Diverse fragment lengths dismiss size selection for serum cell-free DNA: a comparative study of serum and plasma samples.

BACKGROUND

The objective of this study was to determine the features of fragment length for circulating cell-free DNA (cfDNA) from plasma and serum samples.

METHODS

Plasma and serum samples from different sources were randomly collected. Circulating cfDNA was extracted and purified by a precipitation-enriched and spin-column-based kit. The concentration of the purified DNA was immediately measured by a highly sensitive dsDNA quantitative assay, and then the fragment length was analyzed by capillary electrophoresis. The abundance of a specific fragment was estimated by the area under curve (AUC) for the fragment peak in the capillary electrophoresis.

RESULTS

A total of 199 plasma and 117 serum samples were extracted and analyzed. The average yield of cfDNA from the serum samples (131.67 ng/mL) was significantly higher than that from the plasma samples (32.78 ng/mL, p < 0.001). The average abundance of the 20-400 bp fragments in plasma cfDNA (84.4%) was significantly higher than that of serum cfDNA (51.9%, p < 0.001). Fragment peaks in serum cfDNA always presented in regions around 190 bp, 430 bp, and 630 bp, but plasma cfDNA generally showed a sharp peak in the 165-190 bp region and a much lower peak in the 300<uni-2013;400 bp region. Large fragments in plasma cfDNA were longer than 1000 bp and peaked around the 3000<uni-2013;4000 bp region while the large fragments in serum cfDNA were always shorter and peaked around the 1000 bp region.

CONCLUSIONS

The fragment lengths of serum cfDNA and plasma cfDNA have very different features. Fragment size selection is suitable for plasma cfDNA but may not apply to serum cfDNA.