Pathogenbank
© DSMZ

Bioresources, Biodata and Digital Health

The infrastructure supports researchers in the areas of biomaterials, medical data and bioinformatics, among others. In addition to analytical frameworks for modern research, it also offers tools, documents and templates for evaluations, study planning or biomaterial collections.

In future, the infrastructure "Bioresources, Biodata and Digital Health" will enable a cross-cutting standardization of biomedical data and interoperability of database systems as well as improved access to relevant biosamples, (medical) analysis data or digital tools and methods within the DZIF. The infrastructure provides information on biosamples and collections of pathogens, databases, analysis tools or apps, as well as templates, samples or work instructions that are needed more than ever for translational infection research.

Since 2021, the former infrastructures "Biobanking", "Bioinformatics and Machine Learning", "Epidemiology" and the "Pathogen Repository" have been pooling their expertise in this new infrastructure. All DZIF researchers can use and benefit from the services, training courses and workshops. The external presentation of the infrastructure is still under construction and will be continuously expanded.

Our experts at a glance

The picture gallery offers an orientation about expertises and contact persons for your concerns:

Information on the infrastructure

En route to a comprehensive biomedical service structure within the DZIF, we are focusing our work on:

  • Shared access and use of resources and data
  • Support for data analysis
  • Providing key skills and capacity building through training and consultancy
  • Data/IT infrastructure, digital tools and services through specific projects

Projects and use cases

We have already been able to offer and implement our services in a large number of DZIF projects. The following use cases serve as examples and help interested parties to select and search for offers:

Transplant cohort

  • Support in the preparation of standard operating procedures (SOPs) for the biosample collection and cost calculation
  • Establishment of a quality management system with internal audits
  • Advice on the preparation of the ethics application (patient information, informed consent)
  • Quality management for bacterial sample collection (transport, quality control and storage)
  • Quality control of data
  • Development of apps and a recruitment dashboard

COVID-19

  • Support in the preparation of the ethics application
  • Establishment of a comprehensive COVID-19 tissue collective, which will be sustainably expanded during the pandemic through ongoing autopsies of deceased COVID-19 patients
  • Participation in registries of the National Network of University Medicine (NUM) and the liquid sample-based "NAPKON" project
  • Establishment of a repository for individual participant data of large seroprevalence studies in Germany with meanwhile > 40,000 participant data (within the framework of NUM (COVIM))
  • Methodological support for one of the largest seroprevalence studies in Germany (MuSPAD) on SARS-CoV-2
  • Development of the online tool "CoVerage", which analyses and visualises the spread dynamics of SARS-CoV-2
  • Supporting the SORMAS team in methodological issues related to the evaluation of the implementation of digital surveillance software for national and international contact tracing
  • Provision of a comprehensive technology platform - arranging and carrying out analyses (e.g. sequencing)
  • Provision of rapid evidence synthesis, infection modelling and expertise for public communication and expert panels of state and federal ministries e.g. within the European COVID-19 Forecast Hub

How can we support your research project?
Send us an e-mail

„Currently, information on 4,625 patients, 177,160 biosamples and over 2,200 diagnoses is stored in the DZIF Central Biosample Register. These data can be accessed by all DZIF scientists.“
Andrea Kühn
Andrea Kühn-Steven
Project Manager of DZIF Biobanking

Services of the infrastructure Bioresources, Biodata and Digital Health

We offer numerous services for all DZIF researchers: Among other things, we provide advice and support in sample collection and processing and offer state-of-the-art processing and analysis methods with a technology platform.
Service offerings in the field of bioresources:

Service offerings in the field of Bioresources and Biodata:

Biobanking for liquids

The DZIF Liquid Biobanking is located at Helmholtz Zentrum München (HMGU) and is responsible for all issues related to the collection of liquid biosamples. Our goal is to provide safe, high-quality, authenticated and standardised biospecimens for DZIF projects and external partners.

We are happy to support you in the following areas:

  • Preparation of ethics documents taking into account the re-usability of samples and data
  • Data management of biosample collections (LIMS, federated data management)
  • Quality management: for the transplant cohort we have developed a three-tier QM system with SOPs, friendly audits and quality checks on biosamples, which we are happy to adapt to your needs
  • Entry of your biospecimen collection in the German/European Biobank Register

At all DZIF partner sites and with all cooperation partners, we are working on harmonising and standardising these topics. For the Munich Tx partners, we store the biospecimens centrally in the HMGU Biobank. An important task of our group is the operation of the Central Biosample Register (ZBR), which provides an up-to-date overview of available biospecimens at DZIF. Our lead collaborative project is the Transplant Cohort Tx within the research area Infections of the Immunocompromised Host.

Your contact persons for questions and services regarding liquid biosamples are Dr Gabriele Anton and Dr Andrea Kühn-Steven.

Central Biosample Register (DZIF-ZBR)

Biobanks store biological samples such as human tissue, blood and DNA. These samples and the corresponding medical data are of particular value for translational research at the DZIF. They can be used to uncover disease causes in infection research and develop new preventive, diagnostic and therapeutic methods.

In order to utilise the biomaterials from the individual decentralised DZIF storage locations for research purposes, the "Biobanking" unit at the Helmholtz Zentrum München conducts the Central Biosample Register (DZIF-ZBR). The ZBR merges the biomaterial data from the local systems and consolidates the data from the various sites and studies, making it a valuable data harmonisation tool. By providing the DZIF scientists an overview of the collected biomaterials and associated data via individual search queries, the ZBR thus offers an effective instrument for project planning using biomaterials.

More information on the DZIF-ZBR page

Biobanking overview

Biobanks and biosample collections, also with reference to the DZIF, are available at the "German Biobank Directory" of the “Biobanking and Biomolecular Resources Research Infrastructure” (bbmri). Here you will find information about the biobanks and biosample collections of human biomaterials currently available within the DZIF as well as about biobanks of DZIF partners. A brief description and further information of the individual biobanks can be found under the respective acronyms, if you enter the search term "DZIF" under "Biobank network".

To the participating biobanks

If you want to search for biosamples in an international context, you can start your search query here:

https://directory.bbmri-eric.eu

You can also search for and request organic samples at:

https://samplelocator.bbmri.de/search

Would you like to have your biobank or biosample collection listed in the German Biobank Directory or do you have any change requests? Please send an e-mail to Dr Andrea Kühn-Steven.

DZIF tissue bank

The central DZIF tissue bank at the Heidelberg location provides collectives of relevant tissue samples for research projects at the DZIF. The tissue bank also offers state-of-the-art tissue analysis and technology.

In 2020, existing expertise and infrastructures enabled us to respond quickly and in a targeted manner to the challenges of the COVID-19 pandemic and to provide all scientists with access to liquid and tissue samples from COVID-19 patients. To this end, a comprehensive COVID-19 collective was established in the DZIF tissue bank and expanded in the course of the pandemic through continuous autopsies of deceased COVID-19 patients. Studying the tissue included the analysis of the pathophysiological mechanisms of this infectious disease and made it possible to adapt the treatment of severe disease progressions.

Your contact persons for questions and suggestions regarding tissue samples are Dr Isabel Klein and Prof. Dr Peter Schirmacher.

 

A fresh frozen tissue sample is preserved for research.

© BMBH/Stottmeier

Tissue samples and related services can be requested from the DZIF tissue bank using the following forms:

 

Pathogen repository

The DZIF pathogen repository is located at the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures in Braunschweig. In recent years, the DZIF pathogen collections have grown to include over 3,000 microbial pathogen strains and active substance producers. In addition to bacteria, fungi and bacteriophages are also part of the pathogen bank. In addition, the pathogen repository is expanding its collection to include strains that are important for specific research questions (e.g. microbiomes). Thanks to cooperation with the research area Gastrointestinal Infections and other partners, there are collections of microbiome strains from the gastrointestinal tract of mice, pigs, chickens and humans.

Another focus is the collection and characterisation of multi-resistant bacterial strains, which are increasingly leading to outbreaks in hospitals. The DNA of important strains is sequenced and the information is made available in the corresponding databases. To share our expertise and support projects, we offer DZIF training courses on professional pathogen handling.

to the DZIF collection of the DSMZ

Coordinator of the pathogen repository is Prof. Dr Jörg Overmann. Dr Birte Abt and Dr Thomas Riedel are available as contact persons for questions and suggestions.

 

Bacteria, fungi or bacteriophages are preserved for the long term in the pathogen repository.

© DSMZ/Hanno Kessel

Bioinformatics and Machine Learning

Computational analyses of large biomedical datasets are an essential part of modern pathogen research. In particular, the rapid development of omics technologies has led to an increased need for informatics methods in biological and clinical research. To collect and analyse these data in a sensible way requires the expertise of bioinformaticians as well as specialised software and hardware.

Bioinformatics is therefore an essential component in the analysis of data within DZIF projects and requires extensive expertise to either develop new methods or identify the best available software tools for a task. In the field of bioinformatics and machine learning, we have extensive expertise in the evaluation of bioinformatics and machine learning methods for the analysis of microbial pathogens and microbial communities, the implementation of bioinformatics pipelines and their application in DZIF-relevant translational research.

Oriented towards the needs of DZIF researchers, we focus on the following services:

  1. Training Schools
    Regular training courses for all DZIF scientists. In coordination with the DZIF Academy, we offer training courses, for example on general computer-assisted data analysis (pipeline and R programming), on the use of bioinformatics software (e.g. microbiome and clinical pathogen data analyses, phylogenetics, resistance) and on machine learning applications in infection research.
     
  2. Consulting & project support
    Best practice recommendations for DZIF scientists on experimental design and computer-aided data analysis. Support in selecting suitable methods for specific data analyses from a variety of available computer-assisted methods
    Current workshops and events can be found at the bottom of this page.

The coordinator of the Bioinformatics and Machine Learning department is Prof. Dr Alice McHardy. Kristin Sauerland and Adrian Fritz are available as contact persons for questions and suggestions. Please contact us via our central email address bioinformatics@dzif.de.

 

© DZIF/ScienceRelations

Service offerings in the area of Digital Health

Advice, templates, analyses and studies

TI BBD can provide tips and advice on the storage of various biomaterials. Depending on the origin and intended use of the materials, but also on the local infrastructure, solutions can be found. TI BBD can also help with questions on logistics and the transport of biomaterials, which can have both technical and legal backgrounds.
The Nagoya Protocol has regulated the collection and use of biological resources worldwide since 2014. This means that each country now has sovereign rights over its biological resources. We can help researchers find out what is allowed, what permits are required and how to obtain them.

As part of various collaborations within DZIF, a number of sample texts, standard operating procedures and templates as well as recommendations have been developed and can be made available to researchers at DZIF.

We will be happy to advise you on:

Biomaterials and pathogens

  • Storage and logistics
  • Cost calculation for biosample collections
  • Quality management, good biobank practice
  • SOPs (Standard Operating Procedures)
  • Laboratory Information Management System (LIMS)
  • Pre-analytics
  • Compliance with laws, permits
  • Ethics, informed consent and patient information
  • Nagoya Protocol

Bioinformatics analyses

  • Serological analyses
  • Genomic monitoring
  • Microbiome data
  • Pathogens
  • Antimicrobial Resistance (AMR)

Digital tools to support cohort studies

  • Health research apps (e.g. PIA)
  • Biobanking tools like HEnRY (HIV Engaged Research Technology)

Digital tools to support surveillance of infectious diseases

  • e.g SORMAS (Surveillance Outbreak Response Management & Analysis System)

Tools and methods

Epidemiology

Infectious diseases have different prevalence in different regions. They spread differently depending on the pathogen and the route of infection and affect some population groups more than others. With knowledge of these factors, epidemiology can detect infectious diseases more quickly, contain their spread and prevent further illnesses. The close contact with the NAKO Health Study - internationally one of the largest prospective cohort studies - enables us to transfer specific DZIF research approaches to general population cohorts on a large scale and, amongst other things, to investigate previously undiscovered connections between infections and widespread chronic diseases in the population.

Besides providing epidemiological expertise for different projects, we offer tools and resources in the areas of:

  • Study design, sample size calculation and data analysis
  • Systematic reviews and literature search
    Our experienced team is able to quickly and professionally prepare both systematic reviews and systematic literature searches in cooperation with experts from all DZIF research fields. We support both "simple" literature searches and the preparation of comprehensive systematic reviews.
  • Dynamic modelling of infectious diseases
    We have experience in creating our own infection dynamics modelling. We can support modelling through evidence synthesis or methodological capacity. In the context of the COVID-19 pandemic, we supported public communication and work in expert panels through our own modelling as well as the establishment of a communication platform for the German Modelling working group.
  • Meta-analyses and platforms for conducting individual participant data metanalyses
    We conduct meta-analyses both within the context of systematic reviews and outside of them. In particular, we specialise in building, recruiting and maintaining platforms for conducting meta-analyses with individual participant data. For example, in the context of the COVID-19 pandemic, we built the Serohub, which contains individual participant data from serological studies in Germany.

Please feel free to contact us to discuss how we can provide concrete support for your research projects in the above-mentioned areas: Dr Berit Lange.

Education

In training courses, webinars, workshops and at conferences, the infrastructure passes on its knowledge to researchers wanting to expand their knowledge. Whether "Deep Learning" for the free statistical software "R", application meetings for biosample registers or monitoring outbreak events: Oriented to the questions and problems of DZIF researchers, specific research methods are taught and practised using concrete examples from everyday research. An expansion of the cooperation with the DZIFAcademy is intended.

Current events can be found at the bottom of this page.

Do you and your colleagues have a suggestion for a training course and/or workshop? We look forward to receiving your suggestions.

Links and forms

We have summarised important links and forms for you below:

Publications