Have questions? reach out
Have questions? reach out
The methylation industry is transforming, but legacy methods like microarrays and bisulfite sequencing still lack the sensitivity for clinical integration, hindering biomarker discovery and clinical impact. Wasatch BioLabs’ Direct Whole Methylome Sequencing (dWMS) delivers a comprehensive solution, offering whole genome sequencing and methylation analysis with unmatched quality and flexibility.
5x
Screening and regional analyses.
4
10x
Methylation quantification and variant detection.
30x
Comprehensive methylome analysis and detailed variant detection.
1
30-50x +
Genome Assembly
0.5 - 1
Designed to meet the needs of research and biomarker discovery, dWMS delivers scalable multi-omic solutions to advance assay development, epigenetic studies, and beyond.
Traditional methylation technologies leave researchers guessing—are regions uniformly 10% methylated, or is methylation concentrated in just 10% of the region?
Wasatch BioLabs’ dWMS service resolves this uncertainty. By analyzing over 96% of CpGs across the genome, dWMS captures the full methylation context across entire DNA molecules with native reads, enabling precise, molecule-level analyses.
Capturing 30X more CpG sites and 2X more CpG islands without bisulfite or amplification biases, researchers gain a comprehensive view of methylation, hydroxymethylation, and DNA sequence—all in a single run.
Methylation
Hydroxy
methylation
Additional Base Modifications
Bisulfite
Conversion-Free
Approximate CpG Coverage
Up to 900,000 CpGs
Variable*
Over 27 Million CpGs
* Requires Additional Processing And Sequencing
~ Based On Depth And Sequencing Goals
dWMS identifies 2.4x more differentially methylated CpG islands (CGIs) than traditional microarrays. gDNA was extracted from Tissue 1 (n=4) and Tissue 2 (n=4) and analyzed with both methylation array and dWMS. dWMS captured 2.4 times more CGIs containing significant differential methylation between the two tissues, including 91% of those detected by the array.
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WBL’s dWMS demonstrates robust reproducibility with minimal inter-sample variance. DNA samples from Tissue 1 (n=4) and Tissue 2 (n=4) underwent sequencing on two separate PromethION platforms at distinct sites. Correlation analysis (A) and PCA visualization (B) reveal high concordance within both Tissue 1 and Tissue 2 cohorts (r > 0.97), underscoring negligible variation attributable to site-specific batch effects.
Leveraging nanopore sequencing, dWMS long reads resolve repetitive regions, structural variants, phasing, and other complex genomic features. This capability enhances genome assemblies, reveals complex regulatory elements, and provides deeper insights into genomic architecture.
DNA Sequence
Small Nucleotide Variants
Structural Variants
(Deletions, Insertions, Duplications, Inversions, Translocations)
Repetitive Regions
GC-Rich Regons
Multi-omics is accelerating research by providing richer data and deeper biological insights. As an ecosystem-driven platform, Wasatch BioLabs’ Direct Whole Methylome Sequencing (dWMS) for gDNA overcomes the limitations of legacy methylation technologies—enabling seamless progression from biomarker discovery to clinical application, all on a single platform.
Captures over 96% of CpG methylation sites, enabling exploration of methylation linked to gene expression and disease.
Acquires genomic and epigenomic data in single runs, streamlining multi-omics pipelines for comprehensive analyses.
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Enables researchers to bioinformatically target regions of interest for precise assay development and actionable insights.
Supports the identification of methylation and genomic variations associated with cancers for biomarker discovery and treatment research.
Investigate genome-wide methylation and sequence variations to uncover regulatory networks in cellular differentiation.
Figure 1. Tedania ignis, commonly known as the fire sponge, is a vibrant marine sponge found across the Atlantic and Caribbean regions. Known for its striking red coloration and bioactive compounds, this species serves as a valuable model for ecological and biomedical research.
Figure 2. Fire sponge genome assembly workflow. Steps include extracting DNA, selecting for high molecular weight (> 5kb) DNA, dWMS library preparation, long-read nanopore sequencing, and genome assembly using Flye.
Figure 3. Complete BUSCO (%) comparison across sponge species and their taxonomic classes. gDNA was extracted from T. ignis tissue using a methanol-based protocol to inhibit nucleases and reduce DNA degradation, then sequenced with dWMS. A BUSCO analysis was performed, comparing genome completeness across sponge species.
To support genomic research, Wasatch BioLabs offers three scalable solutions that deliver high-quality de novo genome assemblies with long reads and comprehensive methylation data—across any species or genome size:
Wasatch BioLabs introduces MethylSeqR, a user-friendly R package that simplifies the transition from methylation arrays to dWMS. MethylSeqR utilizes proprietary .CH3 files, which compress data by up to 95%, streamlining both analysis and storage.
Seamlessly integrating with familiar pipelines, MethylSeqR makes advanced methylation analysis accessible to both newcomers and experienced users of nanopore sequencing, accelerating research and clinical applications.
Perform genome-wide methylation analyses in record time.
Analyses in just three steps: Import Data, Run QC, and Analyze.
Compress 20 GB outputs to 1 GB, optimizing storage and transfer.
Process large-scale tasks seamlessly with on-disk database support.
(A) Positional Summary
(B) Summaries By Region
Examples of methylation summaries by position (A) and region (B), and methylation visualizations by heatmap (C) and volcano plot (D).
(C) Heat Map
(D) Volcano Plot
Examples of methylation summaries by position (A) & region (B), & methylation visualizations by heatmap (C) & volcano plot (D).
Methylation summs by position, CpG Island
Differential methylation by region, read, position
Sliding window methylation analysis
Multiple quality control functions
From exploratory research to large-scale screenings, Wasatch BioLabs empowers biomarker discovery with unbiased sequencing solutions. Leveraging proprietary technologies like dWMS and MethylSeqR, tailored workflows, and expert bioinformatics support, we deliver actionable insights to advance your research.
Harness advanced tools like dWMS and exclusive DNA repair protocols to sequence challenging sample types, including cfDNA. Our workflows scale to meet your project’s needs, from preliminary exploration to clinical application.
Enhance your data with custom bioinformatics solutions, using tailored workflows and advanced analysis to generate impactful, publication-ready insights.
Simplify methylation analysis with MethylSeqR, our user-friendly R package that transforms raw nanopore data into actionable insights faster than ever.
Work with native-read sequencing experts with decades of experience in genomics, epigenomics, and bioinformatics to guide your project from discovery to clinical success.
Wasatch BioLabs’ dWMS is a next-generation approach to genome wide methylation profiling using native long read DNA sequencing. It enables full methylation analysis across more than 27 million CpG sites without bisulfite conversion, offering a complete and unbiased view of the DNA methylome. This service empowers researchers with accurate epigenetic insights critical for biomarker discovery, clinical applications, and assay development.
Unlike arrays or bisulfite sequencing, dWMS is conversion-free and leverages long read sequencing via nanopore technology. It provides base-resolution detection of methylation, hydroxymethylation, and other modifications—capturing 30X more CpG sites and 2X more CpG islands than arrays. The result is more reliable whole genome sequencing and methylation data with minimal bias or batch effect.
Wasatch BioLabs offers MethylSeqR, a in-house, specialized R package that processes raw nanopore data and compresses it using .CH3 files. It supports standard bioinformatics pipelines and provides intuitive views such as positional summaries, regional profiles, heatmaps, and volcano plots. This tool simplifies long read sequencing analysis and accelerates data interpretation for both novice and advanced users.
dWMS has been verified on 15+ sample types (human tissue, whole blood, saliva, plant & animal, etc.) Coverage levels can be tailored (5x to 50x+), depending on whether the goal is regional screening, methylation quantification, or full genome assembly. You can contact Wasatch BioLabs directly through the site’s contact form or by email to discuss with our technical team.
Getting started is simple—reach out to the Wasatch BioLabs team for one-on-one consultation. Their experts in genomics, epigenomics, and long read DNA sequencing will guide your project from design to data delivery. The service is scalable, with custom workflows built to support both discovery-stage and clinical studies.
Wasatch BioLabs’ dWMS technology offers high-throughput, whole genome sequencing that identifies methylation and hydroxymethylation across over 96% of CpG sites. By using long read sequencing, dWMS uncovers structural variants and CpG island-level differences with unmatched depth and accuracy—delivering rich data for comprehensive genome wide methylation profiling.
