Summarised checklist to consider while choosing a Biobank LIMS (a detailed checklist can be accessed via biorepository.h3africa.org).
Biobanks in low-and middle-income countries need significant infrastructural support to meet ISBER Best Practices to support population-based genomics research. ISBER recommends a Biobank information management system that can manage workflows from biospecimen receipt to distribution. The H3Africa Initiative was set out to develop regional African Biobanks where Uganda, Nigeria, and South Africa were successfully awarded grants to develop state-of-the-art Biobanks. In this chapter, we review the African experiences, processes, and recommendations for information management systems for use in the low-and middle-income country context. We provide a balanced basis on which institutions can deliberate their decision between an out-of-the-box service and a commercial enterprise.
Biobanks require the linkage of high-quality material to data housed in a laboratory information management system (LIMS) which tracks each sample. A founding principle of H3Africa is to ensure that DNA (and possibly other clinical biological material) would be stored in Biobanks for future research purposes [1, 2]. The value of this material is partially determined by the associated phenotypic data. Management of this data and sample tracking in compliance with national and international best practices and ethical guidelines requires a refined data management system [3, 4]. According to the International Society for Biological and Environmental Repositories (ISBER) Best Practices, a computer-based inventory system should be in place to track the location and pertinent annotation of every specimen in the Biobank . The system should also track significant events during a sample’s existence from collection to destruction, including sample thaws, receipt and/or processing delays, processing, transfer of the sample within the repository, specimen distribution and return, and destruction [3, 4, 5]. These ISBER Best Practices, as well as others from around the world, are under consideration to codify an International Organization for Standardization (ISO) norm as the basis for a new international accreditation program for Biobanks . Several factors hinder the successful implementation of a Biobank laboratory information management system (LIMS) in low- and middle-income countries. This chapter discusses the experience of H3Africa Biobanks in the evaluation and setup of a sustainable Biobank information management system.
2. The importance of LIMS sustainability
Biobanks should develop strategies for long-term LIMS sustainability. Reliable and adequate sources of funding are key to the sustainability of LIMS. Commercial LIMS vendors require the payment of annual support fees, unlike open-source LIMS. The risk of liquidation needs to be considered as it impacts LIMS support and maintenance and the long-term viability of the Biobank. Biobanks should employ cost recovery measures for users to ensure sustainability.
3. LIMS harmonization in the case of H3Africa Biobanks
Before the H3Africa program, each Biobank had its LIMS that met their current needs. Since the commencement of the program, the Biobanks have either acquired new LIMS or upgraded their existing systems following a thorough LIMS assessment program. The Biobanks conducted a harmonization exercise to ensure the interoperability of the LIMS across the three sites. Pilot studies conducted between H3Africa Biobanks integrated data sharing and importation protocols through a pilot biospecimen and data exchange. Data exchange harmonization is essential if Biobanks are to operate efficiently in networks like H3Africa to support population genomics studies. Biobanks need to define an agreed sharable set of data and data formats for harmonization and interoperability to facilitate exchange. Pilot projects with virtual data transfer protocols were undertaken successfully suggesting that this harmonization has been effective.
3.1 Checklist for choosing an LIMS and H3Africa Biobank as model
H3Africa required that the three Biobank workflows would be harmonized through interoperable LIMS to enable data integration and exchange. Key elements that were considered while choosing a LIMS for the project included (a) customizability and usability; (b) interoperability with other LIMS; (c) access to revisions, updates, patches, and maintenance releases; (d) cost and access to technical support services; (e) maintenance and associated costs; (f) multiuser/multisite support; (g) robustness to handle large volumes of sample information; (g) security systems (audit trail, user roles, and privileges, etc.); and (h) type of (open-source or commercial) LIMS. Here we presented a summarized checklist (Table 1) we considered while choosing a Biobank LIMS; however, a detailed checklist can be accessed via Biobank.h3africa.org website.
|LIMS general information|
4. IT infrastructure
In addition to high acquisition costs, commercial LIMS requires an IT infrastructure to fully support their function. IT infrastructure is a combined set of hardware (e.g., servers, computers), software (e.g., operating software), and network systems required to deploy and support the LIMS. As biospecimen numbers grow, there is a corresponding decrease in LIMS functionality such as very slow loading and processing speeds, which is linked to the supporting IT infrastructure . Therefore, a LIMS infrastructure should have the ability to scale to meet the needs of the community it serves. Institutions that are unable to support a Biobank LIMS on their own should team with other institutions to develop and deploy a shared Biobank LIMS infrastructure. By using a shared infrastructure, each participating institution could maintain components of the infrastructure independently, while also collectively managing the entire Biobank architecture. This will not only provide an economic benefit but will also provide an environment for harmonizing complex, but still critical, components of a LIMS such as structured data files and data models, as well as standards for data transmission.
4.1 User support services
Commercial LIMS often require user support services such as customization, implementation assistance, annual licenses, maintenance, and update, although the need for these services may vary over time especially as users become experienced with the system. User support can be provided in several forms including telephonic support and on-site support. There is an additional cost to access such services, which may be minimized by conducting thorough initial training and license negotiation. Many commercial LIMS vendors have no support networks or offices in low- and middle-income countries. This increases the costs of user support services because of airfare, accommodation, and other attendant costs to access the services. In such circumstances, low- and middle-income country Biobanks should endeavor to use other remote access technology to access support such as public IP addresses that enable external access and manipulation of the LIMS. Unlike commercial LIMS, open-source LIMS systems do not have user support services, and the user must troubleshoot locally which can be challenging or impossible based on technical capacity.
5. Open-source LIMS and commercial LIMS options
Commercial LIMS are systems whose source code is developed for sale and requires authorization from vendors before licensed use. Open-source LIMS are systems whose source codes are made available for distribution at no cost . During the H3Africa Biobank implementation phases, it was decided to implement commercial LIMS in support of the collections. Commercial LIMS are significantly more expensive upfront than open-source LIMS and are less flexible for end-user adaptations but do not require local expertise to support. Despite some features of modified open-source LIMS that might seem more applicable to the low- and middle-income country setting, there were significant concerns regarding the stability of such systems and the lack of standardization. Additionally, it was clear that the adaptation and maintenance of such a system would require highly specialized staff at each of the Biobanks and that this may create differences among the Biobanks which could cause potential delays in the interlaboratory transfer of data and material.
In general, both open-source and commercial LIMS have some benefits and drawbacks. Open-source LIMS are quite cheap and most are entirely free to acquire, easily customizable, and open to various platforms such as Linux, Window, or Unix. However, they are not secure to data hacking, fixing bugs requires IT expertise, and there are no user support services.
Commercial LIMS are highly secure and reliable and have dedicated user support available in the form of telephone and email support. Software updates are provided regularly most often free but sometimes at a user fee. Some are customizable and adhere to the ISO 20387:2018 . However, they are expensive; in our experience, one commercial LIMS was purchased at US$120,000. Some are associated with annual renewal licenses or user fees which can be very prohibitive and affect the Biobank sustainability. One of the major drawbacks of commercial LIMS is discontinuation of the product without the consultation and consent of users leaving them in jeopardy.
6. Budgeting for LIMS in the H3Africa Biobanks
The functioning of Biobanks requires stability and continuity of the LIMS. In addition to the purchase of commercial licenses, some unforeseen expenses were encountered in the implementation of the commercial LIMS in H3Africa. These included training costs for staff and more complex hardware requirements, unlike for open-source LIMS. In the case of H3Africa, it was possible to budget for these contingencies, but these costs may become prohibitive for smaller Biobanks outside of a funded grant. In these cases, innovative solutions may include forming consortia with other facilities and purchasing a multiuser license. This may have the added advantage of enabling a shared forum for dealing with other problems. However, to keep each repository with separate views, specific role-based security would have to be implemented for each user’s collections. It may also only be necessary to acquire specific modules within a commercial package to keep the costs lower.
Retaining and training staff to operate LIMS has presented some challenges for H3Africa. Some strategies were employed, including actively headhunting individuals with experience, ensuring that the LIMS manager feels integrated into the Biobank management structure, and training junior staff to ensure an adequate succession plan. Also, including training clauses within purchasing agreements have mitigated some of the risks of purchasing complex licenses, but ongoing training represents an essential need and should be part of a Biobank’s quality management system. Discussion regarding formulating in-house training material for LIMS support is ongoing across all three H3Africa Biobanks to stay aligned with training and SOPs.
Developing a state-of-the-art Biobank requires considerable capacity and staff development including the acquisition of formal training, equipment, and software. Key among the Biobank infrastructure is a LIMS. Choosing a LIMS in low- and middle-income countries requires careful consideration of the various factors that could affect its successful and sustainable deployment and utilization. H3Africa Biobanks operating in a consortium have highlighted key factors and recommendations that affect successful LIMS implementation.