Orthanq

Orthanq quantifies haplotypes from DNA sequencing data with transparent, uncertainty-aware predictions for HLA typing and generalizable tasks such as virus lineage quantification.

Key Features:

• Uncertainty-aware predictions: Orthanq reports uncertainty of predictions and transparently observes mutations beyond reported HLA types.
• Pangenome alignment utilization: Orthanq directly utilizes existing pangenome alignments for haplotype quantification.
• HLA locus coverage: Orthanq types all HLA loci.
• Generalizability: The approach extends beyond HLA typing to tasks such as virus lineage quantification.
• Performance: Orthanq provides overall superior accuracy and shorter runtimes than state-of-the-art HLA typers on 99 gold standard samples from 1000 Genomes, Illumina Platinum Genomes and Genome In a Bottle projects.

Scientific Applications:

• HLA typing: Orthanq identifies human leukocyte antigen types from DNA-sequenced human samples for applications in organ transplantation and cancer immunotherapy.
• Virus lineage quantification: Orthanq generalizes to quantify virus lineages from sequencing data.

Methodology:

Orthanq employs a novel statistical model for transparent and uncertainty-aware quantification of haplotypes using pangenome alignments.