Allelespecific

Allele-specific is an adjectival term used in genetics to describe phenomena that pertain to one of the two copies (alleles) of a gene or genomic region rather than both. It is applied across several contexts, including allele-specific expression, allele-specific binding, allele-specific PCR, and allele-specific genome editing. The concept focuses on differences between the paternal and maternal alleles or between variants that distinguish one allele from the other.

Allele-specific expression (ASE) describes a situation where the two gene copies are transcribed at different levels in a diploid organism. ASE can arise from cis-regulatory differences, genomic imprinting, or random monoallelic expression. Detection typically involves sequencing RNA and comparing allele-specific read counts at heterozygous single-nucleotide polymorphisms, while accounting for potential technical biases such as mapping bias and allelic dropout.

Allele-specific PCR uses primers designed to preferentially amplify one allele, enabling targeted detection or genotyping of single-nucleotide variants. In research and clinical diagnostics, such assays help identify pathogenic variants, monitor somatic mutations, or track allelic copy number changes. In genome editing, allele-specific approaches aim to modify only one allele, often leveraging sequence differences like SNPs that create or disrupt editing guides or PAM sites.

Limitations and considerations include the requirement for informative heterozygous variants and the possibility of technical artifacts that mimic or obscure true allelic imbalance. Interpreting allele-specific data also requires awareness of imprinting, X-chromosome inactivation, and somatic mosaicism. Together, allele-specific analyses contribute to understanding how regulatory variation and sequence differences influence gene expression and phenotype.