Design and manufacturing of a microfluidic chip for an integrated ctDNA enrichment assay

Compared to solid biopsy, liquid biopsies comprise many advantages both for the patient and the medical team. In fact, there is no need for an invasive surgery as the procedure only requires a routine blood draw. Liquid biopsies rely on the successful detection of circulating cancer biomarkers, such as circulating tumour cells (CTCs), or circulating tumor DNA (ctDNA). The result of a liquid biopsy can be used to (1) better characterize a cancer after its detection for better choice of treatment, (2) evaluate patient’s response to treatment or (3) cancer screening, applicable in early stage. Amongst the latest technologies developed to facilitate ctDNA detection, the nuclease-assisted minor-allele enrichment with probe-overlap assay (NaME-PrO) was proven to be a fast and robust method, relying on the action
of a nuclease enzyme to digest non-mutant cfDNA[1]. This method was chosen and adapted by our group to the PIK3CA gene’s four most common mutations encountered in breast cancer’s cases[2].

The research carried out by our group focuses on the development of microfluidic tools to process blood samples, from blood plasma separation to cancer detection. Previous work has been made[2][3] to design a microfluidic chip
to perform the NaME-PrO assay, with no requirement from the user other than sample loading. The whole project can be divided into three modules (fig.1A): the NaME-PrO assay (fig.1B) is carried out on the microfluidic chip (fig.1C) and operated by an electronic platform (fig.1D). A first on-chip attempt was performed with freeze-dried reagents. However, the microfluidic result did not meet the ones obtained on bench, and optimization is required before thinking of integrating the developed microfluidic system to an effective sample preparation point-of-care device.

The offered project focuses on subtractive manufacturing techniques for microfluidics. The current prototype consists of bonded layers of polymethyl methacrylate (PMMA) and we aim to increase the reproducibility of its fabrication. The candidate will be in charge of improving the manufacturing reliability of the device (fig.1E). The student will work closely with the PhD candidate in charge of the project. They must be keen on working in a pluri-disciplinary
environment and show creativity and rigorousness in problem solving. Although various training will be offered when needed, the student must as a minimum be comfortable with AutoCAD® design.

[1] Chen Song, Yibin Liu, Rachel Fontana, Alexander Makrigiorgos, Harvey Mamon, Matthew H. Kulke, and G. Mike Makrigiorgos. Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment. Nucleic Acids Res., 44(19), nov 2016.
[2] Ieva Keraite. Strategies for the enrichment of circulating tumour DNA in clinical samples. PhD thesis, Heriott-Watt University, 2020.
[3] Adelaide Lety-Stefanska, Ieva Keraite, Alvaro J. Conde, Linda Marriott, Nicholas R. Leslie, and Ma¨ıwenn Kersaudy-Kerhoas. Microfluidic Rare Allele Enrichment In Circulating DNA Sample. 25th Int. Conf. Miniaturized Syst. Chem. Life Sci. MicroTAS, (Accepted on 13/07/2021), 2021.

Supervisor name: 
Maiwenn Kersaudy-Kerhoas
Supervisor and Deputy email addresses:

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