The Competence Center for Genome Analysis Kiel (CCGA) is a core facility of the Christian- Albrechts-University Kiel, located at the medical faculty and strategically assigned to the Life Sciences (Kiel Life Sciences, KLS).
The core facility CCGA supports NGS-based research and teaching at the University across faculties and priority topics and provides services related to the analysis of high- dimensional nucleotide sequence spaces. These range from advice on experimental design, standardized sequencing and data transfer to bioinformatic analysis of experimental data (in selected cases and on consultation).
The core facility explicitly offers this service also to partners outside the University to promote scientific collaboration and optimal utilization of the equipment. This is part of the identity of the platform.
The core facility is part of the DFG competence centre network and provides 50% of the services exclusively in this context. If through this network there is not enough project capacity (DFG-funded projects) brought forward to the core facility, the capacity can also be used for other projects to streamline the workflow and avoid idle time.
The CCGA is anchored in the Institute of Clinical Molecular Biology for technical reasons. The direct supervision of the personnel lies with the board of directors of the institute. This organization form serves to maintain the ability to act in administrative decisions (for example, recruitment, methodological competence) that can not meaningfully be regulated across institutions.
The primary task of CCGA is the execution of NGS-based analyses. This includes both DNA and RNA- based analyses, principally across all taxa. Input material are the corresponding nucleic acids. If necessary, and upon prior agreement, the nucleic acid extraction of the original samples can be carried out or already prepared libraries are accepted as well. The risk lies with the user in these cases as well. Quality analyses and sample preparation are carried out exclusively by qualified CCGA personnel.
In addition to sequencing, the CCGA offers additional services for the respective sample types. This includes expert advice from platform scientists and, if necessary, the provision of further planning expertise by the CCGA's "Core Expertise Group". The service also includes project-related support for downstream bioinformatic data analyses and / or the provision of further expertise, e. g. by the link to the bioinformatics network de.NBI. The CAU is associated partner of the de.NBI.
The scientific management of the DFG Competence Center ("Project Committee") is responsible for:
the decision on the use of directly allocated laboratory resources, in particular the examination and confirmation / rejection of user applications, including the appointment of the appropriate platform scientist and, where appropriate, the allocation of further scientific expertise of the core expertise group; and
the administration and management of the budget allocated by the DFG.
The board of directors of the Institute hosting the CCGA (IKMB)
legally supervises the employees of the service facility and
is responsible for compliance with health and environmental regulations
The Core Facility CCGA offers scientific consulting and sequencing analyses as services. This service is aimed at all institutions, working groups and doctoral candidates participating in the CCGA, as well as at external project partners. 50% of instrument capacity are primarily available to DFG- funded projects via the competence centre network (see §1 (4)).
The temporal coordination of services and projects is carried out by the management of the service facility (project committee). In principle, all projects are processed in the order in which they are received. To optimize the utilization, the project committee can define a different order of processing. The decisions are communicated transparently. Critical decisions (for example, sample quality issues with larger projects) may be qualified by the SAB on a case-by-case design.
The Scientific advisory board (SAB) of the service facility CCGA is formed by 3 external members with expertise in the field of NGS, Prof. Karsten Kristianssen (University of Copenhagen, DK), Prof. Tuuli Lappalainen (Columbia University and Core Member New-York Genome Center, USA) and Prof. John M. Archibald (Dalhousie University, CA)
The SAB advises the CCGA on technical and scientific planning, capacity issues, and prioritization of projects.
The Advisory Council will mediate in disputed decisions.
The CCGA offers its users early contact during the planning phase of the experiment in order to consult the experiment design with its advisory capacity.
The contact is made via the CCGA web portal. For this purpose, the application must be submitted via the “new request” feature. This contains information on the design of the experiment, the requested type of sequencing, the project manager and the planned bioinformatic evaluation. The information must be provided in advance in the form of a fully completed request. Incomplete requests will not be processed.
The Project Committee will review the request received and, upon acceptance of the project, will appoint a responsible platform scientist to carry out the implementation planning. This includes a calculation of the anticipated costs of the service according to the respectively valid cost and service catalog as well as the prediction of the probable duration of the project.
The management of the CCGA reserves the right to refuse requests in duly substantiated cases. The refusal must be justified in writing.
Before the project is accepted, a binding statement on the legal requirements of the respective analysis must be made. The users of the service facility are responsible for the respective ethics votes, presence of informed consent (human) and the adherence to ethical guidelines, in animals and humans.
Users are subject to due diligence on the basis of the state of the art in order to avoid the occurrence of damage on the part of the CCGA. This applies in particular to the disclosure of relevant details of projects, including those details which are subject to confidentiality, as far as they relate to occupational safety (e.g. highly infectious material).
All users are obliged to comply with the rules of good scientific practice.
All samples will be exclusively accepted in the barcoded sample containers sent by the CCGA, as specified in the application for use. A detailed and complete sample description / list must be enclosed.
The users must ensure that no danger is caused by the samples they have sent, or that the hazard potential is announced in advance and is clearly marked.
The operation of the sequencer and other devices in the CCGA is carried out exclusively by trained specialist employees of the service facility in order to ensure proper operation.
The samples are stored in the CCGA in alarm-protected refrigerators / freezers for the duration of the analysis, for the storage and transport can not be guaranteed. Remaining materials remain the property and responsibility of the user.
Users bear the project-specific costs for all materials and reagents. All quotes contain a 10% financial buffer for repetitions of failed analyses.
For standard methods, a price list can be found on the CCGA Homepage. Displayed prices are non-obligatory and based of scientific collaboration (see § 10.2). Price details may deviate due to batch size affected laboratory consumable usage.
The prices are calculated without profit-orientation and do not include personal costs, service- and maintenance contracts, depreciation, building rent and maintenance.
Each user of the service facility is obliged to observe data secrecy and is subject to secrecy pursuant to § 203 StGB.
Patient material and data should always be handed over in a pseudonymized form.
The project-related generated data (metadata, primary and secondary data files) are stored in a secure form on a file server of the University. Storage modalities and duration will be defined individually in the project request.
The user (project partner) is responsible for the adherence to the guidelines of the respective funding agency for storage and archiving of the data.
All services provided by the CCGA have to be acknowledged in the appropriate places, e.g. in scientific publications.
The CAU considers the use of the platform as a scientific collaboration in principle, the cost compensation for services provided therefore only replaces a part of the costs incurred on the platform side. Thus, all work and results that have been developed together with the CCGA must be clearly identified as "in cooperation with the CCGA" in the acknowledgements of manuscripts or other relevant documents (e.g. grant applications). Corresponding to the intellectual input (for example in the case of extensive bioinformatic analyses), this also includes a co-authorship of the participating CCGA scientists according to the rules of good scientific practice. The scientific contribution of the CCGA will be mutually evaluated and greed upon individually in each project.
When publishing the data, the corresponding manuscripts must be made available in advance for a sufficient amount of time (14 days).
For regulations on exploitation rights, the statutory provisions under the employee invention law apply.