Europe’s leading cancer research facility. Gautheret is in charge of developing tools for basic and clinical research, for example via ICE (Interpretation of Clinical Exome), a collaborative project to develop a scientific software program to help interpret genome sequencing data in order to improve diagnoses for cancer patients and thus offer better treatment.
So what do the Institut Gustave Roussy’s bioinformaticians do? Has big data become key technology for cancer research? How can you guarantee security for patient data? We found out from Daniel Gautheret…
data GALORE… AND bio-informaticiAns
What exactly does your job entail?
At the Institut Gustave Roussy, we develop programs that can analyse patients’ genome alterations. We’re working on the ICE project which involves developing a software program that analyses genome data for cancerology. The final program hasn’t yet been deployed for patients: it will be available in mid-2016. But some parts of it have already been used in clinical trials at Gustave Roussy.
Gustave Roussy’s bioinformatics platform was started four years ago. There are eight of us altogether: bioinformatics engineers and researchers. The tools we create rely heavily on open source programs devised at various research centres all over the world. Our job involves creating treatment chains or pipelines that can link the various programs together in the best possible way in order to address the needs of our clinicians and researchers. Basically, we develop interfaces to make these programs simple and more user-friendly.
Genome sequencing increases its capacities twofold every year, so the computers need to increase their potential and storage power almost every year. And the software has to be able to continue to process data within a reasonable timeframe.
“For our bioinformaticians it’s a constant struggle to keep up with the ever-increasing volumes of data.”
AN active, oPEN COMMUNITY THAT’S constantLY MONITORING THE MARKET
Who are the other players in the ecosystem? How do you work with them?
Bioinformatics is a very open community where information circulates fairly easily. We arrange regular meetings so that bioinformaticians from different organisations can collaborate. For example, the French National Cancer Institute (INCA) organises meetings so we can share best practices and develop ways, together, of addressing the various hospitals’ needs. Also, the Canceropole Ile de France organises seminars whereby we can work with various anti-cancer centres, whilst the Institut Français de Bioinformatique (IBF) enables us to share tools.
The ICE project is a special case in that we’re working with industry members who ultimately plan to develop a commercial tool.
“Bioinformatics is very similar to research: it changes very fast – so fast, that it’s difficult to focus on one tool and put it on the market. When we do take the time to develop a version that we can put on the market, in the meantime loads of other new things have appeared. We have to keep a constant eye on the market.”
HELPING DOCTORS MAKE THE BEST possible dEcisions
You work with substantial volumes of data: do bioinformaticians work a lot with big data technologies?
We do of course use big data because our computing volumes are huge. We also use machine learning to research new genes in cancer or, once we’ve identified mutations, research other related diseases. That said, whilst we do use big data technologies fairly regularly, we don’t do it systematically. Some parts of our software programs are just an interface or for processing genome sequence data.
And what about healthcare professionals: will doctors soon all be using big data to make diagnoses?
Not necessarily. The important thing is that doctors understand what big data can do for them, and that’s not part of medical training!
“Our tools provide very precise information on the characteristics of a patient’s tumour: not all doctors have been trained in how to interpret it and use it as an aid to decision-making.”
It’s a bioinformatician’s job to give the doctor a final report that’s easy to read, interpret and act on, so they can make informed decisions.
Have you come across any reluctance on the part of doctors?
We’re still dealing with clinical research, not day-to-day treatment of patients. We work with doctors who are involved in clinical trials, so they need this data. But soon all patients – and therefore –all doctors will make decisions based on data from bioinformatics platforms. And it’s not just for cancerology: considerable progress is being made in family genetics and concerns a number of illnesses. That too involves big data, which, again, requires training for doctors.
DATA SHARING: AN urgenT ISSUE
How do you ensure security and confidentiality for the data you work with?
We don’t use the cloud: at the moment, there are no centres in France that are both accredited to host medical data and big enough for us. At the moment, our data is hosted at our own data centre: we do all our computing on local servers. We recently received a sizeable donation from Dell for a very powerful computer cluster, which we use to analyse patient data.
Another problem is sharing data. “Real” big data involves comparing the results of patients from several different centres, so we can have as much data as possible. That way, we can provide better-quality statistics and identify rare events that you can’t pick up from a small number of patients.
“The true value of big data can be seen once you accumulate large numbers of patients from different centres and carry out fast analyses.”
At the moment, there is no legal framework governing this: it’s still under discussion, in France and in other countries. It raises a number of questions: what data should be shared? What format? How? We use anonymous data, but the question of how much information centres should be able to share has yet to be determined. We hope this will happen soon, because sharing data enables us to conduct research.
Will research always involve bioinformatics from now on?
Biology is in the process of becoming a quantitative science. There are more and more bioinformaticians in biomedical labs and these platforms are very likely to grow. Medical research is undergoing a real transformation!
==> Read our other profiles of digital makers in the healthcare sector: