Profile
Fern Johnson
My CV
-
Education:
Newbridge School (2005-2010), Crosskeys College (2010-2012), University of Oxford (2012-2015), University of Manchester (2016-2017) (2018-
-
Qualifications:
MSc in Bioinformatics and Systems Biology, BA in Biological Sciencs, A*AAB A levels (Biology Chemistry English Lit German)
-
Work History:
My first full time job was for the charity Marie Curie, who provide palliative care (care for people who are dying). My job was phone based, giving out details of nurse visits to patients or their family, and giving patient details to nurses before their visits. It really gave me a perspective into what it is like to be or care for a terminally ill person, and how much difference care could make. Particularly, that even someone being the scenes is really important in making all this happen. After my MSc I worked for two IT consultancy firms, helping large companies use their data well – this exposed me to useful skills like accessing large databases, and I enjoyed the technical and problem solving aspects of this work. But it definitely wasn’t as fulfilling as working in healthcare, and the lack of science wasn’t as interesting.
-
Current Job:
Trainee Clinical Scientist in Bioinformatics (Genomics)
-
About Me:
Wales born, Manchester based, I like nerd stuff like books and games (and promoting STEM of course)
-
Read more
I’m 25 and live in Manchester with my boyfriend and two cats (one of them is just called Cat). I grew up in Newbridge in South Wales. I can’t speak Welsh very well but I religiously watch the Welsh TV programme Pobol y Cwm (with subtitles on). I’m obsessed with sausage dogs and own way too much stuff with sausage dogs in.
In my spare time I like watching TV or films and going for walks. I dabble in baking as well and can do a mean vegan chocolate chip cookie. I also enjoy gaming on my Switch, I like really story driven adventure or exploration games – because I’m really bad at anything intense where you run around shooting things.
Since I went to university (nearly 7 years ago now) I’ve tried to keep involved in outreach for STEM and/or higher education. I was the first person in my family to go to university and the first to get involved with science, and now work in a niche area that isn’t well known, so I’m very enthusiastic about encouraging young people to think about STEM careers.
-
Read more
To make everything else make sense, first some definitions:
Genomics
Genomics is the study of genes and their functions (as defined by the World Health Organization). Genes are like the blueprint of a person, and make us who we are. We inherit half our genes from our mum and half from our dad, which is why we look a bit like our parents. Sometimes genes get mutations, which can stops them working properly and make us ill. Faulty genes can be passed down generations in families. In the NHS, genomic testing is used to help diagnose disease by looking for mutations within genes that we know can involved in a particular disease.
Bioinformatics
Bioinformatics is the science of collecting and analysing complex biological data such as genetic codes (according to Google, but it’s a good definition). Bioinformatics is a very broad field that can cover almost anything involving both biology and computing, but in genomics it’s focused on processing the complex data genetic testing produces, so that genetic scientists can understand the results of the tests, and report them back to the patient’s doctor. It’s very important that the results are processed correctly, as they could mean that a patient is diagnosed with a specific disease and need special treatment for it, or that their children might inherit this disease.
My Work
I’m a trainee clinical scientist in bioinformatics, specializing in genomics. I’m on the first year of a three training programme, during which time I complete a work-based portfolio , and a part-time master’s, with the aim of becoming a registered clinical scientist in bioinformatics. Bioinformaticians spend almost of their time on computers, running computer programs that translates the genetic testing results into useful information for other clinical scientists scientists, writing new computer programs that allow different genes to be tested or to make current testing better, building databases, researching new tools that might improve the current service, and much more.
Bioinformaticians are just one part of the genetic testing service – clinical scientists in genetics are responsible for arranging patient testing and interpreting the test results, and genetic counselors talk directly to patients about genetic testing, helping them understand the impact of testing, and what their test results mean. There are also technologists who do all the lab work as part of the testing, and doctors and nurses who specialize in genetic diseases. Everyone plays an important part in running a genetics testing service.
I some of my time attending tutorials and having teaching, but a lot of my work is structured into projects, that give me useful skills for the future and tick off my competencies. Not all my projects are directly related to genomics or bioinformatics, but it’s important for a scientist in the NHS to have an appreciation of the health service and the wider issues that surround it.
-
My Typical Day:
Working on different projects, writing computer programs, attending team meetings, solving problems, reading papers, writing up for my portfolio…
-
Read more
My day as a trainee can vary quite a lot depending on which rotation placement I’m doing, or whether I’m at university, or taking a study day. I take one study day a week so that I have time to work on my master’s assignments or revise for upcoming exams, and occasionally I attend university like a regular student, though I don’t have anymore university until November.
Usually I’m working on one or more projects at a given time. This could be working on a simple computer program, or going through an old program that someone else wrote that needs to be updated. It’s easy to spend a lot of time stuck on one problem, and a lot of time on the internet trying to see if anyone else has already solved it. It is very satisfying when you solve the problem and get something working! I’m lucky to be in a department where there is an established team of experienced bioinformaticians who can help me.
If I get stuck with something, or reach a natural place to stop, I’ll switch to something else – I get bored doing the same thing all day and get to manage my own time largely. Trainees are regularly expected to present scientific papers at meetings, along with other staff in the department. It takes time to find an interesting paper, then build a presentation about it. Ideally the paper should be about a new technique or approach that we could start doing in our department. Part of a clinical scientist’s job is to translate ideas from scientific research into new tests in the lab, so we can provide a better service for patients.
I go to bioinformatics team meetings. There is normally at least one of these a week, where everyone discusses how the daily service is running, or how their new projects are going. If it’s relevant I can update the rest of the team on how my projects are going. I don’t always understand everything said in meetings, but it’s important for me to go to know about the bioinformaticians are working on.
I also attend tutorial sessions – qualified clinical scientists in the department spend some of their time teaching trainees like me. This might be about a certain technique or service in the lab, like the cystic fibrosis testing service.
-
What I'd do with the prize money:
I’d spend it on outreach resources that the genetics department can use for events
-
The most exciting thing that's happened this year in my research area:
It’s not ready just yet, but I’m very excited about whole genomic sequencing coming into use in the clinic. At the moment, the tests that are used look at single genes, panels of genes that are involved with a particular disease type, or the exome. In the genome, the exome is the part that has protein-coding genes. Usually these are what we’re more interested in in terms of disease, as normally we would expect a variant in a gene to potentially alter the protein product, causing the a disease – cystic fibrosis is a typical example of this. Looking at the whole exome can be useful if a clinical geneticist (a medical doctor specialising in genetics) isn’t sure which genes or groups of genes are associated with a patient’s condition. However the genome is complex and the DNA that isn’t protein-coding isn’t just ‘junk’ as previously thought, but can have nuanced roles in controlling the expression of protein coding genes. It’s possible that a variant in a non-coding region can ‘switch off’ a protein coding gene, making a perfectly normal gene stop making any protein at all, causing a disease. Whole genome sequencing will look for disease causing variants in the whole genome, helping to find rare disease causing variants. Ultimately this will give more patients an answer or the cause of their condition, and perhaps ways to manage or treat it. In terms of my specialism, bioinformatics, whole genome sequencing presents an exciting challenge due to the vast amount of data that needs to be handled. Clinical whole genome sequencing is due to begin in April next year, and the NHS will be the first National Health Service to offer this.
-
My latest work:
Clinical scientists are usually involved in introducing new tests or improving the genetic testing service, but I’m particularly excited about a project I will be starting next year. As part of my training program I also complete an MSc part time, which includes a work based research project. I’ll be designing an analysis pipeline for a new testing service. Rather than looking for variants in genes, I’ll be looking at microsatellite instability. In the genome, microsatellites are short, repeating sequences – like AGAGAGAGAGAG. The number of repeats should be the same in every cell, though sometime mistakes in DNA replication can result in the microsatellite growing or shrinking in replication, so it’s not the same in all cells – this is called microsatellite instability and can be seen in cancerous tumours with faulty mismatch repair proteins, which normally guard against mistakes in DNA replication. In colorectal cancers, whether a tumour has stable or unstable microsatellites can determine how well some chemotherapy will work. At the moment we look at gene variants in colorectal tumours through next generation sequencing, but microsatellite testing is a separate test. If we could run both tests at the same time, it will help get the results out quicker, so that a patient’s doctors can make faster decisions about their treatment.
-
My favourite misconception about my area of science:
People often talk about having a gene ‘for’ a certain disease. For example, when Angelina Jolie announced that she had had a mastectomy to reduce her risk of breast cancer following BRCA genetic testing, many people with a family history of breast cancer began asking whether they might have the ‘BRCA gene’ or the ‘gene for breast cancer’. Really there are two genes, BRCA1 and BRCA2, and everyone has two copies of each. They place an important role in stopping mistakes in DNA replication leading cancer, so if one of them is faulty, a person’s risk of cancer is increased. I can’t blame anyone for having these misconceptions when genes tend to be named after diseases associated with them – BRCA is short for breast cancer after all.