Introduction

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Cystic fibrosis is caused by a mutation in the CFTR gene that prevents passage of chloride ions from the airway lumen of the lungs. This results in a loss of water from the airway lumens and a thick sticky mucus in the airway.
Single-gene diseases like cystic fibrosis are relatively well understood. In cystic fibrosis mutations in the coding region of the CFTR gene result in a defective protein. This leads to excess mucus production that can damage the lungs and digestive system.

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Figures showing the GWAS Catalog Excerpted from the GWAS Catalog

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Figure showing regulation of gene expression by a SNP Created in BioRender

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Figure showing SNP regulating gene which affects disease Created in BioRender

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Figure showing distal regulation
SNPs can affect gene expression distally from the gene that they regulate, often from a different chromosome altogether.

Genetic Drivers of Pancreatic Islet Function

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Figure showing Type 2 diabetes and insulin. Created in BioRender

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Figure showing the Islet of Langerhans in the pancreas, which is composed of alpha, beta, delta and gamma cells. Created in BioRender

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Figure showing glucose and insulin changes over time.
Glucose and Insulin glucose tolerance test plots

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A plot showing four different curves reflecting insulin levels after administration of glucose starting at time zero
Insulin curves following glucose tolerance test

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Insulin AUC QTL plot
LOD plot for insulin area under the curve

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Keller et al, figure S7
Keller et al, 2018 Supplementary Figure S7

Load and Explore Data

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a residual for one data point located above the line described by a linear model
A linear model showing one residual

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Figure showing relationship between samples, expression, and transcripts.
Data Diagram

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Mapping A Single Gene Expression Trait

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Picture of Environment tab with data objects. Each element of probs is a 3-dimensional array containing the founder allele dosages for each sample at each marker on one chromosome. These are the 8 state allele probabilities (not 32) using the 69k marker grid for the same 500 DO mice that also have clinical phenotypes. We have already calculated genotype probabilities for you, so you can skip the step for calculating genotype probabilities and the optional step for calculating allele probabilities.

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Mapping Many Gene Expression Traits

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Maximum eQTL Peaks and Nearby Genes

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Creating A Transcriptome Map

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Mediation Analysis

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Mediation Analysis
In complete mediation an predictor variable influences a response variable indirectly through a mediator variable.

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mediation figure
A non-coding SNP affects expression of gene 1 locally. Gene 1 mediates expression of gene 2 distally.

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Akr1e1 QTL plot
Chromosome 13 gene Akr1e1 is affected by expression in both local and distant by genes on chromosomes 13 and 4.

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Myo15b QTL plot
Chromosome 11 gene Myo15b is affected by expression of a gene in the chromosome 2 hotspot.

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Hnf4a mediation
Mediating expression of Myo15b identifies Hnf4a as the gene that drops the LOD score from greater than 70 to less than 50.

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