Munia Ahmed

Helios Scholar

The bimodal early screening technique (BESTSeq) is a developing amplicon-based sequencing assay that utilizes a single blood test to measure the fragmentation of cell-free DNA (cfDNA) within a patient. It is an accessible and cost-efficient test for early cancer detection. However, factors upstream of TGen receiving the samples such as how the blood tubes are shipped could cause genomic DNA (gDNA) contamination, affecting cfDNA quality in the plasma and influencing sequencing outcomes. To analyze how possible aberrant shipping conditions affect the quality of cfDNA, gDNA contamination, and BESTseq, four patients with two 10mL blood tubes were collected in Streck cell-free DNA BCT tubes. For each patient, one blood tube had a condition while the other acted as a control. These conditions included physical agitation, adding cold packs, leaving it outside over the weekend, and a delay in the processing of shipments. Controls were processed under ideal conditions at room temperature and within 72 hours of collection. After processing the blood samples and extracting the cfDNA, they underwent quality control. Following tapestation analysis and qubit from experimental quality control, there were no significant differences in the size and concentration of total DNA between the conditions and their controls. After viewing the sequencing quality control results from the iSeq run, there were no significant differences in the read counts and quality scores. These results deepen our understanding on how interferences in blood shipments may affect sample quality, but blood collection should always be strictly regulated as BESTSeq moves into a clinical setting.