In this paper, we explore a simplified variant approach for gas liquid three-equation models.
To properly assess the association between the MMP genes and lung cancer risk and survival, it would be preferable to take a tagging variant approach.
That is, a candidate variant approach may identify novel susceptibility loci, but the variant in question cannot be assumed to be causal, highlighting the importance of rigorous fine-scale mapping analyses, even when an association with a potentially functional SNP has been identified.
In order to identify differentially expressed genes, at statistically significant level, in LV of TRA and CTR rats, we applied a t-statistic variant approach.
For the gene-based association analyses, we performed association tests based on comparison of the numbers of non-reference protein-changing variants alleles exclusive to cases versus those exclusive to controls, a well-established unique variant approach (Cohen et al., 2004; Wain et al., 2014).
The G locus, controlling the peach/nectarine trait, has been recently characterized by a variant discovery approach, identifying an LTR retro-element insertion in exon 3 of the candidate gene PpMYB25 as the cause of the recessive glabrous phenotype.
As such, we compared variant prioritization capabilities of OVA with another recently reported variant prioritization tool, ExomeWalker (Smedley et al., 2014) which uses a current state-of-the-art algorithm for network-based gene prioritization, coupled with a variant scoring approach.
Unlike the variant approach standard process plans are not required.
The sampling was based on the maximum variant approach.
