A comprehensive computational platform to improve liquid biopsies for cancer detection

Project Overview

Background

Although recent advances in cancer research offer new ways to treat cancer, early detection still represents the best opportunity for curing cancer. Earlier stage treatment not only greatly improves patient survival but also costs considerably less. Therefore, a non-invasive, low cost and reliable cancer diagnostic assay could greatly benefit cancer patients and the public. In this regard, circulating cell-free DNA (cfDNA) holds tremendous potential to develop such a diagnostic assay. However, current methods are either not sensitive or not general enough, and cannot distinguish different cancer types. New technologies are needed to effectively extract the tissue and cancer-specific epigenetic information from cfDNA for early cancer detection.

Aims and Objectives

We are establishing a comprehensive cfDNA genetic and epigenetic sequencing platform. As a DPhil student, you will develop a computational workflow to extract and integrate multidimensional data, including epigenetic (methylation and hydroxymethylation) and genetic (base mutations, copy-number variations, and microbiome) information. We are in the process of establishing a database of tissue-specific epigenetic maps that will allow us to deconvolute the relative contributions of tissue and cancer DNA to the observed signal in individual cell-free DNA sequencing samples. As part of this project, you will be involved in building the first map of comprehensive cell-free epigenetic and genetic features for various solid tumours to help achieve the full potential of liquid biopsy. Finally, machine learning techniques will be applied to build classifiers that distinguish different cancer types from healthy controls and precancerous conditions.

Training Opportunities

This project would suit a candidate with a numerical mindset, ideally with good computational skills. However, the most important feature is curiosity and a willingness to learn. Through this project, you will become familiar with using the full spectrum of bioinformatics tools for next-generation sequencing. You will also learn to use a distributed high-performance computing environment and to develop new statistical approaches to analyse and visualise data.

Theme

Genetics & Genomics and Cancer Biology

Admissions

Project reference number: 961

Funding and admissions information

Supervisors

Name Department Institution Country Email
Dr Benjamin Schuster-Böckler Oxford Ludwig Institute Oxford University, Old Road Campus Research Building GBR benjamin.schuster-boeckler@ludwig.ox.ac.uk
Dr Chunxiao Song Oxford Ludwig Institute Oxford University, NDM Research Building GBR chunxiao.song@ludwig.ox.ac.uk

There are no publications listed for this DPhil project.