Category: Automation and High-Throughput Technologies

1262-C - An automated workflow that enables cell-free DNA extraction and whole-genome NGS library preparation from 24 plasma samples in a single workday

Tuesday, February 6, 2018
2:00 PM - 3:00 PM

Clinical research for applications using cell-free DNA has gained traction in the field in recent years. Analysis of cancer-associated sequence variants in circulating cfDNA has garnered significant interest due to the potential for detecting actionable mutations in patients being treated for malignant disease. This approach can enable earlier treatment at a lower cost, while incurring lesser risk compared to traditional approaches that require surgical intervention. Monitoring cfDNA via routine blood tests in healthy individuals for the presence of variants linked to malignancy may also allow early detection of cancer at time points where interventions would be most effective.  In addition to use of these “liquid biopsies” for cancer-related applications, analysis of cfDNA released from fetal tissues into the maternal circulation has become a widely-used method for non-invasive prenatal diagnostics, allowing earlier detection of genetic abnormalities without the risk of fetal injury inherent in invasive procedures such as amniocentesis. A third category of diagnostic tests that rely on analysis of cfDNA relates to monitoring of organ transplant recipients for early signs of organ rejection based on detection of organ donor-specific sequence variants in cfDNA from recipient plasma. In addition to these established diagnostic uses for cfDNA, there is emerging interest in the possibility of identifying epigenetic biomarkers in cfDNA to track pathologies that do not involve differences in primary genetic sequence. To realize the full potential of cfDNA-based diagnostics, clinical research is needed to improve workflows that efficiently extract circulating cfDNA at high yield and purity, convert the cfDNA into libraries to allow massively parallel sequencing of regions of interest, and carry out the bioinformatic analysis steps. This poster describes methodology developed at Bioo Scientific, a PerkinElmer® Company, for both rapid high-throughput automated extraction of cfDNA from plasma and said sample preparation of whole-genome next-generation sequencing libraries in a fully automated fashion. The power of this integrated approach is demonstrated by the successful processing of 24 plasma samples in less than one day or 96 samples in approximately one and a half days. We also highlight the results of our automation workflow when analyzing the size distribution of fetal-derived cfDNA in maternal circulation. The research tools and approaches we have developed for high-throughput cfDNA extraction and analysis will facilitate the use of plasma and other biofluids for an even wider range of non-invasive and cost-effective clinical research applications.

Matt Carter

Application Scientist
Bioo Scientific, a PerkinElmer Company
Austin, TX

Application Scientist responsible for automation of Bioo Scientific workflows for nucleic acid extraction and library preparation for NGS applications. Matt studied at the University of Texas at Austin and has previous work experience at Agilent Technologies and Thermo Fisher Scientific.