NGS-Based HLA Typing Delivers More Comprehensive Information

Used for matching organ transplants to donors and other applications, human leukocyte antigen (HLA) typing is rapidly shifting from older methods to NGS technologies. This is a major step forward, as more complete views of the highly polymorphic HLA genes provide a deeper understanding of how a person’s natural genetic variation might affect transplant matches and other immune-related functions.

Routine HLA Typing

HLA typing has a long history; over time, scientists have added to the number of markers they include to determine the best match between an organ donor and recipient. Today, clinicians evaluate about 10 markers for routine HLA matching. As our characterization of this region improves, however, that number may continue to rise — and with it, the precision and success of organ transplants.

New and Improved HLA Typing Method

Scientists are now adopting NGS platforms for HLA typing to delve deeper into this region, find even more relevant variants, and increase classification accuracy. A recently published protocol, using better library preparation techniques, highlights the wealth of information that can be captured this way. For this method, DNA size selection is an essential step in library preparation for consistently generating reliable results.

HLA Typing Using NGS Requires DNA Size Selection for Library Preparation

In the protocol released in Clinical Chemistry, scientists from The Children’s Hospital of Philadelphia report the development of an HLA typing protocol using next generation sequencing. In the project, the team evaluated the Omixon Holotype HLA assay on samples from 50 people. They used the Pippin Prep DNA size selection system before sequencing, selecting DNA fragments from 650 bp to 1300 bp to optimize next generation sequencing results. The scientists found that HLA results were concordant with other methods, but the big reveal was that more than 7% of samples were characterized by novel alleles — information that could not be detected with other approaches. Even though more than 14,000 HLA alleles have been discovered and curated in public databases, the scientists predict that shifting to sequencing-based methods and kits such as this one will allow the community to find other variants that may have clinical relevance.

Better HLA Matching Results From Better Gene Characterization

The team notes that while there is little research to date into the functional effect of variants in non-coding regions of the HLA locus, some early studies suggest that there may be many important elements to be discovered here. They conclude, “Full-length gene characterization is paramount for unambiguous HLA genotyping and facilitates a deeper understanding of HLA gene polymorphisms and the eventual role they may play in the immune response and the overall physiology of the cell.” Learn more about the Pippin Prep automated DNA size selection platform here.