Personalized onco-genomics group (Pawan Pandoh, Robin Coope, Yongjun Zhao, Richard Corbett)

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This week we profile a recent publication in BioTechniques from Pawan Pandoh
(pictured left) and Dr. Marco Marra at Canada’s Michael Smith Genome Sciences Centre.

Please provide a brief overview of your lab’s current research focus?  

The technology development group at Canada’s Michael Smith Genome Sciences Centre at BC Cancer (GSC) has an unusual mandate within science: it takes emerging tools and methods for novel assays in genomics and turns them into production-ready pipelines which can be offered to collaborators for use on their samples. This requires a higher level of robustness than would be required within a single lab; making processes production-ready typically also involves automating liquid handling so that any assay can be readily scaled to hundreds or thousands of samples.

What is the significance of the findings in this publication?

The advent of next-generation sequencing has enabled researchers to develop assays for diagnosing and managing a variety of diseases, including cancer. Liquid biopsies are one such technique that can assay for circulating cell-free tumour DNA (ctDNA). It is noninvasive and can help clinicians in assessing disease progression and monitor treatment response. Standard isolation of ctDNA involves the separation of plasma by centrifugation followed by column or magnetic bead-based purification of nucleic acids. While magnetic beads are more amenable to automation on liquid handlers, the upstream centrifugation remains largely manual and limits scalability. We present here a magnetic bead-based ctDNA isolation method that eliminates centrifugation steps to allow ctDNA purification directly from whole blood in 96-well plate format. Furthermore, this automated method minimizes manual handling of patient blood, lowering the risk of sample swaps and exposure to staff of blood borne infections.

What are the next steps for this research?

We would like to introduce the automated ctDNA extraction standard operating procedure into production and introduce this in our standard Personalized Onco-Genomics protocol.

This work was funded by:

This work was supported by funding provided by Genome Canada, Genome BC, Canadian Institutes for Health Research (CIHR) and NSERC – Collaborative Health Research Project, BC Cancer Foundation, Canada Foundation for Innovation/BC Knowledge Development Fund and a CIHR Award.

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