Strategies for Retrieving cfDNA of Short Fragment Lengths Using Mag-Bind® cfDNA Kit (M3298) from Omega Bio-tek

The landscape of cfDNA research is constantly evolving with new evidence pointing to the existence of shorter fragment sizes and their importance in terms of tumor detection, early disease diagnosis, and genomic profiling. Circulating tumor DNA is often fragmented and is of shorter length than the nucleosome-bound cfDNA from normal healthy cells1, 2. The difference in size can be exploited to enrich shorter DNA fragments to enhance the sensitivity of detecting genomic level alterations, point mutations and copy number alterations specifically in tumor and cancer diagnostics. Circulating tumor DNA is a subset of cfDNA and its isolation is even more technically challenging since it is present in such low quantities in an already less abundant sample type. To answer this unmet need, Omega Bio-tek has expanded the capability of Mag-Bind® cfDNA kit (M3298) to be able to recover fragment sizes as short as 50bp through certain protocol modifications. This kit provides the customers different protocols to fit their different application needs. Thus, this kit offers researchers and scientists the flexibility to use the same kit for not only large volume sample processing but also for recovering short cfDNA fragments.

 

The standard M3298 protocol can be modified by either addition of supplemental binding buffer (JSB Buffer) or by addition of isopropanol depending on the fragment size of interest. Table 1 elucidates the protocol modifications needed to extract fragments >50bp or >75bp and compared to the standard protocol.