Genotype

A genotype records the inherited alleles carried by an individual at one or more genetic loci. At a two-copy diploid genetic locus with alleles $A,a$, the possible unordered genotypes are $AA,Aa,aa$. The first and last are homozygotes; the middle is a heterozygote. The notation records inherited states, without yet asserting their phenotypes. See NHGRI: genotype.

An unordered $Aa$ combines the two parental orders $Aa$ and $aA$. This small bookkeeping point explains the factor two in Hardy-Weinberg proportions and in an $Aa\times Aa$ cross. If parental origin or arrangement across several genetic loci matters, a phase-known genotype retains extra information about the two haplotypes.

Genotyping determines the alleles carried at chosen genetic loci. A diploid genotype call need not identify its two haplotypes; that additionally requires a phase-known genotype or haplotype estimation.

A genotyping error is an incorrect observed allele or genotype call. A probabilistic observation model replaces the deterministic genetic marker factor by $P(X=x\mid G=g)$, allowing nonzero probability of an observed call inconsistent with the latent genotype. Such error can bias family transmission tests and linkage likelihoods.

Heterozygosity means that the two allele states at a diploid genetic locus differ; an individual with that property is a heterozygote. Heterozygous parental genotypes provide alternative alleles for a transmission disequilibrium test.

Homozygosity means that the two allele states at a diploid genetic locus are the same; an individual with that property is a homozygote. Observed homozygosity does not by itself establish identity by descent.

A heterozygote carries different alleles at a diploid locus. Under ordinary Mendelian segregation each is transmitted to an offspring with probability $1/2$. Only heterozygous parents provide a comparison between alternative transmissions in the transmission disequilibrium test.

A homozygote carries two identical alleles at a locus; a heterozygote carries different alleles. Homozygosity of an observed haplotype is identity by state, and need not be identity by descent.

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 $AB/ab$ or $Ab/aB$; 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.

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At several genetic loci, a phase-known genotype specifies which alleles occur together on each chromosome, hence its two haplotypes. An unphased multilocus genotype may be compatible with several haplotype pairs. For two heterozygous loci, $AB/ab$ and $Ab/aB$ have identical unphased genotypes but different transmission probabilities when genetic linkage is present.