HLA Typing via Segmented NGS and Targeted Sequencing

The method segments the HLA typing process into two distinct phases: first performing standard NGS to obtain moderate sequence depth for initial allele identification, then selectively applying HLA-targetted sequencing only to specific regions (peptide binding cleft exons) where ambiguities exist. This segmentation allows the system to achieve high precision where needed while avoiding the complexity and cost of comprehensive targetted sequencing for all samples.

The invention applies partial targetted sequencing rather than complete targetted sequencing to all samples. By using standard NGS for initial typing and reserving HLA-targetted sequencing only for resolving specific ambiguities in the peptide binding cleft regions, the method achieves sufficient precision for clinical applications without the excessive complexity and resource consumption of full targetted sequencing workflows.

The workflow is segmented into a rapid initial phase using standard NGS that provides moderate sequence depth for most samples, followed by a targeted refinement phase using HLA-specific sequencing only for samples with ambiguities. This time segmentation allows the majority of samples to be processed quickly while dedicating additional time only to cases where higher precision is needed.

The method applies partial targetted sequencing only to the extent necessary for resolving ambiguities in critical regions (peptide binding cleft exons) rather than performing comprehensive targetted sequencing on all samples. This partial application of the time-intensive technique maintains high precision for critical determinations while minimizing overall time loss.

The HLA typing workflow is segmented into two precision levels: standard NGS provides initial typing with moderate precision for the majority of samples, while HLA-targetted sequencing provides high-precision resolution for ambiguous cases. This segmented approach allows the system to maintain simplicity for routine samples while achieving high precision when needed.

The invention applies standard NGS (simpler method) for partial typing of all samples, then selectively applies HLA-targetted sequencing (more complex method) only to the extent necessary for resolving specific ambiguities in the peptide binding cleft regions, achieving sufficient overall precision without consistently requiring the more complex workflow.