A nano-magnetic size selective cfDNA extraction platform for liquid biopsy with enhanced precision

[Display omitted] •For the first time, realized DNA size selection directly from plasma instead of purified DNA, thus removing unnecessary steps for most methodologies.•This is the first developed DNA size selection method using hydroxyl magnetic nanoparticles, which was used in DNA extraction without size selection.•The process could bring the fetal fraction in some samples from undetectable to over 20%, enhancing the precision for non-invasive prenatal test (NIPT).•After the enrichment of cfDNA in plasma sample of cancer patient, the proportion of ctDNA was increased by ∼ 100%, reflected by panel sequencing of specific mutation sites.•This approach combined DNA size selection and DNA extraction in one step, and is automatable, providing a simple method to enhance liquid biopsy precision. As an emerging biomarker, cell-free DNA (cfDNA) carries crucial genetic information for the diagnosis of hereditary disease and cancer. However, test accuracy was severely compromised by the low abundance of cell-free DNA in peripheral blood, frequently diluted by genomic DNA released from white blood cells, resulting in sample rejection, test inaccuracy, and restricted clinical utility. Herein we report a novel strategy for the efficient recovery of cfDNA with significant removal of genomic DNA contamination during the cfDNA extraction process, based on a nano-magnetic size selective cfDNA extraction platform. With this platform, over 90% cfDNA recovery rate was achieved with minimal genomic DNA contamination. For non-invasive prenatal testing, an increase of fetal fraction from 10.10% to 29.94% medially was observed in 11 maternal plasma samples, with two false-negative samples identified by the proposed workflow. Enrichment of cfDNA in plasma sample of cancer patient demonstrated ∼ 100% increase of circulating tumor DNA (ctDNA) percentage by panel sequencing of specific mutation sites. The approach is simple, automatable and cost-efficient, can improve liquid biopsy precision and reduce sequencing depth through significant enrichment of target abundance. The nano-magnetic platform demonstrated its potential application in liquid biopsy, since it exhibited numerous advantages in avoiding false negative results, reducing sequencing cost, improving data quality, and rescuing contaminated samples.