Saamin Cheema (centre above), a recent graduate, joined the Cancer Grand Challenges Mutographs team in January 2021 as a data scientist.
Here, she reflects on her first year working to help tackle the "Unusual Mutation Patterns" challenge.
When I first started working with the Cancer Grand Challenges Mutographs team in January 2021, I had recently completed my bachelor’s degree in biochemistry from University College London and was excited about this incredibly exciting and meaningful opportunity. It was the culmination of a journey that started with a project in cancer genetics during my A levels, up to my final year dissertation in bioinformatics.
Through the Mutographs programme, we are taking on the Unusual Mutation Patterns challenge and our aim is to discover patterns of mutations (called ‘mutational signatures’) that could be linked to a particular lifestyle or environmental factor involved in cancer development. I work at the Wellcome Sanger Institute (Cambridge, UK) and am part of the team responsible for analysing cancer genomes of patients from across the world.
Prior to starting my role, I was aware of the high-impact nature of the work the team is conducting. However, I didn’t realise its sheer scale, with thousands of whole genome samples being analysed, nor the depth and breadth of international collaboration involved, involving researchers and samples from across 26 countries.
Working through the pandemic
Despite the pandemic and remote working, our team has continued to make significant progress over the past year. Over 3,000 samples have now been sequenced and analysed since the team took on the challenge in 2017, and we have managed to analyse over 1,000 in the past year alone.
In 2021, we completed a major component of our programme, revealing new information about oesophageal squamous cell carcinoma, which you can read more about in my colleague Sarah Moody’s blog, here. Since then, we’ve powered on and are now working on kidney cancer. Having finished collecting the samples and generating the data for this cancer type, we’re now at the stage of analysing the mutational signatures and comparing with the information gathered on lifestyles and environment.
It has been exciting to analyse this very large dataset of nearly 1,000 whole kidney cancer genomes – we're starting to see some promising results with the discovery of potential mutational signatures, and the observation that some signatures might be enriched in countries with high kidney cancer incidence when compared to countries with low incidence. We’re currently investigating whether this difference can be linked to lifestyle or environmental factors, which could be contributing to the risk of developing kidney cancer. We hope to share these findings soon.
Cancer Revolution: Science, Innovation and Hope
I was really pleased to learn that our team features in an exhibition on cancer research, which opened in autumn 2021 in Manchester’s Science and Industry Museum and will be moving to London’s Science Museum in spring 2022. The exhibition is called Cancer Revolution: Science, Innovation and Hope and is a partnership between the Science Museum Group and Cancer Research UK.
It takes an honest, uncompromising look at cancer and shares the hopeful side of cancer research. I visited the exhibition in November 2021 and enjoyed seeing how our Cancer Grand Challenges work fits into the broader world of cancer research. From the impact cancer has on patients and their families to the development of modern day therapies, the exhibition provides an extensive overview of the disease in a new and engaging way. It was interesting to learn about the importance of studying animal genetics – for example, I didn’t know that the genes responsible for antler growth in deer are related to genes involved in human cancer. The exhibition also features smart and robotic devices developed to increase efficacy of tumour removal surgeries and new targets for treatments, such as developing drugs to target not only cancer cells directly but the surrounding healthy cells in a tumour which support cancer growth.
Our team's programme of work features as a short film in the exhibition's Seeing and Studying Cancer section, including our investigators based in Cambridge, Lyon and San Diego. The film shares our ambition to uncover underlying causes of cancer and generates optimism that this could lead to new preventative measures. Cancer Research UK predicts that 1 in 2 people will develop cancer in their lifetime, so groundbreaking research like ours is really important.
An inspirational year
In summer 2021, I excitedly moved from my home in the North West of England to Cambridge, where I now work at the Wellcome Sanger Institute. The institute was progressively re-opening its doors, with more staff returning to site, and I was eager to work with my colleagues in person after remote working for 8 months. I really appreciated working on site and benefiting from being part of the scientific community. Unfortunately, due to the rapid spread of Omicron, we’re mostly working from home again – but the team has successfully worked remotely since the start of the pandemic, and we are easily able to continue analysis of data off-site. I’m looking forward to when we can return to the vibrant campus once it is safe again.
I’ve had an inspirational year with the Cancer Grand Challenges Mutographs team, settling into a good working rhythm and cementing my passion for science. I have learned so much and feel proud to be a part of the team. It is a nurturing environment and, with the team’s guidance and encouragement, I have developed my skills and taken on greater responsibilities.
Heading into 2022, I look forward to contributing more to the challenge as we enter the next stages of the kidney cancer study and begin analysis on more cancer types, starting with head and neck cancers.
The header image is of Saamin with her Mutographs colleagues Yichen (left) and Sarah (right) at the Wellcome Genome Campus. Image: Chloe Pacyna.
The Cancer Grand Challenges Mutographs team is generously supported by Cancer Research UK. This article was originally posted on Mutographs.org.
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