Easy-HLA

Easy-HLA: HLA Genotype and Haplotype Inference Suite

Easy-HLA infers high-resolution HLA genotypes and haplotype pairs from low-resolution or partial data using computational and statistical methods with large reference populations.

Key Features:

• Nomenclature and Typing Flexibility: Processes HLA data across evolving nomenclatures and typing methodologies, maintaining compatibility with legacy datasets.
• HLA-Upgrade Tool: Infers high-resolution HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 genotypes from low-resolution inputs using a reference database of >600,000 haplotypes; achieves 92% prediction accuracy for European genotypes.
• HLA-2-Haplo Tool: Imputes HLA haplotype pairs and annotates amino acids and Killer-cell Immunoglobulin-like Receptor (KIR) ligands; demonstrates 96% call rate and 76% accuracy for European haplotype pairs.

Scientific Applications:

• Transplantation Matching: Provides high-resolution HLA typing for hematopoietic stem cell and solid-organ transplantation.
• Immunogenetic Analysis: Enables large-scale studies with functional annotations beyond allelic associations to investigate immune-related pathologies.

Methodology:

Implements computational and statistical inference of HLA haplotypes using extensive reference populations to upgrade incomplete or low-resolution data; validates predictions and annotations across independent cohorts totaling 2,500 individuals.