Comparison of the DNA Preservation Capacity of Two Methods for the Long-Term Cryopreservation of Whole Blood Samples

Comparative studies evaluating the quality of DNA from whole blood samples cryopreserved long-term in commercial PAXgene^® Blood DNA tubes versus anticoagulated all-cell pellet (ACP) samples are limited. Here, we assessed the yield, integrity, and purity of DNA from these two types of samples.

We analyzed 100 randomly selected PAXgene^® samples (3 mL of blood processed per tube) that were stratified by storage duration into five-year (n=50) and 10-year (n=50) groups. In total, 50 randomly selected ethylenediaminetetraacetic acid (EDTA)-ACP samples that had been cryopreserved for 10 years were processed. DNA integrity was assessed using the DNA quality number (DQN), which was generated by a DNA fragment analyzer. DNA yield and purity were measured via spectrophotometry (NanoDrop). The sequencing eligibility criteria were a DNA yield ≥10 μg and a DQN ≥8.

The DNA extracted from the five-year and 10-year PAXgene^® tubes exhibited high-quality metrics (median yield: 111.60 μg vs. 85.32 μg; DQN: 9.45 vs. 9.30; A_260/280: 1.95 vs. 1.96; A_260/230: 2.14 vs. 2.17; all P<0.05). Although the 10-year samples presented slightly lower DNA yields and quality, all PAXgene^® samples met the sequencing criteria. Compared with the 10-year PAXgene^® samples, the 10-year EDTA-ACP samples demonstrated comparable median yields (93.18 μg) and DQN values (9.40) but significantly lower purities (A_260/280: 1.83; A_260/230: 1.96) (P<0.05). The sequencing pass rates were 92% for the EDTA-ACP samples and 100% for the PAXgene^® samples (P>0.05).

After long-term cryopreservation, both methods provided DNA with sufficient yield and integrity for genomic studies. However, compared with the EDTA-ACP samples, the whole blood stored in the PAXgene^® Blood DNA tubes yielded DNA with higher purities and tended to have a higher sequencing pass rate.