HATK

HATK performs fine-mapping analysis of human leukocyte antigen (HLA) genes by expanding HLA alleles into amino acid sequences using the IMGT/HLA database and supporting association testing, nomenclature conversion, and visualization to identify HLA alleles or amino acid positions linked to disease susceptibility.

Key Features:

• Data expansion and preparation: Leverages input from HLA typing, imputation, or inference to expand HLA allele information into detailed amino acid sequences.
• IMGT/HLA integration: Uses the IMGT/HLA database for allele-to-amino-acid mapping to ensure up-to-date sequence representation.
• Fine-mapping analysis: Prepares datasets suitable for fine-mapping and identifies HLA alleles or specific amino acid positions associated with disease susceptibility.
• Association tests: Implements a range of statistical tests to assess associations between HLA variants and diseases.
• Visualization tools: Produces visualizations to aid interpretation of complex HLA association results.
• Nomenclature conversion: Converts HLA nomenclature across formats to standardize allele representation.

Scientific Applications:

• Autoimmune disease research: Identify specific HLA alleles or amino acid positions that drive autoimmune disease susceptibility.
• Disease susceptibility fine-mapping: Pinpoint genetic variations in the HLA region associated with disease risk.
• Translational and clinical research: Support basic and potential clinical applications aimed at improving diagnosis and treatment strategies linked to HLA genetics.

Methodology:

Expands HLA alleles into amino acid sequences using the IMGT/HLA database from inputs including HLA typing, imputation, or inference; prepares datasets for fine-mapping; performs statistical association tests at allele and amino-acid levels; converts HLA nomenclature; and generates visualizations.