PhD Call for Applications at VinUni and the University of Illinois on Detection and quantitation of cancer ctDNA and miRNA for point-of-care lung cancer therapy selection

PhD Call for Applications at VinUni and University of Illinois

Detection and quantitation of cancer ctDNA and miRNA for point-of-care lung cancer therapy selection

Open date: 01/06/2023 – Closing date: 31/12/2023

Description

There is a strong clinical need for a technology platform that performs multiplexed, sensitive, quantitative, rapid, and longitudinal genomic readout of tumor biology through detecting nucleic acid molecules released during initial disease development, treatment, and recurrence. While Next Generation Sequencing (NGS) technologies aid the discovery of new genomic biomarkers for cancer, NGS does not provide the required sensitivity for detecting circulating tumor DNA (ctDNA) in plasma that identifies the presence of genetic variants when only a few target tumor gene copies exist within a diverse pool comprised of millions of non-tumor sequences in circulating free DNA (cfDNA). We seek to address an important gap in the capabilities of existing methods to enable routine point-of-care detection/quantification of tumor-associated genes in the blood before, during, and after treatment. Such an approach would enable more timely initial therapy selection, provide a longitudinal readout of the effects of therapy while it is underway, and enable routine post-therapy follow-up as clonal evolution emerges under selective treatment pressures. In this project funded by VinUni-Illinois Smart Health Center, we will focus specifically on rigorously demonstrating the performance of a novel assay approach called “Activate, Cleave, Capture, and Count” (AC3) for ultra-sensitive detection and quantification of several well-known mutations with clinical relevance for guiding initial therapy selection. Specifically, we will design, demonstrate, and validate AC3 assays for KRAS mutations in lung, colorectal, and pancreatic cancers. However, the technology developed in this project is broadly applicable to any ctDNA target sequence through the design of nucleic acid probes that specifically recognize the base sequence of their target.

We are recruiting Ph.D. students and postdoctoral researchers for the following three aims. Aim 1: Development of an assay format for AC3 that is compatible with multiplexing and enhanced throughput, along with the design and validation of synthetic guide RNA (sgRNA) probes for the most common mutations in Vietnamese lung cancer patients. Aim 2: Rigorous and stepwise characterization of the assay to meet quantitative performance metrics. Aim 3: Measure circulating miRNA and ctDNA biomarkers in plasma samples from VinMec patients. Through these Aims, the project will rigorously characterize the sensitivity, selectivity, and repeatability of multiplexed AC3 and TRAP using target mutations with a high degree of clinical relevance while comparing directly to a standard gold method. Our project culminates in the combined evaluation of miRNA and ctDNA from plasma samples of patients, pre-and post-treatment, providing advantages over current practices using NGS.

Training program

As a Ph.D. student, you will undertake training courses that will lead towards a Ph.D. and allow you to gain various skills and expertise to strongly support your future career, whether in industry or academia. Students will be supported in publishing their research and encouraged to present it at international conferences. The students will be advised by professors at Illinois and VinUni from the following team: Illinois: Brian T. Cunningham and Xing Wang. VinUni: Yi Hyeon Gyu, Nguyen Xuan Hung, and Tran Thi Mai.

Qualifications

This project is suitable for students (Vietnamese only) with a bachelor or master degree in Bioengineering, Chemistry, Biochemistry, Molecular Biology, Biotechnology, or a related field. Academic excellence should be demonstrated, i.e., a GPA of 3.2 or above. A Master’s degree and/or experience in one of the following fields: physics, chemistry, biology, or molecular biology is desirable but not essential. Preference will be given to candidates familiar with the development and characterization of biosensors with an emphasis on optics-based approaches such as fluorescence, nanoparticle tags, or label-free detection. The essential requirements are an interest in the topic and a good work ethic. English language requirements: IELTS Academic: 6.5 or above (or equivalent).

Benefits

Selected candidates will work towards their PhD degree granted by either VinUniversity (VinUni) or University of Illinois at Urbana-Champaign (UIUC), and be co-advised by faculty from both universities. During their PhD studies, VISHC PhD students will spend 2 years to study and research at the other university and can optionally seek a master’s degree from that university. This program will cover all tuition fees, living expenses, health insurance, round-trip airfare, and related expenses for VISHC PhD students. The financial support for VISHC PhD students while they are at UIUC is provided by the Vingroup Scholarship Program for Overseas Study for Master’s and Doctoral Degrees. VISHC PhD students will receive a stipend of 10,000 USD/year when they study at VinUni and 25,000 USD/year when they study at UIUC.

How to apply

To arrange an informal discussion, please email VinUni-Illinois Smart Health Center (shc@vinuni.edu.vn) and copy Dr. Tran Thi Mai (mai.tt@vinuni.edu.vn). You must include your CV, a research summary, and the names of two recommenders who can write letters on their behalf.