MiDAS

MiDAS provides R functions to transform and analyze immunogenetic variation in Human Leukocyte Antigen (HLA) and Killer-cell Immunoglobulin-like Receptor (KIR), enabling HLA amino-acid fine mapping, HLA evolutionary divergence analysis, HLA–KIR interaction analysis, and statistical association testing with phenotypes on various scales.

Key Features:

• Immunogenetic Data Transformation: Recodes raw HLA alleles and KIR types into biologically meaningful variables for downstream analysis.
• HLA Amino Acid Fine Mapping: Identifies and tests associations at the HLA amino-acid level to pinpoint residue-level effects.
• Analysis of HLA Evolutionary Divergence: Computes measures of evolutionary divergence within HLA types to assess diversity and selection-related metrics.
• HLA–KIR Interaction Analysis: Tests experimentally validated interactions between HLA molecules and KIRs for association with phenotypes.
• Comprehensive Statistical Association Workflows: Performs statistical association analyses across phenotypes measured on various scales.

Scientific Applications:

• Genetic association studies: Relates HLA and KIR variation to disease-associated or quantitative phenotypes.
• Immune response and disease susceptibility: Investigates how HLA and KIR differences influence immune-related traits and susceptibility to disease.
• Amino-acid level effect mapping: Maps residue-level HLA variation to phenotypic effects.
• Evolutionary and selection analyses: Studies HLA diversity and divergence to infer evolutionary pressures.
• HLA–KIR functional studies: Examines the contribution of validated HLA–KIR interactions to immune phenotypes.

Methodology:

MiDAS recodes HLA alleles and KIR types into biologically meaningful variables, performs HLA amino-acid fine mapping, computes HLA evolutionary divergence metrics, and conducts statistical association tests including HLA–KIR interaction analyses across phenotypes on various scales.