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Biobanking at the CCG

Biological specimens are widely used for nucleic acid isolation and a critical resource for all genetically motivated studies. Over the years the CCG team acquired a great expertise for major biobanking issues concerning project management, sample storage, DNA isolation and downstream processing. Thus the CCG is well equipped to manage large disease orientated studies whose success also depends on biobanking skills as well as team work. We can help you in identifying weak points, finding collaborators and work out standard operating procedures tailored to your particular needs.

Storage and Safety

A critical point of biobanking is to have sufficient space for storage. The new location of the genomic centre is planed from the outset to maintain freezer footprint and capacity (no storage in liquid nitrogen to date).

The worst cases for biobanking are damaged cooling devices and power failures. All critical components are connected to emergency electricity generators and uninterrupted power supply. Freezers and cooling rooms are externally temperature controlled and monitored.

 

freezer temperature viy network

High throughput DNA isolation

The CCG is running Qiagens Autopure LS system that enables automated purification of genomic DNA from up to 96 samples a day and different sources (e.g. blood, saliva, body fluids, buffy coat) using proven Puregene® chemistry. A long time stability of DNA stored at 4°C for 16 years has been demonstrated.

DNA storage and normalisation

The challenge of DNA storage not only depends on long time stability but secure identification and processability for automated liquid handling systems.

We use an Abgene 2D barcoded storage system with an encapsulated unique data matrix barcode on each tube allowing storage in a compact 96 well format. Together with a pipetting robot integration of a 2d barcode scanner and a tube capper/decapper we developed a full automated DNA normalization system with database-driven sample identification.

Laboratory information management system (LIMS)

Biobanking depends to a high degree on database support. We decided to develop our own LIMS system (DBCCG) to have more flexibility in fitting our project demands. Software programming aims mainly on fast developing time while user interfaces should be as simple to handle as possible.

 

 

freezer

 

DNA quality management

As the success of all further experiments mainly depends on DNA quality we take e deep look at every sample. There are many different techniques allowing the appraisement of DNA - used dependent of the planed experiment.

gel electrophoresis

This is still the method of choice to identify sample degradation

photometric

We photometrical measure DNA with 1 and 8 canal NanoDrop instruments. That method works very well for DNA of good quality and allows the quantification as well as the identification of protein contamination.

fluorescent

The incorporation of fluorescent dyes in double stranded DNA followed by reading out light signals after excitation is the basis of this method. It allows the specific identification of double stranded DNA but is much more expensive.

We have a simple - Invitrogen Qubit - based device to measure single samples on the fly and a plate based (pico green) with integration into a liquid handling system followed by optional normalization.

copy number

ABI offers a validated assay to measure the RNAseP gene copy number (real time PCR) of human DNA samples and therewith the amplificable DNA proportion. As the most genotyping methods depend on PCR or equivalent enzymatic reactions and signal clustering is accident-sensitive for wrong normalized DNA we consider the RNAseP assay as the most faithful method for human DNA quantification that aims to normalize human DNA as even as possible.

lab-on-a-chip

The Agilent lab-on-a-chip (developed by Caliper) microfluidics technology allow the exact measurement of DNA and RNA size distribution in a range of 50-12000bp. We mainly use it to control the process of library creation necessary for next generation sequencing and RNA quantification.