Allelefocused

Allelefocused is a term in genetics describing an analytical approach that centers on information at the level of individual alleles rather than genotypes or haplotypes. In allelefocused analyses, each allele is treated as a separate unit and assessed for frequency, effect, or expression, enabling examination of allele-specific phenomena such as imprinting or allele-specific expression (ASE).

The term is not universally standardized and is used to denote a methodological stance rather than a formal discipline. It covers methods that resolve sequencing data to the allele level, including ASE analyses, allele-specific binding studies, and allele-focused association testing. In population genetics, allelefocused approaches can reveal differences in allele frequency or selection signals between alleles at a locus.

Common applications include detecting ASE in disease genes, fine-mapping causal alleles in association studies, pharmacogenomics where a single allele drives drug response, and evolutionary studies of allele-frequency dynamics. Methods typically combine read-level data with statistical models that compare allele-specific counts or effects, such as binomial or beta-binomial models for ASE and allele-focused tests in association analyses.

Limitations include dependence on high-quality, bias-mitigated sequencing data, sufficient read depth, and potential mapping bias toward reference alleles. Phasing and accurate allele assignment remain technical challenges, and tightly linked variants can complicate interpretation.

Overall, allelefocused represents a perspective within genomics that seeks to maximize allelic resolution to better understand genetic regulation and its phenotypic consequences.