION platform.
  • 4. Data Analysis
    Sequencing data are processed through automated analysis pipelines.
  • 5. Data Delivery
    Results are delivered through the customer portal or AWS S3.

Sequencing Performance

Coverage and yield vary by cfDNA input quantity, sample type, multiplexing strategy, and study goals. Representative performance metrics for human cfDNA samples are shown below.
Genomic visualization showing gene MAP3K2-DT with methylation patterns across two tissues and gene annotations.
  • Metric
    Typical Performance (Human Samples)
  • Samples per Flow Cell
    Up to 24
  • Average Coverage
    0.1x-1.0x
  • Average Read Length
    ~500 bp N50
  • Available CpG Coverage
    > 95% CpG coverage
  • Available Epigenetic Signals
    5mC, 5hmC, 6mA, non-CpG methylation

Bioinformatics and Data Outputs

Data outputs are designed to optimize data storage, transfer, and analysis. Methylation data is provided in a unique CH3 file format which reduces data size by up to 95%. This memory-efficient format stores data in an on-disk database, enabling larger-than-memory tasks.
Renew developed the ModSeqR R package, which converts ONT methylation data into array-like formats compatible with tools such as minfi, DMRcate, and chAMP. This solution empowers researchers to efficiently leverage dWMS data within familiar frameworks, facilitating advanced epigenetic insights.
Get ModSeqR on GitHub
Download panel showing four files for specimen 250409 with names, sizes, dates, and download options.
  • Data Outputs
  • QC Report
    Sequencing metrics and run statistics
  • BAM
    Aligned reads
  • CH3
    Base modifications
  • POD5
    Raw sequencing data (available for an additional fee)
  • Data Delivery Options
  • Client Web Portal
    Manual download | Mac, Linux, Windows
  • AWS S3 Transfer
    Automated process | AWS to AWS
  • Command Line Script
    Manual download | Mac, Linux

Service Inclusions

Each project is supported by dedicated project management and cross-functional expertise across assay development, bioinformatics, and regulatory strategy. Renew provides proactive communication, transparent project tracking, and technical support from study design through data delivery.
Renew combines platform flexibility, nanopore expertise, and operational excellence to resolve areas
of the genome that standard approaches cannot.
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