HLA Typing With PacBio Shown To Improve Transplant Outcomes

By Bio-IT World Staff

April 5, 2019 | Scientists at the Anthony Nolan Research Institute in the UK have demonstrated that ultra-high-resolution HLA typing performed with PacBio sequencing identified stronger matches associated with improved survival rates among patients who received hematopoietic stem cell transplants. The retrospective study was published this week in the Journal of Biology of Blood and Marrow Transplantation.

HLA typing involves analysis of the genes found in the human leukocyte antigen region of the human genome. For stem cell transplants, HLA typing is used to find the best donor/recipient match for the strongest chance of a positive outcome for transplant patients. The HLA genes are highly polymorphic and complex, making them very difficult to resolve fully with conventional technologies. They are also known to be important in immune-related diseases and drug hypersensitivity.

The Anthony Nolan Research Institute, which is funded by Anthony Nolan, a registered UK charity that maintains the world's oldest stem cell registry, has implemented Single Molecule, Real-Time (SMRT) Sequencing from PacBio to fully phase and characterize HLA genes with high accuracy. In this retrospective study, the scientists aimed to determine whether high-resolution HLA typing enabled by SMRT Sequencing would have made a difference for previously matched donors and recipients.

Researchers analyzed 891 donor/recipient pairs, all of which had originally been considered a perfect match (a 12/12 score for all six HLA genes). SMRT Sequencing revealed that 29.1% of those matches were not actually perfect and identified previously undetected variation in nearly a quarter of the pairs. The patients whose 12/12 matches were confirmed by SMRT Sequencing had a significantly improved 5-year overall survival (OS) of 54.8% compared to 30.1% OS for those who were thought to be 12/12 matched using standard technology. Perfectly matched patients were also less likely to die of other transplant-related complications in the 12 months post-transplant, and significantly less likely to develop acute graft-versus-host disease.

"NGS and third-generation sequencing technologies have changed the landscape for HLA typing laboratories, allowing for full gene characterization in a manner that is viable for use in a routine clinical typing laboratory, and thus is becoming current practice," the authors wrote in the paper. "In our opinion the current optimal typing technology is Pacific Biosciences Single Molecule RealTime DNA sequencing, which has the ability to sequence individual molecules of double-stranded DNA of up to 10 kilobase pairs at the high level of accuracy required for HLA typing."

The study highlights the importance of sequencing through previously uncharacterized regions of the traditional HLA genes, showing that polymorphisms in these regions affect patient overall survival.

"We are very excited about this breakthrough, which has told us more than we have ever known about how to match patients and donors," said Neema Mayor, Head of Immunogenetics Research at the Anthony Nolan Research Institute in a press release. "We believe that HLA matching at ultra-high resolution could ultimately enable us to further minimize the risk of complications such as graft-versus-host disease and, consequently, the risk of mortality—potentially saving more lives in the future."