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Here, we attempted to proceed beyond this general description and examine the possibility of deducing the detailed interactions between the checkpoint proteins using the quantitative phenotype of gene deletion mutants.
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Also, using a dichotomized case-control approach would waste considerable statistical efficiency otherwise gained by using the quantitative phenotypes.
Using a dichotomized case-control approach would waste considerable statistical efficiency otherwise gained by using the quantitative phenotypes.
Subsequently, residuals from the polygenic analysis, which are adjusted for polygenic covariation and fixed effects are used as the quantitative phenotype for whole genome association study.
An additional related side project involves annotating QTLs qualitatively with the ontologies/vocabularies used for the quantitative phenotype annotations.
For case/control tests, PLINK 1.9's –tail-pheno 0 command was used to downcode the quantitative phenotype to case/control.
We performed GWAS and GWIS using amyloid imaging as the quantitative phenotype and investigated the genetic interaction effects on cingulate amyloid-beta (A β) load.
The quantitative phenotype used in this article is the percent change of the scale in week 2 relative to scale tallied in the baseline week 0 for each patient.
The method is first tested on simulated data followed by real data obtained from a depression study using Hamilton Depression Rating Scale as the quantitative phenotype for each individual.
The quantitative phenotype Y was calculated using Eq. 3, where the error term ∈ was generated using the normal distribution with mean 0 and standard deviation 1, or the Student's t-distribution with 5 degrees of freedom.
We thus decided to use the average PiB uptake value from these four regions as the quantitative phenotype for the genetic association analysis.
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