Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references.
However, for rare variants, most of these possible genotype groups will not be seen because of low MAF, and, instead, we observe only M + 1 patterns, denoted P0, P1, …, P M, where P 0 represents a pattern of common homozygotes only.
If there are no epistatic incompatibilities among beneficial mutations, and if there is only one most fit genotype out of all possible genotypes, parallel evolution is likely to occur [22], [23].
In most applications SNPs are diallelic, resulting in three possible genotypes.
The probability P(s i = 1) thus depends on the genotype of animal i, denoted g i. Posit a set of n possible genotypes ranked by increasing susceptibility: G1 corresponds to the most resistant genotype, while G n corresponds to the most susceptible one.
Both strategies, selecting the most likely genotype and selecting the posterior distribution of all possible genotypes, have demonstrated the capacity to improve power in follow-up association analysis [5], [6], [16].
For each individual, the genotype at the untyped SNP can be summarized by taking (1) the most likely genotype according to the posterior probability of the three possible genotypes and (2) allele dosage, the expected number of copies of the reference allele (a fractional value between 0 and 2).
Pattern 4 markers represent markers that detect two loci, most likely from the homeologous chromosomes: one polymorphic and one monomorphic resulting in three possible genotypes (AAAA, AAAB, AABB).
These SNP genotyping mistakes are more frequent when most samples in the plate have the same genotype, since reference genotype clouds corresponding to the three possible genotypes per SNP locus are more difficult to establish.
Among the nine possible genotypes, we found only six combined genotypes in schizophrenia cases; the CC/AA was the most frequent (40%), followed by CC/AG (15%).
