Allele-specific expression analysis for complex genetic phenotypes applied to a unique dilated cardiomyopathy cohort

Figures

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  Figure 1. Overview of the pipeline. This analysis plan allows the inclusion of genotyping data to increase data retrieval and statistical power. The data can be evaluated on three distinct levels, with suiting visualizations for all of them in order to create interpretable results. The integration of WGS or WES data, the group comparisons, and the visualizations are novel additions to established ASE analysis pipelines.

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  Figure 2. ASE density by zygosity status. This figure shows the density plots of ASE values for genotyped loci based on the zygosity status of the loci. The ASE threshold for homozygosity in non-genotyped loci is indicated with the dotted line.

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  Figure 3. QQ-plot of p-value inflation. This figure shows the test statistic inflation for SNPs located in 12 genes with established DCM-associated variants compared to the remaining SNPs.

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  Figure 4. Overview of results visualizations for differential imbalance between all four phenogroups. (A) Manhattan plot indicating loci significantly differentially imbalanced between all four phenogroups. Note that each dot represents a SNP, annotated with the gene it is located in. (B) Boxplot showing the distribution of ASE scores and number of measurements by phenogroup for rs9766, located in EZH1, the most significant differentially imbalance SNP between the four phenogroups. (C) Subgraph of the network displaying a group of functionally related genes with median ASE scores for the corresponding SNP per phenogroup.