Research Associate in nanopore sequencing of ultra-short DNA targets
The Clinical Microfluidics group, headed by Dr. Maïwenn Kersaudy-Kerhoas, develops and utilises microfluidic platforms for the preparation of biological blood samples for the recovery of circulating cell-free nucleic acid markers. The laboratory is a friendly multi-disciplinary group fostering numerous collaborations between engineers, physicists, chemical engineers, materials scientists and biologists working towards a common goal: the development of robust, simple tools, to maximise the integrity of emerging circulating nucleic acid markers and potentially transform the way liquid biopsies are currently implemented.
Being able to rapidly identify genomic sequences of an infecting pathogen will help to make rational medical decisions in the management of patient presenting sepsis symptoms. This genomic information can improve treatments, decrease the prescription of broad-spectrum antibiotics, reduce the burden of antibiotic-resistance in the hospital environment, or avoid the use of antibiotics altogether, if cause is viral, fungal or parasitic. Current diagnostic technologies involve long and laborious blood, CSF or urine cultures, which provide answers after broad-spectrum antibiotics are administered. Microbial cell-free DNA (cfDNA), released from lysed pathogens in the infected human circulation, has been shown to have high sensitivity for detection of pathogens. Portable genome sequencing technologies, such as the MinION platform from Oxford Nanopore, are cheap and portable, and have great potential for point-of-care detection of sepsis causes via microbial cfDNA. While nanopore technology is more suited to long reads, library separation strategies have been successfully developed to enable sequencing of short fragments, such as cfDNA.
We are seeking a researcher with experience of portable sequencing Oxford Nanopore MinION workflow, able to confidentially and independently develop this capacity in our group. Your role will be twofold. Firstly, you will implement the Oxford Nanopore MinION platform in the group and develop library preparation protocols in view of sequencing microbial cell-free DNA. Support from the local Nanopore user group “ION BRU” and from collaborators at the University of Birmingham (Dr Josh Quick) is available. Secondly, you will be expected to develop an introductory MinION nanopore sequencing workshop and travel to Nigeria for a 3-4 day trip in late summer 2020, to deliver the workshop, together with other experts, to colleagues at the Nigerian Institute of Medical Research in Lagos. This project is funded by the Royal Academy of Engineering Frontiers of Development and an internal Global Research Challenge fund.
The candidate is expected to have a qualification in Biology or Bioengineering or a closely related discipline, and theoretical and practical knowledge of sequencing, as well as a proven ability to implement Oxford Nanopore MinION protocols. You will be expected to perform clinical blood sample preparation, develop library preparation technique and use state-of-the-art DNA quantification techniques, such as Agilent Tapestation and Qubit. Excellent communication skills, enthusiasm and the ability to work well in a team, and travel internationally, are essential as the role involves active interactions with engineer scientists, biologists and clinical users in multiple locations. You will be expected to be proactive, ambitious and rigorous in your work as well as self-motivated and independent in your implementation of the MinION workflow.
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