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A Novel Nanoparticle-based Approach to Improve Extraction of Circulating Tumor DNA (ctDNA)

Updated: Sep 21, 2021

Introduction: Liquid biopsies, especially those that use plasma ctDNA,

are emerging as a powerful complement, and, in some cases, alternative

to solid tumor biopsies for the molecular characterization of cancer. Nonsmall

cell lung cancer (NSCLC) has proven particularly amenable to liquid

biopsies due to the availability of an FDA-approved tyrosine kinase

inhibitor for patients whose tumors have EGFR exon 19 deletions or exon

21 L858R mutations, as well as the need to monitor disease progression

and treatment response. However, collection of ctDNA is challenged by

the low abundance of ctDNA in blood, the potential for contamination by

genomic DNA, as well as other factors. These challenges can lead to false

negative results that limit utility of liquid biopsy. Methods: We compared

the recovery of ctDNA using a commercial column-based approach

(Roche) to a novel magnetic hydrogel particle (Ceres Nanosciences)

method. We created contrived liquid biopsy specimens by spiking

fragmented EGFR wild-type and mutant DNA sequences into pooled

donor plasma at varying concentrations. Recovered DNA was quantitated

and tested for EGFR mutations using a semi-quantitative multiplex PCR

assay (COBAS 4800). The performance of these 2 ctDNA extraction

methods were further compared using plasma derived from NSCLC

patients with known mutational profiles. Results: In the contrived

specimens, the column-based approach recovered 48% to 63% of spiked

DNA, whereas the magnetic hydrogel particles recovered 79% to 84% of

spiked DNA. Importantly, the hydrogel particle-based approach prevented

genomic DNA contamination for up to 24 hours post-collection. Extracted

ctDNA from both approaches demonstrated comparable performance in

the detection of EGFR mutations, with EGFR exon19del, L858R, and

T790M mutation detection possible at plasma DNA concentrations of 0.5,

4, and 20 ng/mL, respectively. Patient data demonstrated concordance

between ctDNA and tissue analysis in most cases, regardless of ctDNA

extraction method. ctDNA analysis revealed an EGFR L858R mutation not

detected by solid tumor testing. Conclusions: The magnetic hydrogel

particle-based ctDNA extraction technique was highly efficient in

recovering ctDNA from plasma. Moreover, the hydrogel particle-based

technique required less starting material (1 mL plasma) than column based

approaches with similar performance in downstream applications.

These results demonstrate the potential benefit of a magnetic hydrogel

particle-based ctDNA extraction technique in liquid biopsy testing of

NSCLC patients. On-going work is focused on integrating this extraction

technique into a multigene liquid biopsy assay.


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