DNA Methylation Test Matches Flow Cytometry for Measuring Immune Cells in Blood

A simple measurement of DNA methylation patterns in blood can quantify immune cells as accurately as the clinical gold standards, according to a new study published in Clinical Epigenetics. The finding suggests that a technique requiring only DNA, rather than intact cells and specialized laboratory infrastructure, could eventually bring detailed immune profiling to settings where flow cytometry is impractical or unaffordable.

Clinical flow cytometry is currently the standard method for immune cell typing and quantification, but it depends on intact cell membranes, complex reagents, and substantial infrastructure, making it costly and technically demanding. The new research evaluated whether methylation cytometry, which infers cell proportions from DNA methylation measured in a sample, could match both of these established assays.

The underlying principle is that patterns of DNA methylation are specific to each cell type. At cell-type-specific CpG sites, the methylated or unmethylated signal is directly proportional to a cell’s abundance within a sample. By measuring these signals and applying an extended deconvolution library, the researchers could estimate the proportions of different immune cell populations from DNA alone.

To test the approach, the team obtained whole blood from 101 patients who were already undergoing routine clinical flow cytometry and CBC assays. They compared cell quantities derived from methylation cytometry with those produced by CLIA- and CAP-certified clinical flow cytometry and by CBC differentials, including granulocyte subsets such as neutrophils, eosinophils, and basophils.

The results showed strong concordance between the two approaches, with an R-squared of 0.99 and a root mean square error of 2.42. Bland-Altman analysis demonstrated strong agreement and minimal bias, with 95.4 percent of values falling within the limits of agreement, defined as the mean plus or minus 1.96 standard deviations.

Statistical equivalence testing strengthened the case further. Two one-sided tests of equivalence, known as TOST, demonstrated that the mean differences between methylation cytometry and flow cytometry were statistically equivalent within plus or minus 2 percent for all cell types examined.

The researchers also examined a subset of 32 patients with HIV, a group for whom CD4 T-cell monitoring is clinically important. Bland-Altman analysis of CD4 T-cell percentages in this subset revealed a near-zero mean difference between the methods, with 97 percent of observations falling within the limits of agreement.

The study’s authors conclude that methylation cytometry is highly accurate when compared to current clinical assays. They note that, with further development, the approach has strong potential as a scalable option for detailed clinical immune profiling, including in resource-limited settings where the infrastructure required for flow cytometry is not available.

Because methylation cytometry requires only the measurement of cellular DNA methylation, it sidesteps several constraints of conventional immune cell quantification. The study was published as an open access article in Clinical Epigenetics on 26 September 2026, and the version shared at publication is subject to further editorial edits before the final version of record appears.

While the findings are limited to the patient population and clinical assays studied, the reported equivalence across all tested cell types, including granulocyte subsets and CD4 T cells in patients with HIV, indicates that DNA-based immune cell quantification could become a practical complement or alternative to flow cytometry in clinical laboratories.

Subject of Research: Equivalence of DNA methylation-based cytometry with flow cytometry and CBC for immune cell quantification in peripheral blood

Article Title: Equivalence of DNA-based cytometry to clinical flow cytometry and CBC for immune cell quantification in peripheral blood

Article References: Patzke, P. K., Rawson, A. L., Stolrow, H. G., Kaur, P., Kolling, F. W., Salas, L. A., & Christensen, B. C. (2026). Equivalence of DNA-based cytometry to clinical flow cytometry and CBC for immune cell quantification in peripheral blood. Clinical Epigenetics. https://doi.org/10.1186/s13148-026-02246-2

Image Credits: AI Generated

DOI: 10.1186/s13148-026-02246-2

Keywords: DNA methylation, methylation cytometry, flow cytometry, complete blood count, immune cell quantification, deconvolution, peripheral blood, CD4 T cells, granulocytes, clinical diagnostics, epigenetics, Equivalence