TruDiagnostic: Your Partner in Epigenetic Research
We own and operate the largest epigenetic database in the world to provide you with the highest caliber analytics for the lowest cost and fastest turnaround times.
What Makes Our Lab Different
We offer advanced DNA methylation profiling services to academic researchers, clinical practitioners, and commercial partners using Illumina's cutting-edge technology.
Our offerings include: The Infinium Methylation Screening Array (MSA), the Infinium MethylationEPIC v2.0 Array, and several custom arrays. Each platform is designed to meet specific research needs, from large-scale population studies to in-depth epigenetic investigations.
As part of our services, we provide reliable, end-to-end support to you – including study design, participant recruitment, grant funding, testing preparation, algorithmic analysis and data interpretation, helping your team unlock deep biological insights with the speed and efficiency of our in-house lab operations.
High-throughput capabilities
We routinely process large data cohorts with precision, executing 115+ university research partnerships.
Fast turnaround times
Our workflows are built for speed and quality, leveraging our in-house operations to process and deliver results in as little as 2-4 weeks from sample receipt.
Full bioinformatic support
Our services include clock calculations, algorithmic tools, and results interpretation.
Custom Array Design & Validation
We partner with Illumina to design and validate arrays like the EPIC v2.0 and develop custom arrays for specialized epigenome regions, such as CoRSIVs and the Imprintome.
Algorithm Compatibility
We are uniquely prepared to help you with array-array compatibility with our titration correction methods.
Our Array Platforms
We offer four advanced DNA methylation arrays to support a wide range of study types, from targeted interventions to multi-omic population health initiatives.
Methylation Screening Array (MSA)
The Infinium Methylation Screening Array (MSA) is a high-throughput, cost-effective solution tailored for large-scale epigenetic studies. With approximately 270,000 probes, it is optimized for measuring aging, environmental exposures, and metabolic traits. The platform supports up to 48 samples per chip, includes both CpG methylation and SNP probes, and is an excellent choice for large-scale or multi-omic studies where throughput and affordability matter.
Key Features:
- High-throughput Capability: Supports up to 48 samples per BeadChip, facilitating large-scale studies.
- Focused Content: Includes probes associated with traits such as aging, environmental exposures, and metabolic diseases.
- Cost-Effective: Designed to provide comprehensive data at a reduced cost compared to broader arrays.
- Multi-Omic Integration: Incorporates content for CpH methylation and single nucleotide polymorphisms (SNPs), enriching the dataset for integrative analyses.
Many existing DNA methylation algorithms were developed on EPIC array data and don’t always work on the MSA platform. To address this, we developed a suite of custom algorithms trained directly on MSA data to maximize its research utility. In collaboration with research partners at Harvard, Duke, and Yale, we created novel biological age measures specifically validated for the MSA array – several of which are now considered industry-leading standards for longevity, including:
- DunedinPACE → measures the pace of aging
- SymphonyAge → estimates organ-level age
- OMICmAge → measures biological age
Cellular Deconvolution
Beyond aging, we have also engineered Cellular Deconvolution models tailored to MSA data:
- Cellular deconvolution is the process of identifying and quantifying the different cell types present in a biological sample based solely on DNA methylation data.
- We’ve engineered advanced 19-cell immune deconvolution models that allow us to track even subtle shifts in immune cell populations– insight that is essential for aging, inflammation, autoimmunity, and therapeutic response analysis.
Epigenetic Biomarker Proxies (EBPs)
In collaboration with Harvard, we have also developed 1,700 Epigenetic Biomarker Proxies (EBPs) trained on MSA data. These biomarkers predict metabolites, proteins, and clinical values, and have been shown to outperform traditional lab tests in precision and reliability from an at-home dried blood spot sample. Unlike traditional biomarkers that provide momentary snapshots, EBPs reflect biomarker levels averaged over weeks or months, offering a dynamic and comprehensive assessment of health.
Cross-Array Reference Set
Cross-Array Reference & Validation Datasets: With over 2,000 paired EPICv1 and MSA samples, TruDiagnostic has created a robust reference resource to improve cross-array probe reliability and algorithm corrections. In addition, we maintain large replication and validation datasets across multiple array platforms.
Together, these datasets make the MSA a powerful choice for population health studies, disease prediction research, and multi-omic integration projects, delivering both scale and scientific depth.
EPIC v2.0 Array
The EPIC v2.0 array offers a comprehensive genome-wide analysis with approximately 930,000 methylation sites measured. As a result, the EPIC v2.0 provides extensive coverage of CpG islands, enhancers, and other regulatory regions, making it ideal for in-depth epigenetic research, such as studies focused on cancer research, genetic diseases, and molecular epidemiology.
Key Features:
- Extensive Coverage: Targets over 99% of RefSeq genes, including promoter and enhancer regions.
- Enhanced Content: Includes additional probes for regions identified through ATAC-Seq and ChIP-Seq experiments.
- Advanced Analysis Tools: Compatible with bioinformatics tools like SeSAMe and minfi for data processing and analysis.
We helped validate the performance of the EPIC v2.0 array in this publication, which demonstrated expanded enhancer coverage, reliable results across diverse ancestries, support for low-input DNA (~1 ng), and preserved coverage of key tools like epigenetic clocks and immune deconvolution panels.Additionally, we have run over 100,000 EPIC (V1.0 and V2.0) samples since our inception and have a full suite of algorithms trained on both platforms, including:
- 30+ biological age clocks
- 4 mitotic clocks
- 12- and 19-cell immune deconvolution
- 1,700+ Epigenetic Biomarker Proxies described here
- 100+ longitudinal intervention datasets
- Diagnostic and risk predictive Methylation Risk Scores (MRS) for 40+ different disease conditions
Xtra DNAm Array
The Illumina Xtra DNAm Array combines the strengths of the MSA and EPIC v2.0 arrays with an additional 30,000 specially selected regions measured, totaling 1.09 million methylation sites. Notably, these custom regions are designed to include at least 3 CpGs from each Correlated Region of Systemic Interindividual Variation (CoRSIV).
CoRSIVs are genomic regions where DNA methylation patterns show consistent variation between individuals across different tissues. This makes them especially valuable for studies exploring the epigenetic basis of complex traits and diseases. Unlike most CpGs, CoRSIVs capture stable interindividual differences that are often more phenotypically informative. CoRSIVs are related to health outcomes more than any other region, making this array an excellent measure for biological health predictions. For instance, data has shown that these regions are 50-100x more phenotypically penetrant (equivalent to 1.5M-3M CpGs).
“Enrichment of CoRSIV-overlapping probes was observed for most classes of disease, indicating an opportunity to improve the power of EWAS by over 200- and over 100-fold, respectively. EWAS targeting all known CoRSIVs should accelerate discovery of associations between individual epigenetic variation and risk of disease.”
Key Features:
- Comprehensive Coverage: Integrates content from MSA and EPIC v2.0 arrays with additional CoRSIV-targeted regions.
- Enhanced Phenotypic Relevance: CoRSIVs are associated with various human diseases, including obesity, cancer, and neurological disorders.
- High Phenotypic Relevance: CoRSIVs are approximately 50-100 times more phenotypically relevant than other regions, offering deeper insights into disease mechanisms.
Imprintome Array
The Imprintome Array offers dense coverage across all known and predicted imprinting control regions (ICRs), differentially methylated regions (DMRs), and key regulatory elements that influence imprinted gene networks, making this array ideal for imprinting discovery and diagnostics. It’s powered by our proprietary platform for analyzing epigenetic imprinting.
Key Features:
- Targeted Imprintome Coverage: Profiles ~200 known and predicted imprinted regions, including maternal and paternal allele-specific methylation zones.
- Designed for Disease-Relevant Discovery: Ideal for studying disorders of imprinting, developmental syndromes, aging, and transgenerational epigenetic inheritance.
- High-CpG Density Per Region: Each region contains multiple CpG sites (typically 3-15), providing robust statistical power and methylation state clarity.
- Cross-Compatible with Multi-Omic Pipelines: Designed for seamless integration with transcriptomics, proteomics, and single-cell methylation tools.
Epigenetic imprinting is a powerful biological mechanism where gene expression is regulated not by the DNA sequence itself, but by parent-of-origin-specific methylation patterns. Imprinted genes are uniquely susceptible to epigenetic dysregulation. Unlike other loci, they are monoallelically expressed, meaning they rely on precise methylation signals from only one parental chromosome. When these signals go awry, the resulting phenotypes can be severe and systemic.
Recent studies have linked aberrant imprinting methylation to:
- Autism spectrum disorders
- Obesity and insulin resistance
- Cancer progression
- Neurodevelopmental delays
- Accelerated epigenetic aging
Unlike most DNA methylation CpGs, these behave more like genetics with consistency among tissues and throughout time. To address the growing need for precise methylation profiling in these regions, we developed the Imprintome array, the world’s first commercially available DNA methylation array focused exclusively on imprinting control regions, in combination with researchers from North Carolina State University.
The Infinium Methylation Screening Array (MSA) is a high-throughput, cost-effective solution tailored for large-scale epigenetic studies. With approximately 270,000 probes, it is optimized for measuring aging, environmental exposures, and metabolic traits. The platform supports up to 48 samples per chip, includes both CpG methylation and SNP probes, and is an excellent choice for large-scale or multi-omic studies where throughput and affordability matter.
Key Features:
- High-throughput Capability: Supports up to 48 samples per BeadChip, facilitating large-scale studies.
- Focused Content: Includes probes associated with traits such as aging, environmental exposures, and metabolic diseases.
- Cost-Effective: Designed to provide comprehensive data at a reduced cost compared to broader arrays.
- Multi-Omic Integration: Incorporates content for CpH methylation and single nucleotide polymorphisms (SNPs), enriching the dataset for integrative analyses.
Many existing DNA methylation algorithms were developed on EPIC array data and don’t always work on the MSA platform. To address this, we developed a suite of custom algorithms trained directly on MSA data to maximize its research utility. In collaboration with research partners at Harvard, Duke, and Yale, we created novel biological age measures specifically validated for the MSA array – several of which are now considered industry-leading standards for longevity, including:
- DunedinPACE → measures the pace of aging
- SymphonyAge → estimates organ-level age
- OMICmAge → measures biological age
Cellular Deconvolution
Beyond aging, we have also engineered Cellular Deconvolution models tailored to MSA data:
- Cellular deconvolution is the process of identifying and quantifying the different cell types present in a biological sample based solely on DNA methylation data.
- We’ve engineered advanced 19-cell immune deconvolution models that allow us to track even subtle shifts in immune cell populations– insight that is essential for aging, inflammation, autoimmunity, and therapeutic response analysis.
Epigenetic Biomarker Proxies (EBPs)
In collaboration with Harvard, we have also developed 1,700 Epigenetic Biomarker Proxies (EBPs) trained on MSA data. These biomarkers predict metabolites, proteins, and clinical values, and have been shown to outperform traditional lab tests in precision and reliability from an at-home dried blood spot sample. Unlike traditional biomarkers that provide momentary snapshots, EBPs reflect biomarker levels averaged over weeks or months, offering a dynamic and comprehensive assessment of health.
Cross-Array Reference Set
Cross-Array Reference & Validation Datasets: With over 2,000 paired EPICv1 and MSA samples, TruDiagnostic has created a robust reference resource to improve cross-array probe reliability and algorithm corrections. In addition, we maintain large replication and validation datasets across multiple array platforms.
Together, these datasets make the MSA a powerful choice for population health studies, disease prediction research, and multi-omic integration projects, delivering both scale and scientific depth.
The EPIC v2.0 array offers a comprehensive genome-wide analysis with approximately 930,000 methylation sites measured. As a result, the EPIC v2.0 provides extensive coverage of CpG islands, enhancers, and other regulatory regions, making it ideal for in-depth epigenetic research, such as studies focused on cancer research, genetic diseases, and molecular epidemiology.
Key Features:
- Extensive Coverage: Targets over 99% of RefSeq genes, including promoter and enhancer regions.
- Enhanced Content: Includes additional probes for regions identified through ATAC-Seq and ChIP-Seq experiments.
- Advanced Analysis Tools: Compatible with bioinformatics tools like SeSAMe and minfi for data processing and analysis.
We helped validate the performance of the EPIC v2.0 array in this publication, which demonstrated expanded enhancer coverage, reliable results across diverse ancestries, support for low-input DNA (~1 ng), and preserved coverage of key tools like epigenetic clocks and immune deconvolution panels.Additionally, we have run over 100,000 EPIC (V1.0 and V2.0) samples since our inception and have a full suite of algorithms trained on both platforms, including:
- 30+ biological age clocks
- 4 mitotic clocks
- 12- and 19-cell immune deconvolution
- 1,700+ Epigenetic Biomarker Proxies described here
- 100+ longitudinal intervention datasets
- Diagnostic and risk predictive Methylation Risk Scores (MRS) for 40+ different disease conditions
The Illumina Xtra DNAm Array combines the strengths of the MSA and EPIC v2.0 arrays with an additional 30,000 specially selected regions measured, totaling 1.09 million methylation sites. Notably, these custom regions are designed to include at least 3 CpGs from each Correlated Region of Systemic Interindividual Variation (CoRSIV).
CoRSIVs are genomic regions where DNA methylation patterns show consistent variation between individuals across different tissues. This makes them especially valuable for studies exploring the epigenetic basis of complex traits and diseases. Unlike most CpGs, CoRSIVs capture stable interindividual differences that are often more phenotypically informative. CoRSIVs are related to health outcomes more than any other region, making this array an excellent measure for biological health predictions. For instance, data has shown that these regions are 50-100x more phenotypically penetrant (equivalent to 1.5M-3M CpGs).
“Enrichment of CoRSIV-overlapping probes was observed for most classes of disease, indicating an opportunity to improve the power of EWAS by over 200- and over 100-fold, respectively. EWAS targeting all known CoRSIVs should accelerate discovery of associations between individual epigenetic variation and risk of disease.”
Key Features:
- Comprehensive Coverage: Integrates content from MSA and EPIC v2.0 arrays with additional CoRSIV-targeted regions.
- Enhanced Phenotypic Relevance: CoRSIVs are associated with various human diseases, including obesity, cancer, and neurological disorders.
- High Phenotypic Relevance: CoRSIVs are approximately 50-100 times more phenotypically relevant than other regions, offering deeper insights into disease mechanisms.
The Imprintome Array offers dense coverage across all known and predicted imprinting control regions (ICRs), differentially methylated regions (DMRs), and key regulatory elements that influence imprinted gene networks, making this array ideal for imprinting discovery and diagnostics.
Our proprietary platform for analyzing epigenetic imprinting.
Key Features:
- Targeted Imprintome Coverage: Profiles ~200 known and predicted imprinted regions, including maternal and paternal allele-specific methylation zones.
- Designed for Disease-Relevant Discovery: Ideal for studying disorders of imprinting, developmental syndromes, aging, and transgenerational epigenetic inheritance.
- High-CpG Density Per Region: Each region contains multiple CpG sites (typically 3-15), providing robust statistical power and methylation state clarity.
- Cross-Compatible with Multi-Omic Pipelines: Designed for seamless integration with transcriptomics, proteomics, and single-cell methylation tools.
Epigenetic imprinting is a powerful biological mechanism where gene expression is regulated not by the DNA sequence itself, but by parent-of-origin-specific methylation patterns. Imprinted genes are uniquely susceptible to epigenetic dysregulation. Unlike other loci, they are monoallelically expressed, meaning they rely on precise methylation signals from only one parental chromosome. When these signals go awry, the resulting phenotypes can be severe and systemic.
Recent studies have linked aberrant imprinting methylation to:
- Autism spectrum disorders
- Obesity and insulin resistance
- Cancer progression
- Neurodevelopmental delays
- Accelerated epigenetic aging
Unlike most DNA methylation CpGs, these behave more like genetics with consistency among tissues and throughout time. To address the growing need for precise methylation profiling in these regions, we developed the Imprintome array, the world’s first commercially available DNA methylation array focused exclusively on imprinting control regions, in combination with researchers from North Carolina State University.
Bioinformatics & Support
TruDiagnostic doesn’t just deliver raw methylation data. Every project comes with integrated bioinformatic support and access to proprietary algorithms. These tools were trained on the world’s largest private epigenetic datasets and validated with leading academic partners.
Key outputs available to research partners:
- Pace of aging (DunedinPACE)
- Telomere length estimations
- Inflammatory marker proxies
- Immune cell subset deconvolution
- Cellular replication measures
- 1,700+ Epigenetic Biomarker Proxies (EBPs)
This support allows your team to move quickly from raw data to meaningful biological insights – saving time, resources, and external contracting.
Our Process:
From Start to Discovery
How we support your research
Why TruDiagnostic
Partner with TruDiagnostic to leverage our advanced methylation profiling solutions and gain deeper insights into the epigenetic basis of human health and disease.
Market-Leading Pricing
Due to our large volume and specialization in DNA methylation processing, we have the lowest price processing available for researchers and commercial processing partners.
Market-Leading Turnaround Time
Our optimized workflows allow us to process and deliver results in as little as 2-4 weeks from sample receipt, significantly faster than most academic or commercial labs. This speed helps researchers move from data collection to insights without delays.
Sample Type and Array Flexibility
We’ve processed hundreds of thousands of samples from diverse tissue types, including blood, saliva, and solid tissue, and have extensive experience designing and running custom arrays to meet unique research needs.
Bioinformatic Analysis for Publications
Receive access to our bioinformatics team, who provide data analysis, algorithm integration, and support for publication-ready outputs to strengthen your research and speed up the path to dissemination.
Custom Solutions
We offer tailored arrays to meet specific research needs, and provide comprehensive support from array design to data analysis.
Scalability
Leverage the power of our in-house lab and the world's largest DNA methylation database to process large-scale studies with high sample throughput.