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FEN007 - Isolation of specific size ranges in cfDNA samples for target enrichment 
 
 

FEN007 - Isolation of specific size ranges in cfDNA samples for target enrichment.

Cell free DNA (cfDNA) is comprised of short, degraded DNA fragments from necrotic cells of the body, and is found in the bloodstream. Analysis of cfDNA via liquid biopsy is a promising avenue for the development of new tools in the clinical diagnostic field of Oncology. Already, cfDNA analysis is used for non-invasive prenatal testing (NIPT), and the hope that circulating tumour DNA (ctDNA) sequencing will enable early-stage cancer detection is spurring research. The nature of cfDNA work is not trivial, though. Often, target fragments from these samples are characterized as the needle in a haystack, and the need to sequence through cfDNA of normal tissue origin to find fragments of fetal or tumour origin can necessitate high costs, and incur significant false-positive rate1.

It has been put forward that for cfDNA applications, fragments of interest appear to be preferentially associated with specific size ranges that are a subset of the entire cfDNA collection2,3. This phenomenon is currently being further investigated by Dr. Hunter Underhill and his colleagues at the University of Utah. Previous work on this project required manual PAGE size selection to achieve narrow size ranges (+/- 10 bp) to characterize mutant allele frequency across the full fragment length distribution of cfDNA. However, utilization of PAGE is time intensive. A single PAGE extraction, according to Dr. Underhill, can take up to 2 days to complete. The NIMBUS Select with Ranger® Technology was developed for high throughput, fully automated gel electrophoresis. The system has preparative (i.e., size selection) and quality control (i.e., analytical) capabilities. Users can size select up to 96 samples in a single run with industry-leading reproducibility, accuracy, and recovery. Dr. Underhill has generated validation data with the NIMBUS Select that has convinced him to employ the solution for his continuing work with cfDNA.