biobank infrastructure

The biobanking infrastructure is located in the INO building on floor F of the Inselspital. The entire equipment that is dedicated to pre-analytical processing (reception robot, centrifuges, primary tube transport system, pipetting robot, cryo-workbenches, and biobank sample elevator) is fully integrated into the 24/7 emergency and routine diagnostic core lab of the medicine laboratory center ZLM. This set-up enables a full integration of the pre-analytical processes of the core lab for clinical samples. These therefore diverse efficient and quality-assured workflows can be tailored specifically to the needs of individual clinical studies. The fully automated -80°C and <-150°C (N2) storage systems are located one floor below the core lab and are directly connected with a sample elevator. The storage room is an access-controlled environment, which is designed for uninterruptable operation.


If you are interested into processing and/or storing of your samples in our biobank infrastructure, please see Biobank Services. 



For the processing within the fully automated storage systems two sample tube types (0.3ml and 0.7ml nominal, 275ul and 525ul working volume) can be used. They come with external thread screw caps and can be obtained directly from the BBS. These polypropylene tubes are of the highest quality, can be flash-frozen and are certified for temperatures as low as -196°C. The tubes are sterilized and free from DNase, RNase, DNA, and endotoxins. Each tube has a unique ID imprinted as a direct-laser etched 2D barcode on the base. In addition, a linear or 2D barcode and an ID readable by the human eye is imprinted on the side of the tubes. Both tubes fit into standard 96 well format racks, which are widely used in many automation solutions.


automated aliquoting

A specified Microlab STAR Plus pipetting workstation was developed by HAMILTON® especially for the BBS in order to achieve rapid sequential sample processing. Generally, samples are aliquoted in less than 3 minutes and it is possible to feed the system continuously with new samples. The pipetting workstation is composed of two robotic units. One unit aliquots various types of liquid samples from primary tubes into the standard cryotubes of the BBS. The other unit de- and re-caps as well, as allocates the necessary cryo tubes. Key features of this system are displacement pipetting using disposable tips to avoid contamination, automated liquid-level recognition and independent pipetting channels.

The aliquoting is barcode controlled and the time point of aliquoting is tracked for each parent-child sample.

controlled freezing

For the subsequent processing of samples, the BBS offers two ASKION C-line® workbenches that are operational 24/7. Liquid nitrogen pipelines directly feed a reservoir at the bottom of each workbench, which creates cryogenic working areas with temperatures of -170°C to -110°C. Due to the dry nitrogen atmosphere and the cryogenic temperatures, frozen samples can be sorted, repacked and/or temporarily stored. Through internal and external barcode scanners every individual cryotube is recognized and tracked. The controlled and documented sample freezing can be performed based on programmable freezing curves, including a "seeding" procedure for immediate crystallization.


Five independent robotic units move the samples vertically in a predefined and temperature-monitored manner along a measured temperature gradient inside the workbench. This enables a defined and reproducible freezing of various types of samples. All relevant curves are saved along with the sample information data. Frozen samples are then transported without interrupting the cooling chain in a nitrogen-cooled container to the -80°C and <-150°C storage Systems.



Immediate controlled freezing and storing at <-150°C (vitrification temperature plus -20°C security margin) is currently considered to be the gold standard for the long-term preservation of biofluids from the cryobiological point of view (6). However, the technology for storing large sample collections at ultra-low temperatures is still in its infancy. It is associated with high costs as robotics at temperatures far below freezing remain an engineering challenge. Currently available biorepository systems are capable of preserving ultra-low temperatures but are not suitable for large-scale sample throughput or vice versa.


Additionally, many known and established biomarkers are stable at -80°C for reasonable storage periods. At present, the focus for the majority of the samples is therefore on storing biobank samples at -80°C as the market provides technically reliable systems for the automated storage of samples at this temperature, and because it is considered the most cost effective option for research based on biobank samples today (7).


While it has been shown that liquid samples remain stable at a storage temperature of -80°C with regard to most standard clinical laboratory biomarkers, it has also been shown, that some proteins may degrade rapidly in bio specimens stored at this temperature (8, 9), indicating that -80°C is probably not sufficient for omics-based (e.g. proteo-/metabolomics) research. Along with the ever-increasing sensitivity of diagnostic platforms (e.g. mass spectrometry), this problem will become more prominent in the future.



storage at -80°C

The automated sample storage system HAMILTON® BIOS was chosen from a call of proposals to the open market. Stringent performance characteristics were evaluated, such as temperature stability, security, sample tracking, flexibility, energy consumption, efficient storage, and reliability required for the biobanking of clinical samples.

In its current configuration, the -80°C BIOS can store approximately. 2 million cryotubes on standard 96-well racks. The temperature stability for maximum sample integrity is realized by automated lid-covered chest freezer compartments. A -80°C tube picker/sorter is a key component of this system. It has been optimized to minimize warming events during internal processing.


Situated in the center of the front is a blue-lighted double door transfer system. The automated tube picker is located at the front right corner while the robotic arm lifting the rack trays is positioned above the second layer of chests.

Nitrogen-cooled sample containers are transported along an external railway that interconnects the three ASKION - C-line’s®. This allows sample introduction and removal without interrupting the cooling chain.

storage at <-150°C (N2)

BBS also offers a possibility for storage at <-150°C with the ASKION - C-line® system. It is one of the first systems of its kind, as the fully automated sample introduction, sorting and removal is still possible far below sub-zero temperatures.

Samples are stored in stainless steel barrels in the gas phase of liquid nitrogen. The handling of samples is carried out at <-100°C with a fully automated picker. The picking process is over within such a short timeframe, that the temperature of the deep-frozen samples will never reach -130°C. In total BBS provides storage capacity for more than 100’000 cryotubes in three ASKION - C-line® systems.


Nitrogen-cooled sample containers are transported along an external railway that interconnects the three ASKION - C-line’s®. This allows sample introduction and removal without interrupting the cooling chain.


6. Benson, E., Betson, F., Fuller, B. J., Harding, K. & Kofanova, O.2013. Translating cryobiology principles into trans-disciplinary storage guidelines for biorepositories and biobanks: a concept paper. Cryo Letters 34, 277–312.

7. Elliott, P., Peakman, T. C.UK Biobank. 2008. The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int J Epidemiol 37, 234–244.

8. Tworoger, S. S. & Hankinson, S. E. 2006. Collection, processing, and storage of biological samples in epidemiologic studies: sex hormones, carotenoids, inflammatory markers, and proteomics as examples. Cancer Epidemiol Biomarkers Prev 15, 1578–1581.

9. Rai, A. J. et al.2005. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 5, 3262–3277.