Targeted Deep Sequencing Tracks Y Chromosome Loss and Blood Clones Together

Researchers have developed a targeted deep sequencing strategy that can measure mosaic loss of the Y chromosome (mLOY) and mutations linked to clonal hematopoiesis of indeterminate potential (CHIP) in a single test, according to a study published in the European Journal of Medical Research. The work addresses a practical gap in aging research: somatic driver mutations and mLOY are the two major forms of clonal hematopoiesis in men, but they have typically required separate assays, with capture-based deep sequencing used for point mutations and droplet digital PCR (ddPCR) used for mLOY.

Clonal hematopoiesis is prevalent in older adults and is strongly associated with age-related diseases. In male populations, the two dominant manifestations are mutations in known driver genes and the mosaic loss of the Y chromosome, in which a growing fraction of blood cells silently loses the entire male sex chromosome. Because the two phenomena can co-occur, a method that captures both at once could clarify how they interact during aging.

The new approach estimates mLOY from sequencing coverage at two Y chromosome genes, UTY and KDM5D. When blood cells lose the Y chromosome, reads mapping to these loci drop proportionally, so reduced coverage serves as a quantitative proxy for the fraction of cells affected. The team first validated this coverage-based estimation using both whole-genome sequencing and targeted sequencing data, establishing that the signal is reliable across sequencing platforms before moving to clinical cohorts.

The primary validation involved 188 male patients with acute aortic syndrome (AAS). Against ddPCR as a comparator, the sequencing method showed exceptional reliability for detecting high-level mLOY, defined as more than 20 percent of cells affected, with an area under the receiver operating curve of 0.999 and a p-value below 0.001. For this combined detection threshold of mLOY greater than 20 percent, the method achieved a sensitivity of 87.5 percent, a specificity of 100 percent, a positive predictive value of 100 percent, and a negative predictive value of 99.4 percent.

Those performance figures matter because low-level mLOY has historically been difficult to detect. The authors note that existing approaches suffer from limited sensitivity to low-level mLOY and cannot concurrently assess mLOY and point mutations.

To test whether the performance held beyond one disease setting, the researchers verified the strategy in an independent cohort of 240 male patients with acute coronary syndrome (ACS). This second validation strengthens confidence that the method’s accuracy is not an artifact of a single patient population, an important consideration given that clonal hematopoiesis is studied across many cardiovascular and age-related conditions.

Beyond analytical performance, the study explored the relationship between mLOY and CHIP-related mutations. The results revealed a significant trend: individuals with higher mLOY frequencies were more likely to harbor CHIP mutations. Notably, the co-occurrence of CHIP mutations and mLOY was more pronounced when detected with the new method than it would appear with conventional approaches, suggesting that some of the apparent interplay between the two forms of clonal hematopoiesis may only become visible when both are measured simultaneously and sensitively.

This finding carries implications for how genomic instability during aging is dissected. A single cost-effective assay that returns both measurements from one blood sample makes such combined analyses far more practical for large cohorts.

The authors position the strategy as a robust tool for investigating clonal hematopoiesis in age-related disease research rather than as a clinical diagnostic. The published version is a peer-reviewed, accepted manuscript shared early for faster access, citable under a permanent DOI and subject to further editorial revisions before the final version of record. Within those limits, the study offers aging and cardiovascular researchers a validated, simultaneous readout of the two major forms of clonal hematopoiesis in men, with performance benchmarks drawn from more than 400 patients across two independent disease cohorts.

Subject of Research: A targeted deep sequencing method for simultaneously detecting mosaic loss of the Y chromosome and CHIP-related mutations in male patients.

Article Title: An effective method based on targeted deep sequencing to simultaneously estimate mosaic loss of Y chromosome and CHIP-related mutations

Article References: Wang, Y., Yin, C., Zhang, X., Chen, C., Yang, H., Li, G., Gao, Z., Li, K., Ye, C., Zhou, G., Xu, X., Tan, H., Sano, S., & Jin, J. (2026). An effective method based on targeted deep sequencing to simultaneously estimate mosaic loss of Y chromosome and CHIP-related mutations. European Journal of Medical Research. https://doi.org/10.1186/s40001-026-05355-z

Image Credits: AI Generated

DOI: 10.1186/s40001-026-05355-z

Keywords: clonal hematopoiesis, mosaic loss of Y chromosome, CHIP, targeted deep sequencing, ddPCR, UTY, KDM5D, acute aortic syndrome, acute coronary syndrome, somatic mutations, aging, genomic instability