IMPUTE explicitly specifies a set of reference haplotypes (e.g., haplotypes from the HapMap project), as the pool of hidden states of the Markov Chain, and infers haplotypes and missing genotypes in test samples according to these hidden states [5].
For population P, simulate a cohort of 1,000 individuals by selecting pairs of reference haplotypes, at random, from HMP3.
Whereas the original algorithm imputes genotypes from the full set of reference haplotypes, the new approximation imputes each study haplotype from a custom subset of reference haplotypes.
Our method can also use existing panels of reference haplotypes.
By defining a root node, i.e. the hypothetical human ancestral haplotype, ρ between the root node and a descendent haplotype or a group of descendent haplotypes, i.e. a haplotype group, was calculated.
This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local ancestry of admixed individuals.
The use of haplotype blocks improved the prediction reliabilities, even when selection focused on only a group of haplotype blocks.
A group of genetic markers, called the Cohen Modal Haplotype and found in 10percentt of the general population, was found in half of the Jewish Cohens.
We tested the described P2Y12 receptor haplotypes in a group of patients with coronary artery disease.
The introgressant form is characterized by a monophyletic group of mitochondrial haplotypes nested within haplotypes otherwise characteristic of M. rutilus.
When comparing two panels of 200 reference haplotypes drawn from a set of 2000 sample haplotypes, let m be the number of haplotypes that are shared by both panels (0 ≤ m ≤ 200).
