The only difference in the variant test was that the computer screen displayed one octave of a keyboard (12 keys, without labels) instead of the note names arranged in a circle, and the subject had to click on the key corresponding to the perceived musical note (Figure 3).
Markedly, the average difference in the variant to reference ratio at each variant position for these two datasets is only half a percentage (0.544%, SD 0.11%) leading us to conclude that genotype calling from our platform is highly congruent with the genotypes called from the exome sequencing dataset if similar algorithms were used in genotype calling.
The two most consistently identified susceptibility genes for sporadic PD are the α-synuclein (SNCA) and microtubule-associated protein tau (MAPT) genes [ 10, 11] which play independent, but not joint, effects on the risk of developing PD [ 12, 13], although there are significant differences in the variants associated with PD between Asian and Caucasian populations [ 14].
Since no difference in the enzyme variants from the mutants were observed, detailed description of each individual enzyme variant is not described here, and further suggested to refer our recent report (Kumar and Parikh 2015).
These inconsistent calls might be attributable to differences in the variant detection algorithm [ 4] as we used UnifiedGenotyper from GATK [ 22] whereas the 1000 bull genomes project used mpileup from SAMtools [ 46].
This type of underlying difference in the "neurotoxic" variant of AChE may thus contribute to greater vulnerability of neonatal males to neurotoxicant injury in general and not just to the OP pesticides.
Different variant callers follow different underlying models, resulting in differences in the called variants [ 15].
Recently, some studies have shown that there is significant difference in the set of variants called by different variant callers [ 7, 17, 18].
