For CYP2D6, manual interpretation of WGS data in the form of targeted CNV analysis, inspection of allelic read depth and decision-making surrounding missing markers, was necessary here with data generated on the Complete Genomics platform.
The missing markers were replaced by gapped lines, not used for the distance calculation.
The profiles of such individuals were merged, and missing markers were replaced by their counterparts from the other individual.
As such, an initial dataset with only a modest number of missing markers is advisable when employing these methods.
Genotypes of missing markers were generated randomly in each iteration on the basis of the probability inferred jointly from the nearest non-missing flanking markers and the phenotype.
The forms were assumed to be identical if the differences between them did not exceed 2% and if their molecular profiles, except when missing markers, were identical.
The Median LOD of the 400 replicates was used to summarize the replicates as the LOD score distribution at the tested marker were skewed due to changes in the imputed genotypes of missing markers being tested or used as covariates (data not shown).
The multiplex amplification of the Y-chromosomal STRs was successful for 27 of the 38 (71%) male samples, where full profiles or profiles with only one missing marker were obtained (See Additional file 1).
The WHO near miss markers are shown in Table 1, distributed as Group A (organ dysfunction) and Group B (severe dysfunction/failure). Two models of bivariate logistic regression were then developed and tested to describe the relationship between severe morbidity and mortality.
In the two mixed density data sets, 80 to 86% of the markers were missing originally and 93 to 96% of these missing markers were imputed.
