haplotypic

Haplotypic refers to anything relating to a haplotype, a set of alleles or sequence variants that are inherited together on a single chromosome. In diploid organisms, each individual carries two haplotypes for any given region, one on each homologous chromosome, and the combination of these constitutes the diplotype. The haplotypic structure is shaped by historical recombination and mutation events and is often characterized by blocks of high linkage disequilibrium where particular allele combinations occur more frequently than expected by chance.

Haplotypic information is used to describe the arrangement of variants, not merely the presence of variants. It matters in association studies because disease associations may localize to specific haplotypes rather than single variants, and haplotype-based imputation can improve genotype inference.

Haplotyping can be direct via long-read sequencing or family-based methods, or statistical phasing of genotype data with algorithms such as SHAPEIT, Beagle, or EAGLE, often using reference haplotype panels. Haplotype blocks are genomic regions with limited historical recombination where a common set of haplotypes exists.

Applications include population genetics, disease mapping, pharmacogenomics, and forensic genetics, where haplotypic information helps interpret genetic variation and ancestry.

Limitations include phasing errors, dependence on sample size and reference panels, and reduced accuracy for rare variants or highly recombined regions.