Isolation and Detection of Cancer Related DNA Nanoparticulate Biomarkers Directly from CLL Patient Blood “Rapid Sample to Sequence Diagnostics”

M.J. Heller, J. Marciniak, A. Sonnenberg
University of California, San Diego, US

Keywords: cancer, biomarkers, DNA nanoparticulates, DEP, diagnostics


The analysis of cell free circulating (cfc) DNA biomarkers continues to become more widely used for cancer diagnostics and management. Cfc-DNA ranges from nucleosomes and high molecular weight DNA nanoparticulates to 100-200bp fragments. We have demonstrated a dielectrophoretic (DEP) based approach that allows a full range of cfc-DNA biomarkers from chronic lymphocytic leukemia (CLL) patients to be isolated directly from a small volume of unprocessed whole blood. Using a DEP microarray device, cfc-DNA from 50 uls of patient blood is separated and concentrated into DEP high-field regions in about 10-15 minutes. The cfc-DNA concentrated on the DEP microelectrodes is first analyzed by fluorescence, and then eluted with a fluidic wash for subsequent PCR and sequencing analysis. Eluted cfc-DNA was then amplified using VHL specific primers, which correctly verified the CLL patient type for over one dozen CLL patient samples. The CLL patients amplified DNA was then sequenced and correlated with previous patient specific sequencing results from DNA originally isolated from white blood cells. Overall, the use of DEP devices for rapid isolation of cfc-DNA directly from a small volume of blood has considerable potential as a point of care (POC) approach for the detection of incipient, residual, and recurrent cancer.