Capture of Small DNA Fragments for Transplant DNA Analysis

Caryn Tyler
2 hours ago
1 min read

One of the challenges of working with cell-free DNA (cfDNA) is its small size. cfDNA fragments tend to be 167 bp or multiples thereof, and traditional bead-based DNA extraction methods are less efficient at capturing small-size DNA. Traditional DNA extraction methods have a lower fragment size cutoff of ~50 bp, and the yield is typically lower as the fragment size gets closer to 50 bp. This study will compare the recovery of different extraction methods in this size range and use transplant patient DNA as a case study, as DNA fragments from transplanted organs are typically smaller than standard cfDNA and within the 80-120 bp fragment size range.(1)

When transplant patients receive a new organ, it must be monitored for organ health, and the standard of care is typically an organ biopsy. Several studies have looked at using cfDNA biomarkers to monitor the health of the

transplanted organ since a blood draw is less invasive than a biopsy; healthy organs release less cfDNA than failing

organs, and this can be measured by observing changes in the ratio of alleles at a site of genetic difference between

the donor and host.

Differentiation of host and donor DNA can also be difficult; several studies have shown single nucleotide polymorphisms (SNPs) that vary across populations and may provide a site for differences in host and donor

genomes. We utilized PCR assays designed by Kokelj et al. (2021)(2) to evaluate the workflow's ability to capture and

concentrate both spiked cfDNA and transplant patient cfDNA as proof of concept for the detection of these biomarkers from donor organ plasma.