Portable and onsite detection of cancer biomarker or GMO: a new norm in the future
Portable and onsite detection of cancer biomarker or GMO: a new norm in the future.
Department of Biology
Cancer wreaks havoc on global health, thus detecting cancerous biomarkers, the biomolecules produced either by cells within cancerous tumors or in response thereto, is imperative to early detection of the disease. The detection of these biomarkers utilising third generation DNA sequencing coupled with cloud computing in a portable platform may lead to new rapid detection methods for cancer. This system could also be used to detect genetically modified organisms (GMO). A HKBU team is making progress in a project related to the above-mentioned objectives, titled “Development of a portable platform for rapid detection of genetically modified organism (GMO) and de novo discovery of cancer biomarkers using third generation of DNA sequencing coupled with cloud computing.” Relevant findings of the research team were recently published in the journal Genome Research (http://www.genome.org/cgi/doi/10.1101/gr.251512.119).
Significant progress has been made with this project. An efficient methodology for fast DNA library preparation compatible with Nanopore sequencing was established, taking approximately 30 minutes for a sample to be uploaded to the DNA library for Nanopore sequencing. Furthermore, an algorithm increased Nanopore base-call accuracy for DNA sequencing from about 80% to 92%. A GMO database consisting of around 40 different types of transgenes commonly used for GMO has also been developed. Importantly, an algorithm called “TrackCluster,” used for the identification of alternatively spliced RNA transcripts successfully used in C. elegans and Arabidopsis, is currently waiting on a US patent applied for in 2019. The findings of this project will likely provide a significant boost to the indispensable efforts for cancer and GMO detection.
This project is led by Prof Zhongying Zhao of the Department of Biology. Prof Zhao is joined by interdisciplinary Co-Investigators Dr Pan Jun Kim from Biology, Prof Zongwei Cai from the Department of Chemistry, Prof Leihan Tang from the Department of Physics, Dr Hailong Zhu from the School of Chinese Medicine, and Dr Zhihong Zhang from Biotech company Burning Rock Dx.