mhc-typer

mhc-typer V1.1 assigns multilocus MHC genotypes and estimates allele frequencies from genetic data while accounting for duplicated loci and factors that confound allele assignment.

Key Features:

• Simultaneous consideration of multiple factors: Considers identical alleles shared among loci, null alleles, copy number variations (CNVs), negative amplification events, heterozygote excess or deficiency, and linkage disequilibrium when assigning alleles.
• Genotype extraction and frequency estimation: Extracts possible multilocus genotypes for each individual and weights these genotypes to estimate allele frequencies.
• Likelihood optimization with heuristic algorithm: Calculates likelihoods of alternative allele configurations and optimizes allele assignment using a heuristic algorithm.
• Empirical validation: Validated using Monte‑Carlo simulations and evaluations on three empirical MHC data sets under varying conditions.

Scientific Applications:

• MHC genotyping with duplicated loci: Provides accurate genotyping in MHC regions affected by gene duplication and locus sharing.
• Immunogenetics: Supports immunogenetics studies that require precise identification of MHC alleles.
• Disease association analysis: Enables disease association studies by resolving complex allele assignments that could confound association signals.
• Evolutionary biology: Facilitates evolutionary analyses of MHC polymorphism, linkage patterns, and allele frequency dynamics.

Methodology:

Extracts multilocus genotypes, weights genotypes to estimate allele frequencies, computes likelihoods of allele configurations, and optimizes assignments with a heuristic algorithm; validation includes Monte‑Carlo simulations and evaluation on three empirical MHC data sets while explicitly accounting for identical alleles among loci, null alleles, CNVs, negative amplification, heterozygote excess/deficiency, and linkage disequilibrium.