Is it possible to determine ones haplotype from genotype information alone?
A It is sometimes possible – but only if an individual has a genotype compatible with only two haplotypes. For example, an individual homozygous at 10 loci has two obvious and unambiguous haplotypes! If the same individual were heterozygous at an 11th locus, the situation remains unchanged. However, with two or more heterozygous loci, the individual has a (potentially large) set of haplotypes compatible with the genotype, so statistical inference over a sample of individuals is used to estimate the most likely set of haplotypes given the genotypes, and the most likely pair of haplotypes compatible with each individual’s genotypes – Bayesian (eg Phase) and EM (eg SNPHAP) are the two most common statistical inference methods. Like most statistical methods, they only apply to a sample of subjects – one individual is not enough unless that individual is unambiguous as described above.
