HLAssign 2.0

HLAssign 2.0 performs HLA typing from next-generation sequencing (NGS) data to assign HLA alleles and known haplotypes for research and clinical applications.

Key Features:

• Comprehensive workflow: Integrates automatic calling with tools for visual evaluation, read phasing analysis, and strict workflow controls to enhance HLA typing accuracy.
• Automatic caller performance: Provides automatic HLA calling with reported call rates comparable to STC-seq and xHLA.
• Sequencing platform support: Processes Illumina NGS reads and includes preprocessing support for 10x Genomics and PacBio sequencing data.
• Manual inspection and haplotype selection: Enables manual inspection of read mappings, phasing information, and selection of alternative haplotypes to resolve complex genotype compositions.
• Report generation: Produces output reports in PDF and CSV formats for documentation and downstream analysis.

Scientific Applications:

• Bone marrow registry typing: Supports large-scale HLA typing operations for donor matching in bone marrow registries.
• Clinical HLA diagnostics: Facilitates diagnostic HLA allele and haplotype assignment in clinical settings, including cases with complex genotypes.
• Research on HLA diversity and phasing: Enables research analyses requiring visual inspection of read mappings, phasing information, and haplotype assignment from NGS data.

Methodology:

Employs targeted enrichment panels for both PCR-based and capture-based analysis modes to assign known haplotypes to NGS data and integrates automatic calling with manual oversight.