We’ve all met new people where the first question is, “So what do you do?”. When I reply, I usually get a blank face in response. How do you explain it in plain words? I usually say we are the people in between biology and computer science and it does the trick. Otherwise, you have to explain what is DNA, what is DNA sequencing, what is a mutation, things that are “coded” in us. What is the usual jargon to us might be someone else’s rocket science.
Clinical bioinformaticians have become an invaluable part of our modern healthcare system, due to the development of Next Generation Sequencing (NGS) technologies and the increasing demand for clinical automation. The role of a bioinformatician is based on the integration of computer science, biology and mathematics, intertwined together in order to manage, visualise and optimise the increasing amount of data available. The government’s innovative project to sequence 100,000 genomes for people with cancer and rare diseases by the end of 2018 has intensified the need for such a specialist workforce.
The main role of a bioinformatician in a genetics laboratory is to develop and maintain the sequencing analysis pipeline. That means overseeing and troubleshooting what happens to the sequencing data from the minute they are finished from the sequencer, to the report sent to the genomic clinical scientists to analyse. However that’s not all we do. A bioinformatician is essentially the “techy” person in the department. They can use their skills to offer assistance in making clinical databases, helping with data manipulation for research projects or developing new tools that can assist their work or their department.
As not everyone knows what we do, sometimes it is complicated to explain concepts of genomic medicine, even to people already working in healthcare, so bioinformaticians have to possess the ability to convey their role and its importance to others. In the routine of a genetics lab, they have to be able to liaise with the rest of the laboratory scientists to understand the needs of the laboratory and how, with their skills, they can optimise the service. They would then have to be able to communicate with IT and system administrator teams, to ensure their needs of storage, security and infrastructure are met.
The PHG foundation has created a useful infographic about some of the roles a clinical bioinformatician plays in a genetics laboratory.
One of the drawbacks of some of the clinical scientist specialisms, including bioinformatics, is the reduced patient contact. That by no means suggests that clinical bioinformaticians do not care or have patients in the centre of their work, they are still performing at their best to improve the patient’s condition and journey in healthcare. Although our roles are primarily computational we still have numerous essential interactions with other teams in order to provide our service.
How does the STP prepare you to be come a Clinical Bioinformatician?
The training programme curriculum attempts to outline everything that we are supposed to know when we finish and become registered clinical scientists. However, the specialism as part of a clinical environment is still new and keeps evolving, so trainees should be proactive with their time and attempt to broaden their skills without falling back with the competencies. In my opinion, bioinformatics is definitely not all about NGS, yet that is the main focus of our programme and expectation of our departments. So our training is as follows:
Rotational Modules (Year 1):
Introduction to Clinical Bioinformatics & Genomics
This involves the trainees having a basic understanding about essential bioinformatic tools and clinical databases that aid in genetic analysis. Given a sequence, be able to find everything you need to know about the gene in question. It also involves an introduction to variant analysis. How does a clinical scientist decide if a variant found in a patient is pathogenic and cause the patient’s disorder or is it benign- a polymorphism not negatively affecting the patient?
Introduction to Health Informatics
Health informatics is another specialism in the STP. As part of this rotation, trainees have to undertake a clinical audit. Gather the data needed, analyse it and create a report which has to be presented at their department or Trust. This rotation is all about awareness of how information is treated in a clinical environment, how it is transmitted and what guidelines & legislations govern it. You also get to learn about clinical information systems and clinical decision support systems that are essential part of every hospital’s running and management.
Computing for clinical scientists
Our computing rotation is all about gaining some skills in software development and databases. How would you go about making and maintaining your own clinical tool? This rotation introduces you to concepts of project management, database languages and design, in addition to how to create a web interface and connect your database to it. You get to learn about SQL, UML and if you are brave, make your own website using django.
Information and Communications Technology in the Clinical Environment
This one is a tricky one. There’s a specialism in clinical bioinformatics that is focused on physical sciences, although maybe not as well known/understood. This rotation introduces you to the world of Medical Physics and Clinical Engineering. I think experiences of this rotation vary between hospitals. But the main goal is to get an introduction to what happens behind the scenes in those departments. How do their systems work? How would programming and scripting help in their daily routine? Their work is so vast that everyone might observe something completely different. It might sound a bit irrelevant if you are specialising into genomics, but the STP is about experiential learning, so it definitely adds to the experiences you can draw upon.
In the Clinical Bioinformatics – Genomics specialism there are 5 specialist modules that are undertaken during second and third year of your training. Although we haven’t started any of the specialist modules yet, here is a brief overview of what they should be about. As they are a bit more specialised, they rely upon the interest of the trainee and their supervisor in addition to the specific needs of their host department.
Advanced Clinical Bioinformatics
This module builds on the knowledge acquired during the Introduction to Bioinformatics & Genomics in first year. It attempts to teach the trainee the reasons behind the use of specific tools, and how to choose the appropriate ones for your analysis in addition to how to approach different disorders.
In this module, a trainee is called to develop their own clinical tool. This would usually be in regards to the needs of the host laboratory. The trainee will then have to gather the user requirements and using appropriate project management methodology, develop, test and deploy their tool.
Applied Next Generation Sequencing
As one of the main roles of this specialism is developing and maintaining an NGS pipeline, this module strengthens the trainee’s knowledge on how each and every step of the pipeline works and why it is important.
IT for Advanced Bioinformatics Applications
Touching on how the pipeline works, this module expands the trainee’s knowledge on how to build a workflow for clinical and public health analysis.
Whole System Molecular Medicine
This module has more of a genetic focus, enabling the trainee to undertake a more in-depth genetic analysis and focus on specific biological pathway that a gene could be involved with. It tried to enable the trainee to critically evaluate current testing strategies and if needed, try to improve them.
Considering how you could end up in bioinformatics from a variety of disciplines, I think it might have been useful to have a genetics rotation in the first year of your training. It would be a bit more interesting to get a more overall understanding of the laboratory procedures in our own departments and apply that knowledge onto our future work. Despite that, reaching the end of our first year, I think I speak for almost everyone that we are all excited to start our specialist modules. It is an opportunity to be more involved in what our departments do and learn all the things we signed up for when starting this programme. Hopefully, after the end of the three years, all these modules will have prepared us enough to become independent and qualified, Clinical