DNA extraction methods influence telomeric DNA integrity and bias telomere length measurements

Accurate telomere length measurement is essential for investigating the role of telomere dynamics in human disease. However, the impact of pre-analytical factors on measurement precision remains poorly defined. Here, we systematically evaluated the effects of commonly used DNA extraction methods on telomere length measurement using a high-resolution single-telomere assay, DNA-array-FISH. Genomic DNA from human blood samples was extracted using four commercial kits representing three major DNA extraction principles: bead-based, salting-out, and silica membrane–based methods. Compared with salting-out extraction, magnetic bead–based method produced significantly shorter average telomere lengths, increased frequencies of short telomeres (< 2 kb), and decreased frequencies of long telomeres (> 10 kb), indicating selective disruption of telomeric regions despite recovery of high–molecular-weight genomic DNA. In contrast, silica membrane–based extraction resulted in only modest but statistically significant increases in the proportion of short telomeres. These findings identify DNA extraction method as a critical determinant of telomere measurement accuracy and underscore the importance of controlling pre-analytical variables to ensure reliable telomere length assessment in both research and clinical applications.