TABLE 8

Posterior probability distribution of diplotype configuration for each subject: four-locus data

Subject (i)Quantitative
 phenotypeDiplotype
 configurationTrue or falseaPosterior
 distributionbPosterior
 distributionc
 1157.1GCCT  GCCT  True1.00001.0000
 2170.3CCTC  CTCC  True0.99930.9999
CCCC  CTTC  False0.00070.0001
 3173.4CCTC  GCCT  True1.00001.0000
 4158.2CTCT  GCCT  True1.00001.0000
 5170.6CTCT  GCCT  True1.00001.0000
 6162.4CTCC  CTCC  True1.00001.0000
 7161.6CTCC  GCCT  True0.99750.9975
CTCT  GCCC  False0.00250.0025
 8149.4CTCC  CTCC  True1.00001.0000
 9164.3CCTC  GCCT  True1.00001.0000
10165.1CTCC  GCCT  True0.99750.9975
CTCT  GCCC  False0.00250.0025
  • a Possible diplotype configurations for each subject were compared with the diplotype configuration before the phase information was removed. “True” means that the diplotype configuration before the removal of the phase information was the same as the estimated diplotype configuration, while “False” means that they were different.

  • b Posterior probability distribution of the diplotype configuration given only the observed genotype data [P(di = ak|Gobs)].

  • c Posterior probability distribution of the diplotype configuration given the observed genotype and phenotype data [P(di = ak|Gobs, Ψobs)].

  • Simulations were started by assigning diplotype configurations to N = 1000 number of subjects according to the haplotype frequencies employed from the four-locus data for the SAA1 gene. Depending on whether the subject possessed the phenotype-associated haplotype CCTC, a quantitative phenotype was drawn from N1, σ2) or N2, σ2), where μ1 = 165, μ2 = 160, and σ = 5. After removing the phase information, QTLHAPLO was used to determine the posterior probability distribution of the diplotype configuration (diplotype distribution) for each subject either by using only genotype data or by using both genotype and phenotype data.