by Dave Lowe, Senior Director of Research & Development, Transplant Diagnostics, Thermo Fisher Scientific
Over the past few decades, stem cell transplantation has undergone a substantial evolution. What was once a high-risk, experimental procedure has become an established, often life-saving therapy for patients, addressing unmet clinical needs. Yet even as outcomes improve, transplantation continues to face significant challenges. Emerging innovations, particularly in diagnostics, are now reshaping what is possible for patients, clinicians and health systems.
Human leukocyte antigen (HLA) typing is a crucial step in the stem cell transplantation process. HLA compatibility is one of the most important determinants of transplant success, as it directly influences the time to successful engraftment, rejection risk, incidence of graft-versus-host disease (GVHD) and ultimately, long-term survival. Understanding donor-recipient HLA matching is critical. If it’s inaccurate, the recipient’s immune system may reject the graft, or donor cells may attack recipient tissues (GVHD), resulting in serious, sometimes fatal complications.
Next-generation sequencing (NGS) technologies have made HLA typing far more precise, scalable and accessible. High-resolution NGS-based approaches enable more accurate transplant risk assessment, and this improved characterization of HLA mismatches directly supports clinical strategies that can reduce the risk of GVHD and enhance long-term outcomes. At the same time, streamlined workflows and automation are shortening turnaround times and supporting faster, broader access to stem cell transplantation. These advances are not only improving patient care, they are also enabling progress in emerging areas such as personalized and regenerative medicine.
The evolution of NGS and HLA typing
HLA typing has long been recognized as a critical step in the transplantation process. Early HLA testing relied on serology, which offered low resolution and limited sensitivity. These assays could distinguish only broad antigen groups and were unable to capture higher resolution polymorphisms within the HLA system. As a result, many donor-recipient pairs that appeared compatible at a low level of resolution were later discovered to have important mismatches contributing to rejection, GVHD or other complications.
The advent of DNA-based molecular typing represented an important step forward in HLA typing. Traditional molecular typing techniques improved accuracy and resolution, enabling more refined assessment of HLA compatibility. However, these methods still had constraints. Coverage of HLA genes was often partial, and workflows were not easily scalable to the demands of large donor registries and high-volume transplant centers. As the need for broader and deeper HLA characterization became apparent, it was clear that a new generation of technologies would be required.
NGS has fulfilled that need. By enabling comprehensive sequencing across key HLA loci and the resolution of common HLA ambiguities, NGS delivers high-resolution data with far less uncertainty than traditional methods. Its scalability and throughput make it well suited to donor typing across large registries, supporting global transplant programs that serve increasingly diverse patient populations. For clinicians, this means more precise matching with a higher degree of confidence than older technologies.
The journey to this point, however, has not been without challenges. When NGS was first introduced into laboratories, workflows were complex, labor-intensive and time-consuming. Typical turnaround times ranged from three to four days from sample to result. Assay setup required extensive manual intervention, and for laboratories handling smaller sample volumes, the high financial burdens often limited early adoption.
In recent years, the technology and its implementation have evolved significantly. Modern NGS-based HLA workflows can now utilize automation and integrated reagents to simplify assay setup, standardize processes and reduce the potential for human error. Sequencing times have been dramatically reduced, with hands-on set-up times now in the range of approximately five to five-and-a-half hours, contributing to shorter overall sample-to-report turnaround times. This has made NGS more practical in routine clinical settings and time-sensitive scenarios. At the same time, informatics capabilities have advanced, providing laboratories with more robust tools for data analysis, quality control and reporting. Many laboratories have adopted hybrid approaches, combining NGS with other confirmatory methods to balance accuracy, throughput and flexibility.
Ongoing challenges in stem cell transplantation
Even with major advances in HLA typing, stem cell transplantation remains a complex undertaking. Donor selection and matching continue to be central challenges, especially as patient populations grow more diverse and as more individuals seek transplants. For many of these patients, identifying a fully matched donor is still difficult, and the ability to safely use partially matched donors becomes critically important. Increasingly, clinical decision-making focuses not only on the number of HLA mismatches, but also on the specific loci involved and whether mismatches are considered permissive or non-permissive based on emerging clinical evidence.
The risks associated with transplantation extend beyond the matching process itself. Conditioning regimens and post-transplant immunosuppression leave patients highly vulnerable to infection from bacterial, viral and fungal pathogens. Organs such as the liver, kidneys and heart can sustain damage from chemotherapy, radiation and long-term immunosuppressive therapies. Delayed engraftment can prolong cytopenias (low levels of red blood cells, white blood cells or platelets), increasing the risk of bleeding, infection and extended hospitalization. In some cases, an underlying disease, such as leukemia or lymphoma, can relapse despite an initially successful transplant.
Additionally, even with careful HLA matching, mismatches can trigger powerful immune responses, contributing significantly to post-transplant morbidity. High-resolution HLA typing does not eliminate these risks, pointing to the importance of other genetic loci being clinically relevant.
The future of stem cell transplantation
The future of stem cell transplantation will be shaped by continued innovation in donor matching, precision diagnostics and therapeutic approaches. As NGS and related methods continue to advance, laboratories will be able to determine donor matches at unprecedented speed and granularity. Integration with transplant registries and clinical decision-support tools will enable real-time access to comprehensive patient and donor data. This will help clinicians make more informed, data-driven choices at every stage of the transplant journey, from donor selection to post-transplant monitoring and long-term follow-up.
Therapeutic innovations are evolving in parallel. Post-transplant cyclophosphamide, for example, has emerged as an important tool to reduce the risk of GVHD and graft rejection, particularly in the setting of HLA-mismatched transplants. By mitigating the impact of greater HLA variability, this approach is expanding access to stem cell transplantation for patients who previously lacked suitable fully matched donors. Its safe and effective use, however, depends on a detailed understanding of HLA mismatches and individual patient risk, made possible by high-resolution HLA typing and advanced analytics.
Our knowledge of the HLA system is still expanding. The HLA region is one of the most polymorphic in the human genome, and new alleles (different versions of the same gene) are continually being discovered and characterized. There are currently in the region of 43,000 documented HLA variants (termed alleles) and the adoption of NGS based typing methodologies has facilitated a rapid expansion in the identification of new HLA alleles. All of this underscores how much remains to be learned. Looking forward, ongoing research paired with technological progress presents nearly unlimited potential for faster, safer and more personalized stem cell transplantation broadly available to patients around the world.
About the author
Dave Lowe is the Senior Director of Research & Development for the Transplant Diagnostics business of Thermo Fisher Scientific. Dave holds a Ph.D. in Transplant Immunology from the University of Warwick and previously served as the head of the Transplant Immunology Department for the Royal Liverpool and Broadgreen University Hospital NHS Trust in Liverpool, England.