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Graphical Models in Genetics, Genomics, and Metagenomics
Published in Marloes Maathuis, Mathias Drton, Steffen Lauritzen, Martin Wainwright, Handbook of Graphical Models, 2018
Expression quantitative trait locus (eQTL) refers to the genomic regions that carry one or more sequence variants that affect the expression of a gene, typically measured by microarrays or high-throughput RNA sequencing. Such variation may suggest mechanisms under which phenotypic differences arise. Thus eQTL analysis has emerged as a key tool for elucidating the causal effects of regulatory variants on gene expressions and the clinical traits, where tissue-specific gene expressions can serve as possible mediators of the genetic variants.
Inflammatory bowel disease: why this provides a useful example of the evolving science of nutrigenomics
Published in Journal of the Royal Society of New Zealand, 2020
In 2018, a further publication including the IIBDGC amongst several other large consortia (Momozawa et al. 2018) recognised over 240 loci associated with risk for IBD, and utilised newer technologies as well as an even larger set of individuals. These newer technologies included transcriptional profiling of specific cell subsets (Furey et al. 2019; Lee and Cleynen 2019). Transcriptional profiling considers the range of genes that are over- or under-expressed during disease development or progression, but has proved less informative in studying IBD than hoped, because of confounding factors such as medication use and disease severity (Lee and Cleynen 2019). More useful were the genome scale molecular phenotyping approaches used by Furey et al. (2019), to compare diseased and non-diseased subjects in relation to their host gene and microRNA expression, the state of the chromatin landscape and the composition of the gut microbiota. Zhang et al. (2015) defined molecular phenotyping as the technique of quantifying pathway reporter genes, i.e. pre-selected genes that are modulated specifically by metabolic and signalling pathways, in order to infer the activity of these pathways. The analysis by Furey et al. (2019) enabled a more precise redefining of these pathways in IBD. This study generated a large transcriptome dataset (looking at the expression of genes from nine disease-relevant cell types) and identified 23,650 expression quantitative trait loci (eQTL). eQTL have been described as genomic loci that explain all or a fraction of variation in the levels of expression of messenger RNAs (Rockman and Kruglyak 2006). Furey et al. (2019) confirmed the involvement of at least 240 genetic variants in this disease, but identified that approximately ten-fold higher numbers of human subjects would be needed to fully quantify the disease risk associated with individual genes or combinations thereof.