High resolution HLA genotyping with third generation sequencing technology-A multicentre study.

Area of Science:

• Genomics
• Molecular Biology
• Immunogenetics

Background:

• Current molecular HLA typing methods are evolving rapidly.
• Next-generation sequencing (NGS) is crucial for high-resolution HLA typing, essential for stem cell transplantation and disease association studies.
• Real-time PCR is standard for solid organ allocation, but not yet ideal for deceased donors.

Purpose of the Study:

• To evaluate the concordance and practicability of nanopore sequencing (TGS) for high-resolution HLA typing in a multicentre clinical setting.
• To assess the performance of the NanoTYPE™ kit and NanoTYPER™ software for HLA typing.
• To compare nanopore sequencing results with established NGS methods.

Main Methods:

• A multicentre clinical study involving 381 samples.
• Utilized nanopore sequencing (TGS) with the NanoTYPE™ kit and NanoTYPER™ software.
• Analyzed concordance across 11 HLA loci (HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, -DPB1).

Main Results:

• Achieved 99.58% concordance for 11 HLA loci when comparing nanopore sequencing to NGS.
• High-quality sequencing was demonstrated, with over 97% of quality control (QC) values passing.
• Identified that 'inspect' or 'failed' QC warnings do not necessarily indicate incorrect HLA typing.

Conclusions:

• Nanopore sequencing is a fast, flexible, and easily implementable method for high-resolution HLA typing in diagnostic laboratories.
• While challenges like exon coverage and data handling exist, nanopore sequencing shows significant potential for clinical applications and basic research in epigenetics and genomics.