Biobanks and resources have opened up a whole new way of performing research with big cohorts of patients. Anna Perman* investigates.
Biobanks might stir up an image of shelves overflowing with jars containing organs and specimens. In fact modern day biobanks tend to be a slightly sleeker affair, filled with the hum of freezers storing thousands of tiny sample tubes, which comprise most of the samples in today’s bioresources and biobanks, along with urine, saliva, and other biological products, in sub-zero temperatures, and the occasional puff of smoke from liquid nitrogen.
Scientists working with these samples can pull together the rich information contained within them to gain insights into particular medical conditions and search for better treatments. Their research is facilitated by sophisticated infrastructure across academic institutions and hospitals that works to collect the individual samples from patients and healthy volunteers, and to protect them from
damage and decay.
Dr John Cason, from the King’s College London Infectious Diseases Biobank, works closely with partners at hospital trusts like Guy’s and St Thomas’ to collect samples from both healthy patients, and those with infectious diseases, while others are collected by approaching patients when they’re attending clinics. Each sample provides researchers with a biological picture of an individual in a moment in time. ‘There are lots of biobanks with a range of tissue types. But, as a biobank collecting infectious disease samples, we’re pretty unique,’ he says.
Biobank samples give scientists a unique view of how diseases develop. The team stores samples from patients, sometimes before and after infection, and sometimes over the course of their illness. This sits alongside the clinical data collected about when they were diagnosed, and patient consent for the samples to be analysed.
‘In HIV for instance,’ says Cason, ‘we have been able to see the way the disease develops in the blood. From analysing historical samples taken from patients over time, we’ve seen the way immune system cells such as CD4 and T cells die off, and how HIV progresses to AIDS. If you take samples from patients now, they look different, as patients are put on retroviral treatment straight after diagnosis and this affects their cell populations. But having these historical samples stored in the biobank gives us a unique picture of how HIV develops, which can lead to the development of new or improved treatments.
A snapshot of a person
The recruitment process for the biobanks covers the persons’ key information such as height, weight, diet, and whether they smoke, so that their samples give as full and useful a snapshot of that particular person in time. It is also crucial to ensure those donating samples give clear consent for their materials to be used in projects that researchers in the future might undertake.
The National Institute for Health Research (NIHR) BioResource for Translational Research, which includes the BioResource Centre Guy’s and St Thomas’, one of 13 centres, takes a different approach.
One of its main aims is to allow for recall studies, so participants that have consented to join, can be invited to take part in other research studies based on their genetic makeup, and or their physical characteristics – this is the key difference between BioResource and a biobank. Samples collected at these centres are then stored at the NIHR National BioSample Centre in Milton Keynes.
The staff in the NIHR BioResource Centre Guy’s and St Thomas’ find that people are remarkably willing to donate samples and be recalled for future studies, as they understand the value that research has in developing new and improved treatments.
Each sample may preserve a moment in a person’s life, but the collection as a whole is a snapshot of the entire population. If researchers are using the NIHR BioResource to select participants for studies, it’s important that these samples are representative of the UK. As Guy’s and St Thomas’ serves communities in the London Boroughs of Lambeth, Southwark, and Lewisham, it has access to one of the most ethnically diverse populations in the country.
Working against time and temperature
‘Time and temperature are our main enemies,’ says Sam Wadge, Senior Research Laboratory Technician at the NIHR BioResource Centre Guy’s and St Thomas’.
When samples at any biobank or bioresource are collected, best practice is to keep them on ice, to prevent them heating up, and the proteins denaturing. The team in the lab will then process the samples, ensuring accurate records of who gave them, and when, and in the case of the NIHR BioResource Centre Guy’s and St Thomas’, tagging them with a 2D barcode.
In the past, processing samples would have involved technicians breaking up the samples into useable parts. They would measure and extract the DNA – a mark of its quality for use in future studies. The tubes containing the red and white blood cells and plasma would then be labelled, and put in a freezer.
The team then freezes the samples on the same day. While this prevents the samples degrading quickly, it can’t keep them pristine forever. Over time, even frozen samples will degrade, but freezing at sub-zero temperatures mean the samples can last for decades, instead of merely a few hours.
Today, these steps are completed by robots, which bring benefits for standardising the collection. But the technician’s role is still vital. ‘This robot can work out there’s a problem,’ says Wadge, ‘but if something goes wrong, it just stops doing its programmed job. You always need to have someone analysing it’.
Most of the freezers in the BioResource are at -80oC. This is the perfect temperature for DNA taken from blood. Tissue from biopsies is harder to store. Liquid nitrogen is needed to get them to even lower temperatures than the freezers, to keep samples stable.
Sub-zero temperatures come with their own cost however. The rapid change in temperature when samples are frozen creates ice crystals, which may break up proteins.
A further threat comes with actually using the samples for their intended purpose. When researchers request them they are taken from their sub-zero temperatures, and thawed back into liquids. ‘Thawing a sample is always bad news,’ says Wadge, ‘and researchers analysing the data from these samples will need to take these factors into account.’
Biomarkers or other proteins and enzymes tend to be the subject of research using biobank blood samples, and also in selecting patients to be recalled to studies via BioResource.
Yet these are the most vulnerable part of the liquid. The ice crystals breaking up the proteins mean these will be slightly denatured every time the samples are frozen or thawed.
So although these samples take a snapshot of a person in time, the picture loses some of its sharpness over the years.
Time and place
But a freezer is not enough to make a biobank – the technicians and researchers maintaining these collections have to think about their location, and how they protect their samples. They have to strike a difficult balance between having sample tubes with large volumes of fluids in them, and risking the damage that comes with frequently thawing and refreezing, versus dividing a sample into many small tubes, which need only be thawed once, but take up lots of freezer space.
And space is at a premium. In any hospital or university, there are lots of different departments and wards jostling for room – on central London sites, that problem is intensified.
The NIHR BioResource Centre Guy’s and St Thomas’ has taken a unique approach to space, by having individual 2D barcodes on each of their tubes. While other biobanks label their samples indicating where they should go, the barcodes allow the BioResource to make the most of their local storage.
When samples are taken out, a specialised robotic arm can track down the sample by scanning the codes on the lids of the tubes until it reaches it. Then the remaining samples are re-compacted, and put back in the freezer. There’s no need to leave the space empty for a sample to be returned, because the samples are coded by what the tubes contain, rather than where they sit in the freezer.
Between the equipment required to process samples, and the freezers needed to run constantly, biobanks eat up a lot of power. Staff working at the biobanks at Guy’s and St Thomas’ have alerts set up on email, and mobile phones, so if a fridge were to stop working at any time, day or night, the team can respond.
Less likely, but potentially even more catastrophic are risks such as fire or building damage. Some scientific resources manage this by hiding their samples away, for instance the Svalbard Seed Vault deep in a mountain. This isn’t an option for biobanks, which need to be accessible. The recently established NIHR National BioSample Centre manages this by holding samples collected from the NIHR BioResource Centres in different centres.
The staff at the Infectious Diseases Biobank has another concern to consider – biosecurity.
‘Our lab is under high security,’ says Cason, ‘so we make it hard for people to get in, and are really careful about the research that we allow. We also make it hard for anything to get out. Samples are processed under negative pressure, so any infectious particles are contained within the facility.’
How to future proof a biobank
Research can take some unpredictable turns. Scientists are increasingly storing faecal samples in biobanks, as microbiome studies become more popular. Had you told this to people setting up these facilities 10 years ago, they would have been surprised. They focused on blood, as this DNA-rich material is great for genetic studies, and can be taken from patients in a non-invasive way. Now the facilities are keeping an eye on emerging trends and trying to stay ahead of the curve, but this will always be an imprecise science.
A key area of focus is rare disease. The NIHR BioResource has recently brought together a rare disease component and two new cohorts are run by NIHR Guy’s and St Thomas’ Biomedical Research Centre. This focus, alongside the opening of Guy’s and St Thomas’ Rare Disease Centre will bring together clinical and research expertise that could mean real breakthroughs in patient treatment.
While experts can’t predict the future, they do agree that what we have is a valuable resource, and one that scientists will continue to use. That’s why they will continue to fight for the resources required to run biosample facilities such as biobanks and bioresources, and work with patients and healthy volunteers to take as many pictures of the population as they can.
*Anna Perman is the Communications Manager for the National Institute for Health Research Guy's and St Thomas' Biomedical Research Centre, UK.