Laboratory considerations | Contingency plans | Biobank management | IT requirements | Staff and training | Quality control | Questionnaire checklist | Biobank contacts and organisations

Welcome to our biobanking page! Effective control of diseases depends on several pre-requisites and tools available to rapidly identify the responsible pathogen. Adequate biobanking is important as a source of reference materials for developing, improving and implementing diagnostic assays, epidemiological surveillance and global health research. Sustainable in-country sample biobanking allows capacity development, independence of sample management and facilitates the monitoring of infectious diseases outbreaks.

This page will provide you with lots of information and resources to help you plan and set up a biobanking system within your laboratory, or as part of a multi-site biobanking network. We have provided a list of things to consider before setting up, to ensure you can implement a system appropriate to your current needs, as well as ensuring the sustainability of the set-up in the future.

It is important to identify your aims and why you want to set up a biobank in the first place, so that you can pinpoint the most essential factors. It is also vital to identify a budget and remember that ‘a biobank is for life’ and that the set-up costs will only be a fraction of the lifetime costs. Since it is likely to be financed by public funds, it is also important to have clear public communication strategies. The principles and purposes of biobanks can often be unclear to those providing and collecting samples and it is therefore important that the aims are well defined, ensuring the project is supported in the long term.

General resources

The links in this section are to resources and web pages that provide general, or background information about the uses of biobanks and how to set one up:

This blog gives a list of things to consider before setting up a biobank

This paper provides an introduction to starting a biobank (including listing the types of biobanks)

This website from IARC learning has a number of informative videos and articles about setting up a biobank

This article explains H3Africa’s biorepository programme

This paper outlines the current questions and positions on the use of biobanks

This paper outlines the setting up of the GETAfrica consortium to tackle African biobanking, biosecurity and infrastructure developments following the West African Ebola outbreak

Thermo Fisher biobanking learning centre

Thermo Fisher virtual biobank (pipelines and layout)

Thermo Fisher have a blog on new biobanking advances

Things to consider

Before you begin planning your biobank, there are a number of important things to consider. You may have to rank your priorities depending on the aim, funding and scale of your project. We have created a checklist of questions to help you do this.

The practicalities that you will need to consider are likely to depend on the aim of the biobank and therefore what type you will set up. There are different types of biobanks, including:

  • Disease-centric: where you are interested in a specific disease e.g. Lassa fever, and will collect samples relating to it, most likely tissue, body fluid and cultures taken from infected people and animals.
  • Population based: much broader, a population-based biobank may take samples from the general population, both healthy and unwell, for use in broad spectrum research e.g. genetic/epidemiological studies.
  • Genetic (e.g. DNA/RNA): a collection of samples made up of extracted genetic material.
  • Project based: samples collected that relate to a specific research project or clinical trial.
  • Virtual biobank: a collection of data, such as images, sequencing, patient and/or epidemiological data, stored together in a similar way to physical biobanks, but held online.

Your biobank may be a combination of the above types of biobank, depending on your needs.

Laboratory considerations

It is vital to ensure that the physical aspects of your biobank are carefully considered, to ensure that you have the space and equipment to guarantee sample quality and that you can process and store the samples safely.

Samples

What type of sample you will collect will depend on the type of biobank and the overall aim. The more types of sample you plan to include, the more logistical issues you may need to consider.

Sample collection

To have a practical and useful biobank, your samples will need to be of a good standard, enabling the future research conducted using them to be of a high quality. Current standards for human samples in biobanks

Samples must be:

  • High quality
  • Appropriately preserved according to the type of sample
  • Have the associated metadata (which can be easily associated with the sample)
  • Trackable
  • Have multiple backups (see the section on contingency plans)

When collecting and processing samples you will need to consider a number of factors. Before you begin to collect samples for your biobank, you will need to create SOPs for collecting, transporting and processing your samples, so that there is standardisation across all of your collections. You may need separate documentation for each type of sample. Some of the requirements you may need to consider are:

  • Sample transportation (both to and from biobank location)

            - How far is the biobank from the collection point?

            - Does it need to be temperature controlled?

            - Are there extremes of temperature in your country?

            - How will you collect samples (e.g. all in one go, or over a long period)?

  • How will you preserve your samples?  

            - What is the optimum storage fluid/container/temperature

            - Do you have temperature monitoring systems or equipment failure back up plans?

  • How many aliquots are you going to make?

            - Are your samples cultureable/reproducible (e.g. a bacterial isolate) or ‘one of a kind’/finite (e.g. tissue sample)

            - How much of the original sample will you need to collect?

Sample types

The way you process your samples will depend on what type of sample you are going to store. Types of sample include:

  • Human/animal tissue
  • Human/animal body fluids
  • Viral cultures
  • Bacterial isolates
  • DNA/RNA
  • Environmental samples

This study outlines the considerations for processing and preserving samples for biobanking.

Thermo Fisher biobanking sample preparation guide.

The Thermo Fisher biobanking resource library provides information on sample preparation and preservation methods.

UK biobank protocol for processing and storing human blood and urine.

Equipment

The equipment you use will depend on a number of factors: size of biobank, budget, types of sample and physical space. The following is a list of basic items that you may need to consider for your biobank:

  • Freezers – consider the type of sample you will store and the racking options and size of the units
  • Liquid nitrogen systems – if you are collecting samples that require storage in liquid nitrogen, you will need to purchase the equipment required
  • Generators – you will need to ensure you have the appropriate number of generators/power to provide back up for all your electrical equipment
  • Uninterrupted power supplies (UPS) - you will need to ensure you have the appropriate number of UPS to provide back up for all your electrical equipment until your generators can be started
  • Equipment monitoring systems, such as electronic temperature monitoring systems for your freezers.  (too hot or cold could affect integrity of specimen)
  • Back up freezers/storage systems (kept empty!) and monitored in the same way
  • You will also need to consider the smaller things too, such as racks, freezer-proof gloves and storage boxes

Physical space

You will need to consider the physical space required by all parts of a biobank:

  • Freezer space. How many freezing units do you plan to have? Ensure you include empty space around each freezer to help reduce the chance of overheating. Consider temperature control for this room as well.  Will you have dedicated freezers for the biobank, or can you ensure that they are used minimally by other users?
  • Laboratory space for processing the samples (the biological safety level of the laboratory must also be considered (see the section below)). You may need multiple rooms to reduce the potential for contamination
  • Space for back up freezers
  • A cold room
  • Space for incubators if you are culturing isolates
  • Space for generators/uninterrupted power supplies (UPS)
  • Space for staff (e.g. offices, break rooms, toilets)
  • Paper-based archive space (if required)
  • Reagent/consumable storage space

You will also need to consider the layout of your biobank to reduce the risk of sample contamination.

Disinfectants and waste

Your biobank is likely to be linked to a laboratory or hospital, so the waste it produces can be incorporated into waste pipelines of your current institution. It is important to consider the hazard level of the organisms you will be storing (and the biological safety level the waste will be), as well as the types of chemicals that you may be using. The WHO biosafety manual provides information for waste disposal for all biosafety levels of laboratories.

The type of disinfectant(s) used will depend on the types of organisms and samples you are working with. It is vital that you reduce the likelihood of cross-contamination of your biobanked samples and so a good disinfection policy is of high importance. The CDC have provided an overview of the different types.

Biosafety requirements

The level of biosafety you will need to put in place will depend on the types of sample that you wish to process and store. If you plan to store isolates of infectious diseases, you must consider the hazard group level of the organisms. The WHO have provided a biosafety manual that explains what biosafety requirements should be in place for biosafety level (BSL) 1, 2, 3 and 4 laboratories.

Contingency plans

It is important to anticipate any problems that may arise during the lifetime of the biobank. This may include short term issues such as power surges or internet outages, or may be more problematic, such as funding or staff shortages, or problems with the physical space or equipment.

This article outlines the potential hazards that you may need to take into consideration when building a biobank contingency plan.

Before you set up your biobank, it is important to identify the risks that may occur and assess how you can mitigate or manage them. This link may help you to consider the risks involved and how to prepare for and manage them.

It may be useful to consider the following:

  • Build emergency response tests and equipment monitoring into your system, to help prevent and prepare for problems
  • You will need to ensure back up aliquots of samples. In case of a freezer or general power problem, are you able to store alternative samples in a different location such as:

            - An alternative freezer

            - On a different power circuit

            - At an alternative site (e.g. different country)

  • You will need to have power backups in place, such as generators and uninterrupted power supplies (UPS)
  • Consider your reagent and consumable supply chain. If there is a bottleneck in the supply of a certain item, do you have a back up company/procedure to ensure you do not run out?
  • If you rely on the cloud-based LIMS, can you put alternatives in place, e.g. hot spots, in an emergency? Alternatively, can you choose a local-based LIMS?
  • If there are long-term power issues, are you able to transfer samples to alternative locations for short/medium/long term storage?
  • Agreement with companies for emergency delivery of liquid nitrogen/CO2/generators/alternative freezers
  • Emergency contact list (including on-call staff, management team, sample collection owners, back up locations, transport companies etc.) It is also vital that there is clear and frequent communication between these stakeholders to ensure efficient disaster management (e.g. regularly check the contact details of suppliers etc.)
  • Creation of an emergency plan: to include staff roles and responsibilities, list of priority samples or processes etc. It is important to run through mock disaster scenarios, to ensure staff are aware of what to do

Biobank management

Overall governance

You will need an overall management team, depending on the size and structure of your biobank system. If it is large and multi-site, you may need a governance committee along with an external independent advisor, which will be responsible for advising, monitoring and establishing the governance rules of engagement and decision making. The members will also define the roles of each partner and will be responsible for advising, ensuring commitment to ethical principles and governance on samples ownership and usage.

You may also need an administrative team, who will be responsible for the budget management and will assist the leading the training, laboratory assessment and monitoring.

Ethics, consent and legal requirements

The ethical considerations of biobanks are complex and are likely to differ depending on the country or countries that the biobank is based in.

  • This article gives an overview of the ethical problems that are linked to biobanks
  • If you are utilising patient samples, you will need to consider consent forms and patient information leaflets. You will also need to consider the future applications of the samples and who may have access to the samples. You will need to cover all potential future uses.

            - A template consent form from IARC can be found here:

            - This article discusses the requirements of a simplified consent form for biobanking samples

  • You will also have to consider patient privacy and confidentiality, as well as the provision of results to participants, involvement of children and/or vulnerable populations and public engagement.
  • If you plan to allow other researchers to utilise your samples, you will need to put a Material transfer agreement in place.

            - Drafting biological material transfer agreements

            - Use and misuse of MTAs

            - If it’s a multi-country biobank, consider country sample ownership, import/export and usage agreements

Budget

  • Sustainability

            - Chatham houses’ sustainability prior assessment tool

            - Business planning for biobanking

  • To help you identify potential costs, we have created a budget template that you can modify here. We have split it into tabs, which cover:

            - Cost of set up

            - Consumables

            - Yearly servicing charges

            - Staffing costs

IT requirements

Your biobank, however small, will require computers to help run and manage it.

Software/LIMS

A laboratory information management system (LIMS) is an important part of a biobank, enabling ease of tracking, processing and storing samples, we well as improving standardisation. There are many different LIMS available, so you can choose one that fits your purpose and budget. Some LIMS operators provide ‘off the shelf’ models, and some provide customisable systems. Some options to consider when choosing a LIMS:

  • Biological specimen management

            - Can it manage tests and test results?

            - Does it print labels or use a barcode system?

            - Does it provide a chain of custody?

            - Traceability

  • Interoperability

            - Can it manage the training records and schedules of staff?

            - Can it manage documentation and quality control processes?

            - Can it be integrated with (third party) equipment monitoring systems and hospital records systems?

            - Is it designed for single or multiple sites?

            - Ease of use – can your staff easily follow the procedures, or does it require special training?

  • Data protection and storage

            - Does it follow best practice regulatory guidelines?

            - How does it back up the data?

            - Does it have appropriate confidentiality and data protection?

            - Can it manage patient consent?

            - Does it run on a local computer, or is it cloud-based? (consider the reliability of your internet connectivity)

Whichever LIMS you choose, it must be fit for (your) purpose. Below are some useful links to help you choose a system:

  • This link provides a list of popular biobanking LIMS systems, including their features and pros and cons 
  • This link provides information on important LIMS features
  • ASLM biobanking presentation

As well as a LIMS system, you may also need to set up and install software for specific pieces of equipment, so access to these and updates must be considered in the budget. This includes anti-virus software.

Hardware

You will require computers to run equipment, as well as process samples and data. If you are linked to a laboratory, you may already have a computing system in place, but some things to consider include:

  • How many pieces of equipment will need a computer/laptop to run (e.g. a Nanodrop)?
  • If you are going to be doing data analysis, will you need high-powered computers to do this?
  • Will you need extra hard drives to store your data, or will it be cloud-based?
  • Will you need printers, barcode printers and scanners, photocopiers, a phone system?
  • What office-based equipment will you need?

You will also need to consider how you are going to share your data with partners. Data protection is vital to protect patient confidentiality, so how you do this is important to think about. Your institution should have data protection guidelines. Can you use a cloud-based, password protected system? Or encrypted emails? This article provides information on sharing data sets.

Staff and training

A vital consideration for any biobank is the staff that you will hire. You will need to consider the number of people you will employ, as well as what qualifications they will need. You should ensure all staff are trained appropriately, and that you have records of their training, usually in the form of competency assessment forms (CAFs). You will need to consider training on the following, as well as any other areas that may be appropriate to your biobank:

  • Standardised sampling collection
  • Processing of samples
  • Characterisation of samples
  • Storage of samples
  • Aseptic technique
  • Use of the LIMS
  • Emergency and contingency procedures
  • Health and safety
  • Shipping of (infectious) biological materials
  • BSL3 or 4 training (if appropriate)

Staff salaries will be a large part of your budget, so ensure you allow enough of your funds to cover the staff required over the period that you plan to maintain the biobank.

Quality Control

To ensure that all of your samples are collected, processed and stored to the same standards, it is important to centralise and standardise standard operating procedures as much as possible. Putting documentation, equipment servicing and staff training in place will help achieve this, as will working to ISO standards and achieving accreditation. Information about quality management and accreditation programmes can be found in the capacity development section of our resources page.

Servicing, contracts and calibration of biobank equipment

You will need to keep a record (or use a LIMS) of the equipment servicing and contracts for all of the necessary items in your biobank system. These may include:

  • regular deliveries (e.g. dry ice and liquid nitrogen etc.)
  • Equipment servicing (e.g. freezers, generators etc.)
  • Equipment calibration (e.g. pipettes, balances etc.)
  • Contract renewal (e.g. equipment monitoring services, LIMS etc.)

Documentation

Your biobank will rely on well organised and thorough documentation to keep it running smoothly. Documentation can be paper-based, electronic or a combination of the two, and should tie into the LIMS that you implement. You will require general laboratory-based documentation, such as those that can be found in the capacity development section of our resources page. As well as policies and training records, examples of some of the more biobank-specific documents that may be required can be found below:

Forms required

  • Sample consent form
  • Emergency contact list
  • Sample request form

SOPs required

There may need to be multiple SOPs depending on the types of samples you collect

  • Sample collection and transportation
  • Sample processing
  • Emergency procedure/contingency plans
  • Sample request – removal from storage and transportation
  • Reagent/consumable ordering checklist/procedure (to ensure you do not run out of items)

Accreditation

Accreditation is not vital, but it will ensure a good level of quality within your system. You may choose to get accreditation for your entire system, or for individual processes. Information about quality management and accreditation programmes can be found in the capacity development section of our resources page. Other resources for biobanking accreditation and best practices can be found below:

Questionnaire checklist

Below is a list of questions that you may need to consider when planning your biobank. This list is not exhaustive and there are likely to be other things, specific to your set up that you may need to consider:

  • What is the overall purpose of your biobank?
  • How many samples do you plan to store?
  • What types of samples do you plan to store? What level of biosecurity will you need to put in place? E.g. if they are hazard group 3 pathogens, do you have appropriate safety equipment in place to protect staff?
  • How long do you plan to store your samples?
  • Do you plan to obtain samples from other countries/export them to other countries? If so, consider the ethical/legal documentation required (e.g. MTAs)
  • How many staff will you need to set up and maintain the biobank?
  • Do you plan to get accreditation for your biobank set up? Have you considered the extra costs for obtaining accreditation?
  • Physically, what sized space do you have to accommodate freezers, laboratories, generators etc.?
  • Where is your funding going to come from, how long does the funding last and what is the likelihood of this being renewed/refunded?
  • What back ups do you have in place in case of emergencies? E.g. power, internet?
  • How reliable is your power and internet connection?

Biobanking organisations and contacts

H3Africa biorepository group

B3AfricaL Bridging Biobanking and Biomedical Research Across Europe and Africa

European, Middle Eastern and African Society for Biopreservation and Biobanking

Global Emerging Pathogens Treatment Consortium (GETAfrica)