haplotypes

A haplotype is a set of alleles at multiple adjacent loci on the same chromosome that are transmitted together from parent to offspring. In diploid organisms, an individual carries two haplotypes for any region, one from each parent. A haplotype represents the arrangement of variants along a chromosome, whereas a genotype is the pair of alleles observed at each locus. Phasing is the process of inferring the two parental haplotypes from genotype data.

Haplotypes arise through linkage and limited recombination within blocks, so certain allele combinations occur more frequently than expected by chance. The genome is often described in terms of haplotype blocks, within which variants tend to be co-inherited. Haplotype information is essential for many analyses because it captures the inherited structure of the genome beyond single-variant genotypes.

Applications include mapping disease-associated variants, pharmacogenomics, studying population history and ancestry, and improving genotype imputation in genome-wide association studies. Haplotypes can be defined for a specific region or for whole genomes; microhaplotypes are very short haplotypic blocks used in forensic genetics and high-resolution typing.

In population genetics, the term haplotype is related to but distinct from haplogroup. A haplogroup refers to a lineage defined by shared mutations across a population, frequently used for mitochondrial DNA or Y-chromosome analyses, whereas a haplotype is a specific combination of alleles on a chromosome.

Methods for haplotype determination include statistical phasing (using reference panels such as 1000 Genomes or HapMap), family-based phasing, and sequencing-based approaches. Accurate haplotype information improves downstream analyses and imputations.