The MND Association is custodian of the UK MND DNA Bank. Over 3,000 people with MND, carers and family members donated blood samples to the Bank, from which DNA was extracted, ready for use by the MND research community. The logistics of managing, storing and sending out the correct samples for researchers to use is a huge task. This is managed by a unit at the University of Manchester called BioBanking Solutions. Below some of the key steps in looking after the samples are explained.
Work on biobanking at the Centre for Integrated Genomic Medical Research (CIGMR) at the University of Manchester covers most of the steps in the life of a human sample. So much so that there is a dedicated unit within CIGMR called BioBanking Solutions!
This means they have an ISO 9001:2008 certified biobanking facility for researchers from across the world. They undertake work for collection, processing, storage and distribution of samples for the research community. There are 120 collections under their management, covering a range of different conditions from diabetes, to eczema to motor neurone disease. So, if you think that one collection equals one biobank, then BioBanking Solutions has 120 biobanks!
BioBanking Solutions currently stores 553,887 aliquots in a variety of sample types. The MND Association collection has 11,207 aliquots from 3,362 individuals.
Here’s a description of how we handle the samples from door to door:
Blood tubes are fragile!
Blood samples arrive at the lab in the postal service. When the technician unpacks them they confirm that the tubes are intact and that the labels, identifying the samples, are readable and securely fixed to the sample tubes.
Many of the steps of sample processing within BioBanking Solutions are done with robotics, so its important that the robots know what’s what. After the sample has been checked over, the technician then enters the code on the tube into the laboratory database. The database is used to track everything that happens to the samples; from receipt to storage to shipping, including who handled the sample and when they handled it.
The database-generated barcode label is attached to the sample tube. This barcode is then used to track the sample for the rest of its life through every BioBanking Solutions procedure.
High quality DNA in a high tech way
An hour and a half after a 9ml blood sample is loaded onto the robotics system, DNA is isolated into 1ml of liquid. (The liquid is a ‘buffer’, carefully worked out as the best way to keep DNA as close as possible to how it was in the original blood sample). 1ml is approximately equivalent to the volume in a fifth of a teaspoon of liquid.
At this point it’s not known how much DNA has been extracted from a sample, as each will yield different amounts. The concentration of the DNA needs to be measure next.
How much have we got?
DNA concentration is determined by two techniques: measurement by optical density and by fluorescence. These two readings give the laboratory an indication of the concentration and quality of the sample. Optical density uses the UV absorption of DNA – if you shine UV light at some chemicals, a certain amount of it is absorbed or soaked up. Every chemical soaks up different amounts – so its a way of confirming that you’ve extracted the right thing. The way the fluorescence assay works is more complicated! The fluorescent tag temporarily sandwiches itself (intercalates) within the DNA. It only fluoresces when it is within the chemical. (A way of visualising this fluorescent tag might be to picture a pair of shoes sitting on an open plan, spiral staircase – with ‘80s pink fluorescent socks sticking out the tops of the shoes!).
When researchers request DNA from the DNA bank, they will want the same amount, in the same concentration from every sample they select – to make the results of their experiments comparable. However, as mentioned above, for each person’s 9ml blood sample, different amounts of DNA will be extracted. To make things easier when distributing the samples, the concentration of the samples is standardised, in a process called normalisation. A small amount of DNA is removed from the original sample, and standard dilutions are made, where the volume is adjusted so each is the same concentration.
All of this is done on a robotic platform to ensure accuracy and consistency. When it is complete the robot updates the laboratory database with the location of the aliquots, the 2D barcode of the tubes, the concentration of the aliquots and the volume in each tube. The aliquots are then transferred to a temperature monitored freezer for storage at -80°C, until they are requested by a researcher.
Preparing the samples ready for use
A set of samples is prepared for shipping to a researcher once BioBanking Solutions have a list of which samples are required, and authorisation from the MND Association to release the samples. From the list, the database produces a list of locations from which the samples must be removed – it specifies which location the tube can be found, in which rack of samples, in which freezer. Humans are not relied on to choose the right samples, once again, the tubes are picked out from the racks by ‘cherry picking’ robots.
When all the samples have been chosen, these new racks are defrosted, shaken to mix the DNA and then placed onto (another) robot to remove the required amount of DNA into a new plate (sample grid). Just before shipping, these new aliquots are quality controlled to ensure that the DNA is suitable for research use.
The plate is then heat sealed before being shipped to the researcher on a bed of dry ice. All of these steps are recorded by the laboratory database so that we know what has happened to every sample while BioBanking Solutions have been responsible for it.
“At every step where there is manual work to be done, the possibility of human error creeps in. That’s why we need a really robust quality management system like ISO9001. What’s more, every collection has different requirements: that’s the essence of research. So we need to introduce new procedures – and therefore new risks – all the time. This can be anathema to a commercial entity where just one flavour – vanilla – is preferred. But new procedures are the lifeblood of a research environment like BioBanking Solutions’ ” – commented Kate Dixon, Operations Manager at BioBanking Solutions.