Analysis of the first small boxes of samples from the international START study commenced this week at the Unit of Genomic Medicine. More than 4,000 samples will be transported from the US to Blegdamsvej in Copenhagen over the next few months. The samples will be analysed in the laboratory at the Unit, after they have been prepared at the AIDS laboratory. Costs totalling almost DKK 5 mill. are being financed by the American National Institute of Health, and the work is part of a research project to improve treatment for people with HIV throughout world.
Rigshospitalet was selected for the task because of its unusually strong competences within advanced gene analysis.
- The HIV virus is composed of many different variants. “There must usually be at least 20% of a specific virus variant in a sample before it can be identified. However, with the equipment and people we have here at Rigshospitalet, we can identify individual virus variants down to just 1% concentration in the sample,” said Rasmus Lykke Marvig, MSc in engineering and project manager for the task.
Knowledge about the different virus variants is crucial if correct, targeted treatment is to be offered to the individual patient. Some variants spread extremely rapidly, for example, while others are resistant to certain types of medicine.
Targeted investment behind the success
“Several years’ investment in genomic medicine have now been realised in this prestigious task,” said Prof. Finn Cilius Nielsen, Head of Department.
“The technology behind the analyses is called Next Generation Sequencing, and it is well-known on small scale in several other places. However, with financial support from the hospital and external funds, we have established a larger unit for this area. Setting up the precision analyses is demanding on resources and requires highly skilled specialists. We now have both in the structure we have developed over the past four to five years.
The analysis itself is based on nanotechnology, by which many reactions are carried out simultaneously on a microchip.
“In the first phase we prepare the sample and spread a very thin layer on a microchip 2 cm wide and 10 cm long. The sample is then photographed with a special high-resolution device. The picture shows how several billion small DNA sequences are distributed. We compare the pattern with databases of different variants of HIV and identify the types of HIV in the sample,” explained Rasmus Lykke Marvig.
From research to treatment
Work on the samples will also benefit patients at Rigshospitalet.
“At the moment we conduct ordinary standard type-determination on the hospital’s own HIV patients. It will be an obvious next step to use the more accurate test, in which we are now gaining extensive experience, routinely on our own patients,” said Finn Cilius Nielsen.
This will enable more targeted treatment for the individual patient.
- The team from the Unit of Genomic Medicine who are to analyse the samples is composed of Marc Bennedbæk (MSc in engineering), Rasmus Lykke Marvig (MSC in engineering, PhD) and Prof. Finn Cilius Nielsen (Head of Department).
- The task is carried out as part of the research infrastructure provided by Centre of Excellence for Personalised Medicine of Infectious Complications in Immune Deficiency (PERSIMUNE).
- The more than 4,000 samples to be analysed at the Unit of Genomic Medicine come from the international START study being managed by the International Network for Strategic Initiatives in Global HIV Trials (INSIGHT).
- START stands for “Strategic Timing of AntiRetroviral Treatment” and focusses on studying the best time to commence treatment for HIV patients.
- The study has collected 4,688 samples from people with HIV in 35 countries.
- Prof. Jens Lundgren from the Department of Infectious Diseases and Rheumatology at Rigshospitalet is part of the steering group for the START study.
- Results from the START study published in the New England Journal of Medicine, with Jens Lundgren as the main author, caused WHO to change its recommendation in summer 2015 for when to commence treatment, after the study demonstrated unequivocally positive results from starting treatment early.