Another early application of simulation methods is in estimating the
power of a linkage study. The idea is to simulate marker data on the
pedigrees available for a genetic study under an hypothesized genetic
model before genotyping pedigree members.
The method presented here was introduced by Ploughman and
Boehnke [12]. Ott [10] presents a similar idea. The first
step is to simulate genotypes conditional on the observed
phenotypes. This is done by peeling the pedigree up to one of the
ancestors, saving all the 
and 
terms computed along
the way. The procedure gives the probability distribution of the
genotype of the last individual conditional on the phenotype data on
all the people. The genotype of the last individual is generated
from that distribution. Then, the genotype of the next before last
person in the peeling order is simulated given the genotype of the
last individual and the phenotypes of the rest of the pedigree
members. The operation is iterated on the other individuals in the
pedigree. This is called reverse peeling.
Once the disease locus genotypes of all the individuals have been
generated, the genotypes at a marker having a recombination fraction
with the disease locus can be simulated by first sampling the
founder genotypes according to the marker allele frequencies and then
simulating the gene flow down the pedigree according to 
.