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Custom Library Adaptors Via Enzymatic DNA Synthesis Improve Precision of Real-Time Nanopore Sequencing

Presented by:
Tim Mercer, Associate Professor 
Australian Institute of Bioengineering and Nanotechnology, University of Queensland, AUSTRALIA 
Date: December 7, 2022
Time: 7 am AEST | 1 pm PST | 10 pm CET
Benchtop enzymatic DNA synthesis enables the rapid creation of oligonucleotides that can be combined with real-time nanopore DNA sequencing to accelerate the iterative design and testing cycles in synthetic biology. Here, we use enzymatic DNA synthesis to build novel, custom library adaptors, termed CAPTORS, that contain functional sequence elements that can measure the qualitative and quantitative accuracy of an DNA sequencing library. We show how CAPTORS are used to prepare libraries from patient samples, with the functional information retrieved in during nanopore sequencing. We show how the analysis of CAPTORS using adaptive sequencing allows real-time evaluation of sequencing accuracy at per-read, -pore and time level during metagenome experiments in the Nevada Toluca volcano near Mexico City. CAPTORS can also analyse quantitative accuracy, improving measurements of gene expression in mRNA samples, and enabling best-in-class normalisation between samples across large patient cohorts, longitudinal patient timelines and point-of-care testing. These benefits can also be employed to improve clinical diagnosis, with CAPTORS able to sufficiently mitigate nanopore sequencing errors to improve the diagnosis of pathogenic BRCA1/2 variants in breast cancer. Together, this demonstrates how the enzymatic synthesis of CAPTORs can affix information within patient samples during library preparation that is later retrieved by sequencing. The information encoded within CAPTORS can act as internal ‘software’ that interfaces with external bioinformatic software for responsive analysis, and can integrate patient samples into a large decentralised global network or a clinical IT infrastructure. 
Speaker Biography

Tim Mercer leads a research team in genomics and bioinformatics at the AIBN, University of Queensland (mercerlab.org), and co-leads the BASE Facility, Australia’s foremost nucleic-acid biomanufacture facility that drives academic and commercial research into mRNA therapies and synthetic biology (www.basefacility.org.au). Tim Mercer and his team have undertaken basic research in genomics, noncoding RNAs and splicing that have been translated into biotechnologies widely adopted for research and clinical applications. Notable examples include the development of targeted RNA sequencing for the diagnosis of fusion-genes and the use of synthetic NGS controls for improving the accuracy of clinical genomics (www.sequinstandards.com). 

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