A haplotype is the set of alleles on one chromosome across specified genetic loci. Closely linked markers without intervening genetic recombination are transmitted as one haplotype; they are not independent observations of inheritance.
A haplotype frequency is the proportion of chromosome copies carrying specified alleles together across chosen genetic loci. Its marginal distributions give allele frequencies; its departures from products of those frequencies are linkage disequilibrium.
Haplotype estimation reconstructs which alleles share a chromosome from observed genotypes and other information, such as pedigrees. A doubly heterozygous genotype can be or ; a phase-known genotype distinguishes them. Uncertainty in that reconstruction must propagate to estimated haplotype frequencies and linkage disequilibrium.
A haplotype block is a chromosomal region with limited historical genetic recombination, strong local linkage disequilibrium and comparatively few common haplotypes. Its definition is operational and population-dependent; it does not mean that recombination never occurs within it.
// Target: biology.bigb
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