Integrative Cancer Genomics: Single-Cell Transcriptomics and Oxford Nanopore Long-Read Sequencing for Biomarker Discovery

About the Project

Details of the Project

Sarcomas are rare and biologically diverse cancers, comprising more than 70 histological subtypes, each with distinct genomic and molecular characteristics. Their heterogeneity leads to significant clinical uncertainty, with limited reliable biomarkers available to guide diagnosis, prognosis, or treatment decisions. Although traditional short-read sequencing has uncovered a complex mutational landscape, many critical regulatory mechanisms, particularly transcript isoforms, gene fusions, RNA splice variants, and tumour-cell subpopulations, remain poorly characterised. To address these gaps, this project aims to generate an integrative, high-resolution molecular map of sarcoma using a combination of single-cell RNA sequencing (scRNA-seq) and Oxford Nanopore long-read transcriptomics across a diverse cohort of patient samples.

The student will generate and analyse single-cell transcriptomic profiles to identify tumour subclones, immune microenvironment states, stromal interactions, and transcriptional programs associated with metastatic progression and treatment resistance. This fine-grained cellular resolution will allow the discovery of distinct malignant cell states, lineage trajectories, and rare subpopulations that may drive aggressive behaviour. Complementary long-read sequencing will enable full-length transcript reconstruction, detection of novel isoforms, and validation of structural and splice variants that are often missed by conventional short-read approaches. This dual sequencing strategy provides a comprehensive view of both cellular heterogeneity and transcriptomic complexity.

Using advanced bioinformatics, machine learning, and multi-omics integration, the project will:

1. Characterise intra-tumour heterogeneity and identify clinically relevant cellular states.
2. Detect novel fusion transcripts, isoform switches, and long-noncoding RNAs associated with metastasis.
3. Validate biomarkers across the full sample cohort and correlate molecular signatures with available clinical and pathological metadata.
4. Generate a comprehensive biomarker catalogue to inform translational research and potential diagnostic or prognostic assays.

This project provides extensive training in wet-lab methods, multi-omics data analysis, long-read informatics, single-cell analysis pipelines, and computational oncology. The outcomes have the potential to directly inform future sarcoma diagnostic tools, patient stratification strategies, and precision oncology approaches.

Overseas Applicants

Overseas applicants may apply for this studentship but will need to pay the difference between the ‘Home’ and the ‘Overseas’ tuition fees. Currently the difference between ‘Home’ and the ‘Overseas’ tuition fees is £17,712 for 2026/7. As part of the application, you will be required to confirm that you will provide this additional funding. Please indicate this on the application form in the funding section.

Location

This position will be based on the Aston Campus in Birmingham, UK. The successful candidate will need to be located within a reasonable distance of the campus, and will be expected to visit in person regularly.

Person Specification

Candidates should have been awarded, or expect to achieve, EITHER:

a] a First or Upper Second Class award in their Undergraduate Degree (Bachelors or UG Masters) from a UK institution, in a subject judged by Aston to be relevant to the proposed research.

OR

b] a Merit (or above)* in a Postgraduate Masters degree in a relevant subject AND an Undergraduate Degree (Bachelors or UG Masters), both from UK institutions.

*where appropriate.

Qualifications from overseas institutions will be also considered but performance must be equivalent to that described above, and the University reserves the right to ascertain this equivalence according to its own criteria.

Contact information

For formal enquiries about this project contact Dr Mohammed ‘Mo’ Elasrag at m.elasrag@aston.ac.uk

Submitting an application

We can only consider applications that are complete and have all supporting documents. Applications that do not provide all the relevant documents will be automatically rejected.Your application must include:

1. English language copies of the transcripts and certificates for all your higher education degrees, including any Bachelor degrees.
2. A Research Statement detailing your understanding of the research area, how you would approach the project, and a brief review of relevant literature. Be sure to use the title of the research project you are applying for. There is no set format or word count.
3. A personal statement which outlines any further information which you think is relevant to your application, such as your personal suitability for research, career aspirations, possible future research interests, and further description of relevant employment experience.
4. A Curriculum Vitae (Resume) which details your education and work history.
5. Two academic refereeswho can discuss your suitability for independent research. References must be on headed paper, signed and dated no more than 2 years old. At least one reference should be from your most recent University. You can submit your references at a later date if necessary.
6. Evidence that you meet the English Language requirements. If you do not currently meet the language requirements, you can submit this at a later stage.
7. A copy of your passport. Where relevant, include evidence of settled or pre-settled status.

Interviews

Interviews will be conducted online via Microsoft Teams. If you are shortlisted, you will be contacted directly with details of the interview.

Apply for this position here

Please select “Research - Biomedical Sciences” from the application form options.

If you require further information about the application process please contact the Postgraduate Admissions team at pgr_admissions@aston.ac.uk

Funding Notes

This project covers the Home tuition fees. Candidates who do not have Home status will be responsible for the difference in tuition fees. Currently the difference between ‘Home’ and the ‘Overseas’ tuition fees is £17,712 for 2026/7.