Using the simulated genotypic data for markers within the glutathione metabolism pathway, a binary phenotype (Z i ) for each subject i was generated conditional on their genotypic values from a Bernoulli distribution, Z i ∼ Ber(p i ) with log(p i /1− p i )= X i T β.
To demonstrate the contribution of each EPO producing organ, various mice in which VHL can be inactivated tissue specifically were generated using conditional gene targeting technology based on Cre-loxP mediated recombination [ 52].
Odds ratios (OR) and 95% confidence intervals (CI) were generated by conditional logistic regression models.
To assess whether individual loci were inconsistent with expectations under the best-fit neutral demographic model, coalescent samples of ARGs conditional on the best-fit model were generated placing mutations on the ARG conditional on the scaled mutation rate estimated for all loci within the coding and promoter locus classes, respectively.
The CrT construct and conditional founder mice were generated and maintained on a C57BL/6J background through the University of Cincinnati Embryonic Stem Cell Core according to standard techniques [22].
We then simulated survival times for the ith individual were generated randomly using the exponential distribution, conditional on genotype and HR, where the HR was drawn from a normal distribution with mean = 1.067 and standard deviation (as a percentage of mean) matching that seen for age in the Cox Proportional Hazards model.
Each participant's recurrence time (X) is generated from a hypothetical PH model conditional on the five auxiliary variables, where the hazard function is λ r (x) = t0.5 * exp -2.0 Z1 + 0.5 Z2 -2.0 Z3 + 1.5 Z4 + 0.5 Z5).
In a situation with dependent censoring, time to early colonoscopy is generated from a hypothetical PH model conditional on auxiliary variables with a hazard function λ e (t; Z1,..., Z5) and truncated at three years.
Using SLINK, replicates were generated for each given pedigree structure conditional on affection status by generating a marker with a minor allele frequency of 0.0001 completely linked (recombination fraction =0.0) to a fully penetrant autosomal recessive disease locus with an allele frequency of 0.0001.
Distributions of CNV sizes, probe spacing, and log2 values were generated for gains, normal copy, and losses conditional on the observed distributions of these quantities in each sample.
