Mason Lab BSc project - Multiomic analysis of bladder cancer
This site contains helpful information for completing your 28H final year BSc dissertation project in the Mason Lab. General information on the module is available on the VLE - check this regularly.
Expectations, meetings and assessments
Across the year you are expected to spend 1.5-2 days per week on your project, balancing this 40 credit module with your other module topics. As this is a data project, you can be very flexible with when you are working. Remember, this is an individual project (and must be completed and submitted independently), but it is likely the other students who also selected this topic will face similar issues, so support each other! You may enjoy arranging to meet in a computer lab or in the library at the same time in small groups. Whatever works for you.
28H does have some workshops, so make sure you check the Module Planner on the VLE site and look out for any announcements from the module organiser. There is a useful checklist of expectations available here.
During semester 1, we will have our group supervision meetings on Wednesdays 2-3 in B/M/049. Some particular dates to note are tabled below:
| Week | Date | |
|---|---|---|
| S1 W2 | W 01/10/25 | First group supervision meeting |
| S1 Consolidation Week | W 29/10/25 | No supervision meeting |
| S1 Week 6 | T 04/11/25 | Meeting is on Tuesday at 1pm (not Wednesday) in B/M/049 |
| S1 Week 8 | W 19/11/25 | Extended session to include formative presentations |
| S1 Week 11 | W 10/12/25 | Last meeting of semester |
| S2 Week 1 | w/c 09/02/26 | First supervision meeting of semester 2 (day/time TBC) |
| S2 Week 6 | w/c 16/03/26 | Final supervision meeting of project (day/time TBC) |
As your project develops I will set aside an open office hour where I will be available in case you want to drop in to discuss your project. This will be on a first come, first served basis.
The main assessment is your 4000 word scientific report. Deadline: Tuesday 5th May at 12 noon (S2 W11).
There is also the formative oral presentation in semester 1 (S1 W8). There are multiple opportunities for feedback on your writing (S2 W0, S2 W8) - these are for you to make the most of, and are not compulsory.
Scope and aims of your project
Bladder cancer is an incredibly diverse disease, characterised by a very high mutational burden and the highest number of different driver genes among solid cancers. The challenge is to understand the drivers in each patient’s cancer so that we can select, repurpose or develop more personalised treatment.
In this project you will use different types of sequencing data generated from 408 advanced bladder cancers included in The Cancer Genome Atlas (TCGA), an international programme built to understand over 30 different cancer types from over 10,000 patients. Whilst the power of TCGA was having multiple data types, most studies have only looked at one. In your project you will combine datasets to better understand the impact of mutations and gene expression changes on bladder cancer biology. The overall aim of my lab is to better understand existing bladder cancer subtypes, or to find new subtypes which could have a route to clinic.
So, how about your project? You will do the following:
- Familiarise yourself with muscle-invasive bladder cancer literature
- Devise a relevant, sensible and testable investigation where you can compare different types of muscle-invasive bladder cancers using the multiple data types you have available to you
- Perform a systematic data investigation to answer your question
- Critically review your results and determine how this fits within the wider literature - what have we learned and is it clinically relevant?
- Consider and plan the future work you would propose to further understand your results and their relevance (incl. wet lab work, further data analysis, clinical follow up etc.)
Coming up with your own study might feel daunting just now, but don't worry - there are some useful starting points below including some key papers. If you are doing the Cancer cell & molecular biology module, or the Genomics module, you should get some useful context and help from lectures and workshops - don't worry if you don't take either of these. A minimal project would be to identify tumours with/without a mutation in a relevant cancer gene, and then to use RNA sequencing data to compare the gene expression profiles of these cancers, and to try and work out what that means. We have lots of different data (and there are >400 cancers in the dataset) so the project can grow, develop, extend in lots of different ways - the best approach is to try and find a question where you'd be interested in finding out the answer.
Introduction to bladder cancer
To get you started I've recorded a mini lecture on muscle invasive bladder cancer. This is enough to get you going, but you'll want to dig deeper in areas relevant to your project (including looking at studies from other cancer types). Remember - what I've said is my scientific assessment based on the literature and my own research experience - your critique is welcome and expected!
PLACEHOLDER
Relevant (big) starting papers
Robertson et al, 2017, Cell - the paper which describes the full TCGA MIBC cohort
Kamoun et al, 2020, European Urology - the paper which introduces the MIBC "consensus classifier"
Shi et al, 2020, Genome Medicine - the paper which describes bladder cancer hotspot mutations, particularly those created by APOBEC mutagenesis
Baker et al, 2022, Oncogene - paper from our unit which attempts to link viral infection to bladder cancer
Martincorena et al, 2017, Cell - paper identifies recurrent driver genes across all cancers in TCGA - see Figure 2
Cotillas et al, 2024, The Journal of Molecular Diagnostics - an alternative view to bladder cancer classification (all disease stages)
The data