Biobanking Science: Lessons from African Biobanks

Lessons learnt from setting up biobanks in Africa as part of the H3Africa project.

H3Africa biobanks and studies.
The H3Africa project is setting up biobanks and running large-scale population studies in Africa.
Advertisement

With the recent advances in genomic sequencing, proteomics and precision medicine, biobanks are becoming more prevalent around the world. So are large-scale population studies such as the UK Biobank.

H3Africa Project and Biobanks

The Human, Hereditary and Health in Africa (H3Africa) initiative is a large biobanking project funded by the US National Institutes of Health (NIH) and the Wellcome Trust (1). The goals of H3Africa are to facilitate large-scale population studies and build new infrastructure, biobanks and research capabilities in Africa, and also to foster collaborations between African, European and American researchers.

H3Africa researchers are collecting biological samples, phenotypic and environmental data from thousands of volunteers in order to study the causes of infectious and non-infectious diseases. Data and samples are stored in H3Africa biobanks and will be available to other H3Africa researchers. Researchers not affiliated with the H3Africa project can apply to access samples and data collected by the project

An important part of the H3Africa project is building more biobanks and biorepositories in Africa and increasing public awareness about biobanks among African populations.

Advertisement

SIREN Study and Biobanks

As part of the H3Africa initiative, researchers in Nigeria and Ghana are conducting the Stroke Investigative Research and Educational Network (SIREN) project, a multicenter study with over 6,000 participants across 16 different sites (2). SIREN researchers are studying the genetic and environmental factors that lead to stroke in African populations. Patients in Low and Middle Income Countries (LMIC), including African countries, suffer from 86% of all worldwide stroke-related deaths (3).

SIREN patients are recruited in hospital within 10 days of their first stroke episode and are matched with control volunteers based on age, sex and ethnicity. SIREN biobanks now store over 90,000 blood fractions, as well as brain images and extracted DNA from over 6,000 study participants.

SIREN is a multicenter, multicountry project. Therefore, to maintain quality of all biological samples and data for this project, researchers had to develop reliable, standardized procedures to collect, process, store and ship biological samples and brain images in a challenging field environment. The scientists have published their experiences to help other researchers in LMIC countries overcome infrastructure challenges.

Quality Control, Safety and Staff Training in SIREN Biobanks

The SIREN study complies with best practice guidelines from the International Society for Biological and Environmental Repositories (ISBER) and the International Stroke Genetics Consortium (ISGC).

In order to comply with these guidelines and maintain sample quality, SIREN researchers developed standard operating procedures (SOPs) to standardize each aspect of sample handling across the multiple study sites. They also implemented quality control plans with periodic visits to sites to make sure SOPs were being followed. SIREN researchers used multiple communication channels to stay up to date with different research teams, including emails, teleconferences and WhatsApp messaging.

All SIREN biobanks are staffed by dedicated, trained personnel. To protect staff, all SIREN sites implement safety protocol and safety training, and all staff use personal protective equipment.

Data and Sample Collection, Processing and Storage in Biobanks

The SIREN project has been designed to minimize the risk of pre-analytical variables which are known to affect sample and data quality (4). All SIREN sites use standardized phenotype data collection and follow the same standardized protocols for patient enrolment, sample collection, processing, storage, transport and biomarker analysis. The SIREN Central Laboratory procures and distributes sample kits to all peripheral sites to ensure there is no variation in kit contents.

Staff at peripheral study sites collect blood and urine from participants  and process samples within two hours of collection. All tubes are barcoded. All samples are de-identified to protect patient privacy and coded by barcode. All SIREN research sites use the Freezerworks Basic 7.2® laboratory management system (Dataworks Development, Seattle, USA) to label and track all samples. This system provides a complete audit trail.

Some blood biomarkers are analyzed immediately at peripheral sites, then samples are temporarily stored until they can be transported on dry ice to the central SIREN biobank. Whole blood from each participant is also sent to one of three processing labs for DNA extraction. Extracted DNA is then shipped to the central SIREN biobank for long-term storage. An aliquot from each DNA sample is also shipped to the H3Africa central biobank.

Cold Chain Continuity

Biological samples degrade if kept at room temperature and temperature fluctuations during transport and storage can compromise the quality of biobanked samples. Therefore, as part of the study design, SIREN made sure every study site had at least one -20°C/-40°C freezer. In some sites, SIREN installed freezers and/or hybrid solar-powered inverter systems to provide backup power.

The central SIREN biobank has three -30°C freezers for short-term storage, four -80°C freezers for long-term storage and two backup -80°C freezers for emergency storage. The central site also has solar-powered hybrid inverter batteries as a backup power source for the -80°C freezers. Freezer temperature is monitored at all sites and recorded twice a day.

Packaging and Shipment

SIREN researchers developed a Material Transfer Agreement (MTA) to ship samples to the central site from peripheral sites and to ship to international collaborators. All samples are shipped on dry ice following IATA protocols and standards.

Brain Imaging Databank

As part of the project, SIREN researchers have developed an independent brain imaging databank called ACCESS (Annotation and Image Markup on Clear Canvas Enriched Stroke-phenotyping Software). ACCESS stores over 3,000 MRI and CT brain scans and allows reproducible classification of stroke subtypes by different investigators across the various sites within the study.

Conclusions

SIREN researchers overcame infrastructure challenges with careful planning, standardized protocols, staff training, multi-channel communication and quality control measures. They also worked to ensure cold chain continuity by installing freezers and backup power at study sites as needed. This study shows that high quality biobanks can be set up in LMIC countries where existing research infrastructure is limited.

 

References

  1. Human Heredity and Health in Africa: H3Africa
  2. Akinyemi et al. Biobanking in a Challenging African Environment: Unique Experience from the SIREN Project. Biobank. 2018
  3. Owolabi et al. The burden of stroke in Africa: a glance at the present and a glimpse into the future. J. Afr. 2015.
  4. NCI Best Practices for Biospecimen Resources. National Cancer Institute. 2016