The Human Leukocyte Antigen (HLA) is a complex and diverse area of the genome and plays an important role in transplantation. A lack of bone marrow registries means that variation in HLA is poorly understood. Advances in genetic and sequencing technologies have enabled the identification of novel HLA types in African populations, with important implications for future research and patient care.
The HLA is responsible for antigen presentation and the subsequent activation of the active immune system. Matching of HLA typing is critical for the matching of individuals’ HLA types in organ and stem cell transplantation to avoid transplant rejection. This immunoregulatory region of the genome is complex and thus its direct mechanism of action with respect to disease is not well understood, however it has been associated with auto-immune disease, infectious and non-infectious disease, cancer, and vaccine response.
The HLA typing of individuals from African populations using gene sequencing technologies is an important area of research. For these populations, typing falls short due to a shortage of bone marrow registries and biobanks across the continent. Without these resources, there is very little information on the variability of this important gene region in these populations, posing challenges for tissue matching and both basic and applied research. Consequently, these populations are often missed when testing safety and efficacy of interventions. It is therefore important to sequence HLA genes in populations across Africa to further our understanding of genetic variation in the region and ultimately improve patient care. However, this scale of sequencing is costly and requires a large number of donors to consent to the use of their DNA for research and biobanking.
Known and novel HLA types are usually identified through genetic sequencing. Until recently, the majority of HLA sequencing was carried out using a technique known as PCR (polymerase chain reaction), followed by capillary (“Sanger”) sequencing. This method is limited by the short length of output reads and the resulting HLA type ambiguity in the test results. The development and maturity of the PacBio RS II has revolutionised HLA sequencing by enabling the sequencing of reads of up to 60 kilobases and eliminating the problem of type ambiguity. However, even with the reduced cost of PacBio’s new Sequel machine, cost remains a limiting factor and scaling to the tens or hundreds of thousands of samples required for population genetics is expensive.
Our pilot project explored the genetic variation in African populations using both traditional and novel sequencing technologies. Samples were taken from 125 individuals in five African populations and were subjected to the traditional “Sanger” capillary method of sequencing, whilst a subset was typed using PacBio technology. Our PacBio results revealed significant novel HLA type variation in the African populations, implying that a larger sample size would yield even more variation. These novel types are particularly problematic for conventional clinical typing as they may not be recognised, or worse misidentified, as a known type leading to negative clinical outcomes. We plan to scale-up our research to sequence hundreds of samples, whilst exploring ways to further type thousands of samples with the aim of creating a comprehensive reference to aid disease research in Africa. However, with significant cost implications, there is ultimately a need for a commercial technology that allows the typing of thousands of samples in parallel. This would be valuable in the determination of allele frequencies or as a screening technique for identifying potential transplant donors. Once developed, this would provide the basis for future research into genetic diseases worldwide.